orcs-full.obo

format-version: 1.2
data-version: orcs/releases/2021-11-13/orcs-full.owl
subsetdef: attribute_slim ""
subsetdef: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension ""
subsetdef: http://purl.obolibrary.org/obo/valid_for_go_gp2term ""
subsetdef: http://purl.obolibrary.org/obo/valid_for_go_ontology ""
subsetdef: http://purl.obolibrary.org/obo/valid_for_gocam ""
subsetdef: ro-eco ""
subsetdef: RO:0002259 ""
ontology: orcs/orcs-full
property_value: http://purl.org/dc/elements/1.1/contributor "Amanda Hicks" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Josh Hanna" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Mathias Brochhausen" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Matthew Diller" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "S. Clint Dowland" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string
property_value: http://purl.org/dc/elements/1.1/date "2019-08-03" xsd:string
property_value: http://purl.org/dc/elements/1.1/title "Ontology for Representing CDM Semantics" xsd:string
property_value: owl:versionInfo "2021-11-13" xsd:string

[Term]
id: APOLLO_SV:00000008
name: software development
def: "A planned process that has specified output a software product and that involves the creation of source code." []
is_a: OBI:0000011 ! planned process
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
property_value: IAO:0000117 "William R. Hogan" xsd:string
property_value: IAO:0000119 http://en.wikipedia.org/wiki/Software_development xsd:string
property_value: IAO:0000600 "A planned process resulting in a software product involving the creation of source code." xsd:string

[Term]
id: APOLLO_SV:00000032
name: count
def: "A measurement datum that is the output of counting." []
is_a: IAO:0000109 ! measurement datum
intersection_of: IAO:0000027 ! data item
intersection_of: OBI:0000312 APOLLO_SV:00000033 ! is_specified_output_of counting
relationship: OBI:0000312 APOLLO_SV:00000033 ! is_specified_output_of counting
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
property_value: IAO:0000600 "A measurement datum that is the output of counting." xsd:string

[Term]
id: APOLLO_SV:00000033
name: counting
def: "The planned process of finding the number of elements in a finite set of objects." []
is_a: OBI:0000011 ! planned process
intersection_of: OBI:0000011 ! planned process
intersection_of: OBI:0000299 APOLLO_SV:00000032 ! has_specified_output count
relationship: OBI:0000299 APOLLO_SV:00000032 ! has_specified_output count
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
property_value: IAO:0000119 http://en.wikipedia.org/wiki/Counting xsd:string
property_value: IAO:0000600 "The planned process of finding the number of elements in a finite set of objects." xsd:string

[Term]
id: APOLLO_SV:00000242
name: name of temporal interval
def: "A name of temporal region that specifies a time span on a specified time scale by giving a start time and a duration." []
is_a: APOLLO_SV:00000395 ! name of temporal region
property_value: APOLLO_SV:0000040 "TimeSpanCategoryDefinition" xsd:string
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/apollo_sv/v4.1.1./apollo_sv.owl xsd:string
property_value: IAO:0000600 "An information content entity that specifies a time span on a specified time scale by giving a start time and a duration." xsd:string

[Term]
id: APOLLO_SV:00000376
name: name of a temporal boundary
def: "A name of temporal region that designates a temporal boundary" []
is_a: APOLLO_SV:00000395 ! name of temporal region
property_value: APOLLO_SV:0000040 "RealTimePointCategoryDefinition" xsd:string
property_value: IAO:0000117 "Matthew Diller" xsd:string
property_value: IAO:0000117 "William R. Hogan" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/apollo_sv/v4.1.1./apollo_sv.owl xsd:string
property_value: IAO:0000600 "An information content entity that designates a temporal boundary" xsd:string

[Term]
id: APOLLO_SV:00000395
name: name of temporal region
is_a: IAO:0020000 ! identifier
property_value: IAO:0000412 http://purl.obolibrary.org/obo/apollo_sv/v4.1.1./apollo_sv.owl xsd:string

[Term]
id: APOLLO_SV:00000429
name: date
def: "A name of a temporal region that is systematized according to a particular calendar system, such as the Gregorian calendar." []
is_a: APOLLO_SV:00000395 ! name of temporal region
property_value: APOLLO_SV:0000040 "date" xsd:string
property_value: IAO:0000117 "Matthew Diller" xsd:string
property_value: IAO:0000117 "William R. Hogan" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/apollo_sv/v4.1.1./apollo_sv.owl xsd:string
property_value: IAO:0000600 "A name of a temporal region that is systematized according to a particular calendar system, such as the Gregorian calendar." xsd:string

[Term]
id: APOLLO_SV:00000480
name: geographical migration of organism
def: "A behavior of one or more organisms that is characterized by the displacement from one geographic region to some target geographic region, and is the realization of either a biological function or (a concretization of) an objective specification." []
is_a: GO:0007610 ! behavior
property_value: IAO:0000117 "Matthew Diller" xsd:string
property_value: IAO:0000117 "William R. Hogan" xsd:string
property_value: IAO:0000600 "A behavior of one or more organisms that is characterized by the displacement from one geographic region to some target geographic region, and is the realization of either a biological function or (a concretization of) an objective specification." xsd:string

[Term]
id: APOLLO_SV:00000522
name: source code repository
def: "A document that comprises at least one source code module and provenance data about who contributed the set of files making up the module(s), and optionally comprises also multiple versions of files with detailed change history about who committed files and when, a license for the software, readme files, documentation, executables, etc." []
comment: Refers to the stuff that lives on GitHub, not to GitHub or the git software on which it is based
is_a: IAO:0000310 ! document
relationship: BFO:0000051 IAO:0000096 ! has part source code module
property_value: IAO:0000111 "software source code version control repository" xsd:string
property_value: IAO:0000117 "William R. Hogan" xsd:string

[Term]
id: APOLLO_SV:00000524
name: compiling software
def: "A planned process that converts human-written or curated software into a machine-executable or interpretable set of instructions." []
comment: It's compiling "software" (scare quotes) and not "source code" because you can compile Java bytecode to machine code, and Java bytecode is not technically "source code".  Compiling source code would be a subclass of this class (as would compiling Java bytecode, etc.).
comment: Source code can be automatically generated to some extent, but we're assuming humans still curate it minimally. Also, in the case of Java and its JVM, it's machine interpretable instructions, not directly executable. Ditto for other languages with intermediate form like Java byte code.
is_a: APOLLO_SV:00000008 ! software development
property_value: IAO:0000111 "process of compiling software" xsd:string
property_value: IAO:0000117 "William R. Hogan" xsd:string

[Term]
id: APOLLO_SV:00000532
name: human travel
def: "A geographical migration of an organism belonging to the species Homo sapiens." []
is_a: APOLLO_SV:00000480 ! geographical migration of organism
property_value: IAO:0000117 "Matthew Diller" xsd:string
property_value: IAO:0000117 "William R. Hogan" xsd:string

[Term]
id: APOLLO_SV:00000796
name: dataset creating
def: "A planned process that has a data set as its specified output." []
is_a: OBI:0000011 ! planned process
intersection_of: OBI:0000011 ! planned process
intersection_of: OBI:0000299 IAO:0000100 ! has_specified_output data set
relationship: OBI:0000299 IAO:0000100 ! has_specified_output data set
property_value: IAO:0000111 "creating a data set" xsd:string
property_value: IAO:0000117 "William R. Hogan" xsd:string
property_value: IAO:0000118 "data set creation" xsd:string
property_value: IAO:0000118 "dataset creation" xsd:string

[Term]
id: BFO:0000001
name: entity
property_value: BFO:0000179 "entity" xsd:string
property_value: BFO:0000180 "Entity" xsd:string
property_value: IAO:0000112 "Julius Caesar" xsd:string
property_value: IAO:0000112 "the Second World War" xsd:string
property_value: IAO:0000112 "Verdi’s Requiem" xsd:string
property_value: IAO:0000112 "your body mass index" xsd:string
property_value: IAO:0000116 "BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81" xsd:string
property_value: IAO:0000116 "Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000004", comment="per discussion with Barry Smith", http://www.w3.org/2000/01/rdf-schema#seeAlso="http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf"}
property_value: IAO:0000600 "An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/001-001"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl

[Term]
id: BFO:0000002
name: continuant
def: "An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts." []
is_a: BFO:0000001 ! entity
disjoint_from: BFO:0000003 ! occurrent
relationship: BFO:0000050 BFO:0000002 ! part of continuant
relationship: RO:HOM0000000 BFO:0000002 ! continuant
property_value: BFO:0000179 "continuant" xsd:string
property_value: BFO:0000180 "Continuant" xsd:string
property_value: IAO:0000116 "BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240" xsd:string
property_value: IAO:0000116 "Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000007"}
property_value: IAO:0000600 "A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/008-002"}
property_value: IAO:0000601 "if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/126-001"}
property_value: IAO:0000601 "if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/009-002"}
property_value: IAO:0000601 "if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/011-002"}
property_value: IAO:0000602 "(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/009-002"}
property_value: IAO:0000602 "(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/126-001"}
property_value: IAO:0000602 "(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/008-002"}
property_value: IAO:0000602 "(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/011-002"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl

[Term]
id: BFO:0000003
name: occurrent
def: "An entity that has temporal parts and that happens, unfolds or develops through time." []
is_a: BFO:0000001 ! entity
relationship: BFO:0000050 BFO:0000003 ! part of occurrent
relationship: RO:HOM0000000 BFO:0000003 ! occurrent
property_value: BFO:0000179 "occurrent" xsd:string
property_value: BFO:0000180 "Occurrent" xsd:string
property_value: IAO:0000116 "BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region" xsd:string
property_value: IAO:0000116 "BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players." xsd:string
property_value: IAO:0000116 "Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000006", comment="per discussion with Barry Smith"}
property_value: IAO:0000116 "Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000012"}
property_value: IAO:0000600 "An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/077-002"}
property_value: IAO:0000601 "b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/079-001"}
property_value: IAO:0000601 "Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/108-001"}
property_value: IAO:0000602 "(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/108-001"}
property_value: IAO:0000602 "(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/079-001"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl

[Term]
id: BFO:0000004
name: independent continuant
def: "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything." []
def: "b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/017-002"}
is_a: BFO:0000002 ! continuant
disjoint_from: BFO:0000020 ! specifically dependent continuant
disjoint_from: BFO:0000031 ! generically dependent continuant
relationship: BFO:0000050 BFO:0000004 ! part of independent continuant
property_value: BFO:0000179 "ic" xsd:string
property_value: BFO:0000180 "IndependentContinuant" xsd:string
property_value: IAO:0000112 "a chair" xsd:string
property_value: IAO:0000112 "a heart" xsd:string
property_value: IAO:0000112 "a leg" xsd:string
property_value: IAO:0000112 "a molecule" xsd:string
property_value: IAO:0000112 "a spatial region" xsd:string
property_value: IAO:0000112 "an atom" xsd:string
property_value: IAO:0000112 "an orchestra." xsd:string
property_value: IAO:0000112 "an organism" xsd:string
property_value: IAO:0000112 "the bottom right portion of a human torso" xsd:string
property_value: IAO:0000112 "the interior of your mouth" xsd:string
property_value: IAO:0000601 "For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/134-001"}
property_value: IAO:0000601 "For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/018-002"}
property_value: IAO:0000602 "(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/018-002"}
property_value: IAO:0000602 "(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/134-001"}
property_value: IAO:0000602 "(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/017-002"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl

[Term]
id: BFO:0000005
name: obsolete dependent continuant
def: "A continuant  that is either dependent on one or other independent continuant  bearers or inheres in or is borne by other entities." []
is_a: ObsoleteClass ! Obsolete Class
is_obsolete: true

[Term]
id: BFO:0000006
name: spatial region
is_a: BFO:0000141 ! immaterial entity
disjoint_from: BFO:0000029 ! site
disjoint_from: BFO:0000140 ! continuant fiat boundary
property_value: BFO:0000179 "s-region" xsd:string
property_value: BFO:0000180 "SpatialRegion" xsd:string
property_value: IAO:0000116 "BFO 2 Reference: Spatial regions do not participate in processes." xsd:string
property_value: IAO:0000116 "Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000002", comment="per discussion with Barry Smith"}
property_value: IAO:0000600 "A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/035-001"}
property_value: IAO:0000601 "All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/036-001"}
property_value: IAO:0000602 "(forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/036-001"}
property_value: IAO:0000602 "(forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/035-001"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl

[Term]
id: BFO:0000008
name: temporal region
is_a: BFO:0000003 ! occurrent
disjoint_from: BFO:0000011 ! spatiotemporal region
disjoint_from: BFO:0000015 ! process
disjoint_from: BFO:0000035 ! process boundary
property_value: BFO:0000179 "t-region" xsd:string
property_value: BFO:0000180 "TemporalRegion" xsd:string
property_value: IAO:0000116 "Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000003", comment="per discussion with Barry Smith"}
property_value: IAO:0000600 "A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/100-001"}
property_value: IAO:0000601 "All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/101-001"}
property_value: IAO:0000601 "Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/119-002"}
property_value: IAO:0000602 "(forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/119-002"}
property_value: IAO:0000602 "(forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/101-001"}
property_value: IAO:0000602 "(forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/100-001"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl

[Term]
id: BFO:0000009
name: two-dimensional spatial region
is_a: BFO:0000006 ! spatial region
disjoint_from: BFO:0000028 ! three-dimensional spatial region
property_value: BFO:0000179 "2d-s-region" xsd:string
property_value: BFO:0000180 "TwoDimensionalSpatialRegion" xsd:string
property_value: IAO:0000112 "an infinitely thin plane in space." xsd:string
property_value: IAO:0000112 "the surface of a sphere-shaped part of space" xsd:string
property_value: IAO:0000600 "A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/039-001"}
property_value: IAO:0000602 "(forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/039-001"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl

[Term]
id: BFO:0000011
name: spatiotemporal region
is_a: BFO:0000003 ! occurrent
property_value: BFO:0000179 "st-region" xsd:string
property_value: BFO:0000180 "SpatiotemporalRegion" xsd:string
property_value: IAO:0000112 "the spatiotemporal region occupied by a human life" xsd:string
property_value: IAO:0000112 "the spatiotemporal region occupied by a process of cellular meiosis." xsd:string
property_value: IAO:0000112 "the spatiotemporal region occupied by the development of a cancer tumor" xsd:string
property_value: IAO:0000600 "A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/095-001"}
property_value: IAO:0000601 "All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/096-001"}
property_value: IAO:0000601 "Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/099-001"}
property_value: IAO:0000601 "Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/098-001"}
property_value: IAO:0000601 "Every spatiotemporal region occupies_spatiotemporal_region itself." xsd:string
property_value: IAO:0000601 "Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/107-002"}
property_value: IAO:0000602 "(forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/107-002"}
property_value: IAO:0000602 "(forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/099-001"}
property_value: IAO:0000602 "(forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/096-001"}
property_value: IAO:0000602 "(forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/098-001"}
property_value: IAO:0000602 "(forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/095-001"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl

[Term]
id: BFO:0000015
name: process
def: "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t." []
def: "p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/083-003"}
is_a: BFO:0000003 ! occurrent
property_value: BFO:0000179 "process" xsd:string
property_value: BFO:0000180 "Process" xsd:string
property_value: IAO:0000112 "a process of cell-division, \\ a beating of the heart" xsd:string
property_value: IAO:0000112 "a process of meiosis" xsd:string
property_value: IAO:0000112 "a process of sleeping" xsd:string
property_value: IAO:0000112 "the course of a disease" xsd:string
property_value: IAO:0000112 "the flight of a bird" xsd:string
property_value: IAO:0000112 "the life of an organism" xsd:string
property_value: IAO:0000112 "your process of aging." xsd:string
property_value: IAO:0000116 "BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/ido.owl
property_value: IAO:0000412 http://purl.obolibrary.org/obo/omrse.owl
property_value: IAO:0000602 "(iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/083-003"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl

[Term]
id: BFO:0000016
name: disposition
is_a: BFO:0000017 ! realizable entity
disjoint_from: BFO:0000023 ! role
property_value: BFO:0000179 "disposition" xsd:string
property_value: BFO:0000180 "Disposition" xsd:string
property_value: IAO:0000112 "an atom of element X has the disposition to decay to an atom of element Y" xsd:string
property_value: IAO:0000112 "certain people have a predisposition to colon cancer" xsd:string
property_value: IAO:0000112 "children are innately disposed to categorize objects in certain ways." xsd:string
property_value: IAO:0000112 "the cell wall is disposed to filter chemicals in endocytosis and exocytosis" xsd:string
property_value: IAO:0000116 "BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type." xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/ido.owl
property_value: IAO:0000600 "b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/062-002"}
property_value: IAO:0000601 "If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/063-002"}
property_value: IAO:0000602 "(forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/063-002"}
property_value: IAO:0000602 "(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/062-002"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl

[Term]
id: BFO:0000017
name: realizable entity
def: "A specifically dependent continuant  that inheres in continuant  entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances." []
is_a: BFO:0000020 ! specifically dependent continuant
disjoint_from: BFO:0000019 ! quality
relationship: BFO:0000050 BFO:0000017 ! part of realizable entity
property_value: BFO:0000179 "realizable" xsd:string
property_value: BFO:0000180 "RealizableEntity" xsd:string
property_value: IAO:0000112 "the disposition of this piece of metal to conduct electricity." xsd:string
property_value: IAO:0000112 "the disposition of your blood to coagulate" xsd:string
property_value: IAO:0000112 "the function of your reproductive organs" xsd:string
property_value: IAO:0000112 "the role of being a doctor" xsd:string
property_value: IAO:0000112 "the role of this boundary to delineate where Utah and Colorado meet" xsd:string
property_value: IAO:0000600 "To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/058-002"}
property_value: IAO:0000601 "All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/060-002"}
property_value: IAO:0000602 "(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/060-002"}
property_value: IAO:0000602 "(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/058-002"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl

[Term]
id: BFO:0000018
name: zero-dimensional spatial region
is_a: BFO:0000006 ! spatial region
disjoint_from: BFO:0000028 ! three-dimensional spatial region
property_value: BFO:0000179 "0d-s-region" xsd:string
property_value: BFO:0000180 "ZeroDimensionalSpatialRegion" xsd:string
property_value: IAO:0000600 "A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/037-001"}
property_value: IAO:0000602 "(forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/037-001"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl

[Term]
id: BFO:0000019
name: quality
is_a: BFO:0000020 ! specifically dependent continuant
relationship: BFO:0000050 BFO:0000019 ! part of quality
property_value: BFO:0000179 "quality" xsd:string
property_value: BFO:0000180 "Quality" xsd:string
property_value: IAO:0000112 "the ambient temperature of this portion of air" xsd:string
property_value: IAO:0000112 "the color of a tomato" xsd:string
property_value: IAO:0000112 "the length of the circumference of your waist" xsd:string
property_value: IAO:0000112 "the mass of this piece of gold." xsd:string
property_value: IAO:0000112 "the shape of your nose" xsd:string
property_value: IAO:0000112 "the shape of your nostril" xsd:string
property_value: IAO:0000600 "a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/055-001"}
property_value: IAO:0000601 "If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/105-001"}
property_value: IAO:0000602 "(forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/105-001"}
property_value: IAO:0000602 "(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/055-001"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl

[Term]
id: BFO:0000020
name: specifically dependent continuant
def: "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same." []
def: "b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1  i < j  n, ci  and cj share no common parts, are such that for each 1  i  n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])" []
def: "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/050-003"}
is_a: BFO:0000002 ! continuant
disjoint_from: BFO:0000031 ! generically dependent continuant
relationship: BFO:0000050 BFO:0000020 ! part of specifically dependent continuant
property_value: BFO:0000179 "sdc" xsd:string
property_value: BFO:0000180 "SpecificallyDependentContinuant" xsd:string
property_value: IAO:0000111 "specifically dependent continuant" xsd:string
property_value: IAO:0000112 "of one-sided specifically dependent continuants: the mass of this tomato" xsd:string
property_value: IAO:0000112 "of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates." xsd:string
property_value: IAO:0000112 "Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key" xsd:string
property_value: IAO:0000112 "the disposition of this fish to decay" xsd:string
property_value: IAO:0000112 "the function of this heart: to pump blood" xsd:string
property_value: IAO:0000112 "the mutual dependence of proton donors and acceptors in chemical reactions [79" xsd:string
property_value: IAO:0000112 "the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction" xsd:string
property_value: IAO:0000112 "the pink color of a medium rare piece of grilled filet mignon at its center" xsd:string
property_value: IAO:0000112 "the role of being a doctor" xsd:string
property_value: IAO:0000112 "the shape of this hole." xsd:string
property_value: IAO:0000112 "the smell of this portion of mozzarella" xsd:string
property_value: IAO:0000116 "Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000005", comment="per discussion with Barry Smith"}
property_value: IAO:0000412 http://purl.obolibrary.org/obo/ido.owl
property_value: IAO:0000412 http://purl.obolibrary.org/obo/omrse.owl
property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl
property_value: IAO:0000602 "(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/050-003"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl

[Term]
id: BFO:0000023
name: role
def: "A realizable entity  the manifestation of which brings about some result or end that is not essential to a continuant  in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant  in some kinds of natural, social or institutional contexts." []
is_a: BFO:0000017 ! realizable entity
property_value: BFO:0000179 "role" xsd:string
property_value: BFO:0000180 "Role" xsd:string
property_value: IAO:0000112 "John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married." xsd:string
property_value: IAO:0000112 "the priest role" xsd:string
property_value: IAO:0000112 "the role of a boundary to demarcate two neighboring administrative territories" xsd:string
property_value: IAO:0000112 "the role of a building in serving as a military target" xsd:string
property_value: IAO:0000112 "the role of a stone in marking a property boundary" xsd:string
property_value: IAO:0000112 "the role of subject in a clinical trial" xsd:string
property_value: IAO:0000112 "the student role" xsd:string
property_value: IAO:0000116 "BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals –  professor, sergeant, nurse – only during certain phases in their lives." xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/omrse.owl
property_value: IAO:0000600 "b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/061-001"}
property_value: IAO:0000602 "(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/061-001"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl

[Term]
id: BFO:0000024
name: fiat object part
is_a: BFO:0000040 ! material entity
property_value: BFO:0000179 "fiat-object-part" xsd:string
property_value: BFO:0000180 "FiatObjectPart" xsd:string
property_value: IAO:0000112 "or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29" xsd:string
property_value: IAO:0000112 "the division of the brain into regions" xsd:string
property_value: IAO:0000112 "the division of the planet into hemispheres" xsd:string
property_value: IAO:0000112 "the dorsal and ventral surfaces of the body" xsd:string
property_value: IAO:0000112 "the FMA:regional parts of an intact human body." xsd:string
property_value: IAO:0000112 "the upper and lower lobes of the left lung" xsd:string
property_value: IAO:0000112 "the Western hemisphere of the Earth" xsd:string
property_value: IAO:0000116 "BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions" xsd:string
property_value: IAO:0000600 "b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of  c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/027-004"}
property_value: IAO:0000602 "(forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/027-004"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl

[Term]
id: BFO:0000026
name: one-dimensional spatial region
is_a: BFO:0000006 ! spatial region
disjoint_from: BFO:0000028 ! three-dimensional spatial region
property_value: BFO:0000179 "1d-s-region" xsd:string
property_value: BFO:0000180 "OneDimensionalSpatialRegion" xsd:string
property_value: IAO:0000112 "an edge of a cube-shaped portion of space." xsd:string
property_value: IAO:0000600 "A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/038-001"}
property_value: IAO:0000602 "(forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/038-001"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl

[Term]
id: BFO:0000027
name: object aggregate
is_a: BFO:0000040 ! material entity
property_value: BFO:0000179 "object-aggregate" xsd:string
property_value: BFO:0000180 "ObjectAggregate" xsd:string
property_value: IAO:0000112 "a collection of cells in a blood biobank." xsd:string
property_value: IAO:0000112 "a swarm of bees is an aggregate of members who are linked together through natural bonds" xsd:string
property_value: IAO:0000112 "a symphony orchestra" xsd:string
property_value: IAO:0000112 "an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team)" xsd:string
property_value: IAO:0000112 "defined by fiat: the aggregate of members of an organization" xsd:string
property_value: IAO:0000112 "defined through physical attachment: the aggregate of atoms in a lump of granite" xsd:string
property_value: IAO:0000112 "defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container" xsd:string
property_value: IAO:0000112 "defined via attributive delimitations such as: the patients in this hospital" xsd:string
property_value: IAO:0000112 "the aggregate of bearings in a constant velocity axle joint" xsd:string
property_value: IAO:0000112 "the aggregate of blood cells in your body" xsd:string
property_value: IAO:0000112 "the nitrogen atoms in the atmosphere" xsd:string
property_value: IAO:0000112 "the restaurants in Palo Alto" xsd:string
property_value: IAO:0000112 "your collection of Meissen ceramic plates." xsd:string
property_value: IAO:0000116 "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000301"}
property_value: IAO:0000116 "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000011"}
property_value: IAO:0000116 "BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee)." xsd:string
property_value: IAO:0000119 "ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000300"}
property_value: IAO:0000600 "b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/025-004"}
property_value: IAO:0000602 "(forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/025-004"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl

[Term]
id: BFO:0000028
name: three-dimensional spatial region
is_a: BFO:0000006 ! spatial region
property_value: BFO:0000179 "3d-s-region" xsd:string
property_value: BFO:0000180 "ThreeDimensionalSpatialRegion" xsd:string
property_value: IAO:0000112 "a cube-shaped region of space" xsd:string
property_value: IAO:0000112 "a sphere-shaped region of space," xsd:string
property_value: IAO:0000600 "A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/040-001"}
property_value: IAO:0000602 "(forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/040-001"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl

[Term]
id: BFO:0000029
name: site
is_a: BFO:0000141 ! immaterial entity
property_value: BFO:0000179 "site" xsd:string
property_value: BFO:0000180 "Site" xsd:string
property_value: IAO:0000112 "a hole in the interior of a portion of cheese" xsd:string
property_value: IAO:0000112 "a rabbit hole" xsd:string
property_value: IAO:0000112 "an air traffic control region defined in the airspace above an airport" xsd:string
property_value: IAO:0000112 "Manhattan Canyon)" xsd:string
property_value: IAO:0000112 "the cockpit of an aircraft" xsd:string
property_value: IAO:0000112 "the Grand Canyon" xsd:string
property_value: IAO:0000112 "the hold of a ship" xsd:string
property_value: IAO:0000112 "the interior of a kangaroo pouch" xsd:string
property_value: IAO:0000112 "the interior of the trunk of your car" xsd:string
property_value: IAO:0000112 "the interior of your bedroom" xsd:string
property_value: IAO:0000112 "the interior of your office" xsd:string
property_value: IAO:0000112 "the interior of your refrigerator" xsd:string
property_value: IAO:0000112 "the lumen of your gut" xsd:string
property_value: IAO:0000112 "the Piazza San Marco" xsd:string
property_value: IAO:0000112 "your left nostril (a fiat part – the opening – of your left nasal cavity)" xsd:string
property_value: IAO:0000600 "b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/034-002"}
property_value: IAO:0000602 "(forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/034-002"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl

[Term]
id: BFO:0000030
name: object
is_a: BFO:0000040 ! material entity
property_value: BFO:0000179 "object" xsd:string
property_value: BFO:0000180 "Object" xsd:string
property_value: IAO:0000112 "atom" xsd:string
property_value: IAO:0000112 "cell" xsd:string
property_value: IAO:0000112 "cells and organisms" xsd:string
property_value: IAO:0000112 "engineered artifacts" xsd:string
property_value: IAO:0000112 "grain of sand" xsd:string
property_value: IAO:0000112 "molecule" xsd:string
property_value: IAO:0000112 "organelle" xsd:string
property_value: IAO:0000112 "organism" xsd:string
property_value: IAO:0000112 "planet" xsd:string
property_value: IAO:0000112 "solid portions of matter" xsd:string
property_value: IAO:0000112 "star" xsd:string
property_value: IAO:0000116 "BFO 2 Reference: an object is a maximal causally unified material entity" xsd:string
property_value: IAO:0000116 "BFO 2 Reference: BFO rests on the presupposition that at multiple micro-, meso- and macroscopic scales reality exhibits certain stable, spatially separated or separable material units, combined or combinable into aggregates of various sorts (for example organisms into what are called ‘populations’). Such units play a central role in almost all domains of natural science from particle physics to cosmology. Many scientific laws govern the units in question, employing general terms (such as ‘molecule’ or ‘planet’) referring to the types and subtypes of units, and also to the types and subtypes of the processes through which such units develop and interact. The division of reality into such natural units is at the heart of biological science, as also is the fact that these units may form higher-level units (as cells form multicellular organisms) and that they may also form aggregates of units, for example as cells form portions of tissue and organs form families, herds, breeds, species, and so on. At the same time, the division of certain portions of reality into engineered units (manufactured artifacts) is the basis of modern industrial technology, which rests on the distributed mass production of engineered parts through division of labor and on their assembly into larger, compound units such as cars and laptops. The division of portions of reality into units is one starting point for the phenomenon of counting." xsd:string
property_value: IAO:0000116 "BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below)." xsd:string
property_value: IAO:0000116 "BFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47" xsd:string
property_value: IAO:0000116 "BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74" xsd:string
property_value: IAO:0000600 "b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/024-001"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl

[Term]
id: BFO:0000031
name: generically dependent continuant
def: "A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time." []
def: "b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/074-001"}
is_a: BFO:0000002 ! continuant
relationship: BFO:0000050 BFO:0000031 ! part of generically dependent continuant
property_value: BFO:0000179 "gdc" xsd:string
property_value: BFO:0000180 "GenericallyDependentContinuant" xsd:string
property_value: IAO:0000112 "The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity." xsd:string
property_value: IAO:0000112 "the pdf file on your laptop, the pdf file that is a copy thereof on my laptop" xsd:string
property_value: IAO:0000112 "the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule." xsd:string
property_value: IAO:0000602 "(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/074-001"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl

[Term]
id: BFO:0000034
name: function
is_a: BFO:0000016 ! disposition
property_value: BFO:0000179 "function" xsd:string
property_value: BFO:0000180 "Function" xsd:string
property_value: IAO:0000112 "the function of a hammer to drive in nails" xsd:string
property_value: IAO:0000112 "the function of a heart pacemaker to regulate the beating of a heart through electricity" xsd:string
property_value: IAO:0000112 "the function of amylase in saliva to break down starch into sugar" xsd:string
property_value: IAO:0000116 "BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc." xsd:string
property_value: IAO:0000600 "A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/064-001"}
property_value: IAO:0000602 "(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/064-001"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl

[Term]
id: BFO:0000035
name: process boundary
def: "p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/084-001"}
is_a: BFO:0000003 ! occurrent
property_value: BFO:0000179 "p-boundary" xsd:string
property_value: BFO:0000180 "ProcessBoundary" xsd:string
property_value: IAO:0000112 "the boundary between the 2nd and 3rd year of your life." xsd:string
property_value: IAO:0000601 "Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/085-002"}
property_value: IAO:0000602 "(forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/085-002"}
property_value: IAO:0000602 "(iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/084-001"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl

[Term]
id: BFO:0000038
name: one-dimensional temporal region
is_a: BFO:0000008 ! temporal region
disjoint_from: BFO:0000148 ! zero-dimensional temporal region
property_value: BFO:0000179 "1d-t-region" xsd:string
property_value: BFO:0000180 "OneDimensionalTemporalRegion" xsd:string
property_value: IAO:0000112 "the temporal region during which a process occurs." xsd:string
property_value: IAO:0000116 "BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks)." xsd:string
property_value: IAO:0000600 "A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/103-001"}
property_value: IAO:0000602 "(forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/103-001"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl

[Term]
id: BFO:0000040
name: material entity
def: "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time." []
is_a: BFO:0000004 ! independent continuant
disjoint_from: BFO:0000141 ! immaterial entity
property_value: BFO:0000179 "material" xsd:string
property_value: BFO:0000180 "MaterialEntity" xsd:string
property_value: IAO:0000112 "a flame" xsd:string
property_value: IAO:0000112 "a forest fire" xsd:string
property_value: IAO:0000112 "a human being" xsd:string
property_value: IAO:0000112 "a hurricane" xsd:string
property_value: IAO:0000112 "a photon" xsd:string
property_value: IAO:0000112 "a puff of smoke" xsd:string
property_value: IAO:0000112 "a sea wave" xsd:string
property_value: IAO:0000112 "a tornado" xsd:string
property_value: IAO:0000112 "an aggregate of human beings." xsd:string
property_value: IAO:0000112 "an energy wave" xsd:string
property_value: IAO:0000112 "an epidemic" xsd:string
property_value: IAO:0000112 "the undetached arm of a human being" xsd:string
property_value: IAO:0000116 "BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60" xsd:string
property_value: IAO:0000116 "BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity." xsd:string
property_value: IAO:0000116 "BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here." xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/ido.owl
property_value: IAO:0000412 http://purl.obolibrary.org/obo/omrse.owl
property_value: IAO:0000600 "A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/019-002"}
property_value: IAO:0000601 "every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/021-002"}
property_value: IAO:0000601 "Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/020-002"}
property_value: IAO:0000602 "(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/021-002"}
property_value: IAO:0000602 "(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/020-002"}
property_value: IAO:0000602 "(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/019-002"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl

[Term]
id: BFO:0000140
name: continuant fiat boundary
def: "b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/029-001"}
is_a: BFO:0000141 ! immaterial entity
property_value: BFO:0000179 "cf-boundary" xsd:string
property_value: BFO:0000180 "ContinuantFiatBoundary" xsd:string
property_value: IAO:0000116 "BFO 2 Reference: a continuant fiat boundary is a boundary of some material entity (for example: the plane separating the Northern and Southern hemispheres; the North Pole), or it is a boundary of some immaterial entity (for example of some portion of airspace). Three basic kinds of continuant fiat boundary can be distinguished (together with various combination kinds [29" xsd:string
property_value: IAO:0000116 "BFO 2 Reference: In BFO 1.1 the assumption was made that the external surface of a material entity such as a cell could be treated as if it were a boundary in the mathematical sense. The new document propounds the view that when we talk about external surfaces of material objects in this way then we are talking about something fiat. To be dealt with in a future version: fiat boundaries at different levels of granularity.More generally, the focus in discussion of boundaries in BFO 2.0 is now on fiat boundaries, which means: boundaries for which there is no assumption that they coincide with physical discontinuities. The ontology of boundaries becomes more closely allied with the ontology of regions." xsd:string
property_value: IAO:0000116 "Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000008"}
property_value: IAO:0000601 "Every continuant fiat boundary is located at some spatial region at every time at which it exists" xsd:string
property_value: IAO:0000602 "(iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/029-001"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl

[Term]
id: BFO:0000141
name: immaterial entity
is_a: BFO:0000004 ! independent continuant
property_value: BFO:0000179 "immaterial" xsd:string
property_value: BFO:0000180 "ImmaterialEntity" xsd:string
property_value: IAO:0000116 "BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl

[Term]
id: BFO:0000142
name: one-dimensional continuant fiat boundary
is_a: BFO:0000140 ! continuant fiat boundary
disjoint_from: BFO:0000146 ! two-dimensional continuant fiat boundary
disjoint_from: BFO:0000147 ! zero-dimensional continuant fiat boundary
property_value: BFO:0000179 "1d-cf-boundary" xsd:string
property_value: BFO:0000180 "OneDimensionalContinuantFiatBoundary" xsd:string
property_value: IAO:0000112 "all geopolitical boundaries" xsd:string
property_value: IAO:0000112 "all lines of latitude and longitude" xsd:string
property_value: IAO:0000112 "The Equator" xsd:string
property_value: IAO:0000112 "the line separating the outer surface of the mucosa of the lower lip from the outer surface of the skin of the chin." xsd:string
property_value: IAO:0000112 "the median sulcus of your tongue" xsd:string
property_value: IAO:0000600 "a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/032-001"}
property_value: IAO:0000602 "(iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/032-001"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl

[Term]
id: BFO:0000144
name: process profile
def: "b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/093-002"}
is_a: BFO:0000015 ! process
disjoint_from: BFO:0000182 ! history
property_value: BFO:0000179 "process-profile" xsd:string
property_value: BFO:0000180 "ProcessProfile" xsd:string
property_value: IAO:0000112 "On a somewhat higher level of complexity are what we shall call rate process profiles, which are the targets of selective abstraction focused not on determinate quality magnitudes plotted over time, but rather on certain ratios between these magnitudes and elapsed times. A speed process profile, for example, is represented by a graph plotting against time the ratio of distance covered per unit of time. Since rates may change, and since such changes, too, may have rates of change, we have to deal here with a hierarchy of process profile universals at successive levels" xsd:string
property_value: IAO:0000112 "One important sub-family of rate process profiles is illustrated by the beat or frequency profiles of cyclical processes, illustrated by the 60 beats per minute beating process of John’s heart, or the 120 beats per minute drumming process involved in one of John’s performances in a rock band, and so on. Each such process includes what we shall call a beat process profile instance as part, a subtype of rate process profile in which the salient ratio is not distance covered but rather number of beat cycles per unit of time. Each beat process profile instance instantiates the determinable universal beat process profile. But it also instantiates multiple more specialized universals at lower levels of generality, selected from   rate process profilebeat process profileregular beat process profile3 bpm beat process profile4 bpm beat process profileirregular beat process profileincreasing beat process profileand so on.In the case of a regular beat process profile, a rate can be assigned in the simplest possible fashion by dividing the number of cycles by the length of the temporal region occupied by the beating process profile as a whole. Irregular process profiles of this sort, for example as identified in the clinic, or in the readings on an aircraft instrument panel, are often of diagnostic significance." xsd:string
property_value: IAO:0000112 "The simplest type of process profiles are what we shall call ‘quality process profiles’, which are the process profiles which serve as the foci of the sort of selective abstraction that is involved when measurements are made of changes in single qualities, as illustrated, for example, by process profiles of mass, temperature, aortic pressure, and so on." xsd:string
property_value: IAO:0000600 "b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/094-005"}
property_value: IAO:0000602 "(forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/094-005"}
property_value: IAO:0000602 "(iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/093-002"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl

[Term]
id: BFO:0000145
name: relational quality
def: "b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/057-001"}
is_a: BFO:0000019 ! quality
property_value: BFO:0000179 "r-quality" xsd:string
property_value: BFO:0000180 "RelationalQuality" xsd:string
property_value: IAO:0000112 "a marriage bond, an instance of requited love, an obligation between one person and another." xsd:string
property_value: IAO:0000112 "John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married." xsd:string
property_value: IAO:0000602 "(iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/057-001"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl

[Term]
id: BFO:0000146
name: two-dimensional continuant fiat boundary
is_a: BFO:0000140 ! continuant fiat boundary
property_value: BFO:0000179 "2d-cf-boundary" xsd:string
property_value: BFO:0000180 "TwoDimensionalContinuantFiatBoundary" xsd:string
property_value: IAO:0000600 "a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/033-001"}
property_value: IAO:0000602 "(iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/033-001"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl

[Term]
id: BFO:0000147
name: zero-dimensional continuant fiat boundary
is_a: BFO:0000140 ! continuant fiat boundary
property_value: BFO:0000179 "0d-cf-boundary" xsd:string
property_value: BFO:0000180 "ZeroDimensionalContinuantFiatBoundary" xsd:string
property_value: IAO:0000112 "the geographic North Pole" xsd:string
property_value: IAO:0000112 "the point of origin of some spatial coordinate system." xsd:string
property_value: IAO:0000112 "the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet" xsd:string
property_value: IAO:0000116 "zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000001", comment="requested by Melanie Courtot", http://www.w3.org/2000/01/rdf-schema#seeAlso="ZDRnpiIi:TUJ"}
property_value: IAO:0000600 "a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/031-001"}
property_value: IAO:0000602 "(iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/031-001"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl

[Term]
id: BFO:0000148
name: zero-dimensional temporal region
is_a: BFO:0000008 ! temporal region
property_value: BFO:0000179 "0d-t-region" xsd:string
property_value: BFO:0000180 "ZeroDimensionalTemporalRegion" xsd:string
property_value: IAO:0000112 "a temporal region that is occupied by a process boundary" xsd:string
property_value: IAO:0000112 "right now" xsd:string
property_value: IAO:0000112 "the moment at which a child is born" xsd:string
property_value: IAO:0000112 "the moment at which a finger is detached in an industrial accident" xsd:string
property_value: IAO:0000112 "the moment of death." xsd:string
property_value: IAO:0000118 "temporal instant." xsd:string
property_value: IAO:0000600 "A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/102-001"}
property_value: IAO:0000602 "(forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/102-001"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl

[Term]
id: BFO:0000182
name: history
is_a: BFO:0000015 ! process
property_value: BFO:0000179 "history" xsd:string
property_value: BFO:0000180 "History" xsd:string
property_value: IAO:0000600 "A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/138-001"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl

[Term]
id: BFO:0000202
name: temporal interval
is_a: BFO:0000038 ! one-dimensional temporal region
property_value: definition "(Elucidation) a temporal interval is a one-dimensional temporal region that is continuous, thus without gaps or breaks" xsd:string
property_value: example "The year 2018. " xsd:string
property_value: http://purl.org/dc/elements/1.1/identifier "155-BFO" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/bfo/2020/bfo.owl xsd:string
property_value: prefLabel "temporal interval" xsd:string
property_value: scopeNote "A one-dimensional temporal region can include as parts not only temporal intervals but also temporal instants separated from other parts by gaps. " xsd:string

[Term]
id: BFO:0000203
name: temporal instant
is_a: BFO:0000148 ! zero-dimensional temporal region
property_value: definition "(Elucidation) a temporal instant is a zero-dimensional temporal region that has no proper temporal part" xsd:string
property_value: example "The millennium." xsd:string
property_value: http://purl.org/dc/elements/1.1/identifier "209-BFO" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/bfo/2020/bfo.owl xsd:string
property_value: prefLabel "temporal instant" xsd:string

[Term]
id: C49474
name: obsolete International Classification of Diseases
is_a: IAO:0020020 ! code set
is_obsolete: true

[Term]
id: ENVO:00002004
name: mesoscopic physical object
name: physical object of mesoscopic geological size
def: "An environmental feature that is, or can be, contained and is predominantly composed of one or a few types of stuff." []
def: "An object which is large enough to be visible to humans, but small enough that humans can handle the object (i.e. transport it, examine it, etc) in its entirety with little to no technological assistance." []
comment: https://en.oxforddictionaries.com/definition/mesoscopic
comment: This is a legacy class from ENVO's early versions. It will be depopulated and filled in by inference using a PATO quality. Not to be confused with "mesoscopic" as defined in physics, which deals with objects typically between 10e-6 and 10-8 meters in diameter.
xref: MA:ma
is_a: BFO:0000030 ! object
property_value: IAO:0000118 "mesoscopic physical object" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/envo.owl xsd:string

[Term]
id: ENVO:00003074
name: manufactured product
def: "A material entity that has been processed by humans or their technology in any way, including intermediate products as well as final products." []
comment: https://en.wikipedia.org/wiki/Manufactured_product
synonym: "manufactured good" EXACT []
is_a: ENVO:00003075 ! anthropogenic abiotic mesoscopic feature
property_value: IAO:0000412 http://purl.obolibrary.org/obo/envo.owl xsd:string

[Term]
id: ENVO:00003075
name: anthropogenic abiotic mesoscopic feature
namespace: ENVO
is_a: ENVO:01000010 ! abiotic mesoscopic physical object
property_value: IAO:0000412 http://purl.obolibrary.org/obo/envo.owl xsd:string

[Term]
id: ENVO:01000010
name: abiotic mesoscopic physical object
namespace: ENVO
is_a: ENVO:00002004 ! mesoscopic physical object
property_value: IAO:0000412 http://purl.obolibrary.org/obo/envo.owl xsd:string

[Term]
id: ENVO:01000254
name: environmental system
def: "A system which has the disposition to environ one or more material entities." []
comment: In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class "system". The relation "environed_by" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised.
synonym: "environment" EXACT []
xref: DOI:10.1186/2041-1480-4-43
xref: EcoLexicon:environment
is_a: RO:0002577 ! system
property_value: IAO:0000412 http://purl.obolibrary.org/obo/envo.owl xsd:string
creation_date: 2013-09-23T16:04:08Z

[Term]
id: ENVO:01000604
name: vehicle
def: "A vehicle is a mobile machine which transports people or cargo." []
xref: https://en.wikipedia.org/wiki/Vehicle
is_a: ENVO:00003074 ! manufactured product
property_value: IAO:0000412 http://purl.obolibrary.org/obo/envo.owl xsd:string

[Term]
id: FMA:49443
name: Anatomical cluster
is_a: FMA:67135 ! Anatomical structure

[Term]
id: FMA:55457
name: vocal fold
is_a: FMA:64854 ! Subdivision of larynx

[Term]
id: FMA:64854
name: Subdivision of larynx
is_a: FMA:64989 ! Heterogeneous cluster

[Term]
id: FMA:64989
name: Heterogeneous cluster
is_a: FMA:49443 ! Anatomical cluster

[Term]
id: FMA:67135
name: Anatomical structure
is_a: FMA:67165 ! Material anatomical entity

[Term]
id: FMA:67165
name: Material anatomical entity
is_a: BFO:0000040 ! material entity

[Term]
id: GAZ:00000448
name: geographic location
def: "A reference to a place on the Earth, by its name or by its geographical location." []
is_a: BFO:0000029 ! site
property_value: IAO:0000412 http://purl.obolibrary.org/obo/gaz.owl

[Term]
id: GO:0003674
name: molecular_function
is_a: BFO:0000015 ! process
property_value: IAO:0000589 "molecular process" xsd:string

[Term]
id: GO:0003824
name: catalytic activity
is_a: GO:0003674 ! molecular_function

[Term]
id: GO:0007610
name: behavior
def: "The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity." [GOC:ems, GOC:jl, ISBN:0395448956, PMID:20160973]
comment: 1. Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation reviews.\n2. While a broader definition of behavior encompassing plants and single cell organisms would be justified on the basis of some usage (see PMID:20160973 for discussion), GO uses a tight definition that limits behavior to animals and to responses involving the nervous system, excluding plant responses that GO classifies under development, and responses of unicellular organisms that has general classifications for covering the responses of cells in multicellular organisms (e.g. cell chemotaxis).
xref: Wikipedia:Behavior
is_a: GO:0050896 ! response to stimulus

[Term]
id: GO:0008150
name: biological_process
def: "A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence." [GOC:pdt]
comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.
xref: Wikipedia:Biological_process
is_a: BFO:0000015 ! process
disjoint_from: OBI:0000011 ! planned process

[Term]
id: GO:0016301
name: kinase activity
is_a: GO:0016772 ! transferase activity, transferring phosphorus-containing groups

[Term]
id: GO:0016740
name: transferase activity
is_a: GO:0003824 ! catalytic activity

[Term]
id: GO:0016772
name: transferase activity, transferring phosphorus-containing groups
is_a: GO:0016740 ! transferase activity

[Term]
id: GO:0050896
name: response to stimulus
is_a: GO:0008150 ! biological_process

[Term]
id: IAO:0000001
name: conditional specification
def: "A directive information entity that specifies what should happen if the trigger condition is fulfilled." []
is_a: IAO:0000033 ! directive information entity
property_value: IAO:0000111 "conditional specification" xsd:string
property_value: IAO:0000114 IAO:0000120
property_value: IAO:0000117 "PlanAndPlannedProcess Branch" xsd:string
property_value: IAO:0000119 "OBI branch derived" xsd:string
property_value: IAO:0000119 "OBI_0000349" xsd:string

[Term]
id: IAO:0000003
name: measurement unit label
def: "A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure." []
is_a: IAO:0000009 ! datum label
property_value: IAO:0000111 "measurement unit label" xsd:string
property_value: IAO:0000112 "Examples of measurement unit labels are liters, inches, weight per volume." xsd:string
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000116 "2009-03-16: provenance: a term measurement unit was\nproposed for OBI (OBI_0000176) , edited by Chris Stoeckert and\nCristian Cocos, and subsequently moved to IAO where the objective for\nwhich the original term was defined was satisfied with the definition\nof this, different, term." xsd:string
property_value: IAO:0000116 "2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI." xsd:string
property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string
property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string

[Term]
id: IAO:0000005
name: objective specification
def: "A directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved." []
is_a: IAO:0000033 ! directive information entity
property_value: IAO:0000111 "objective specification" xsd:string
property_value: IAO:0000112 "In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction." xsd:string
property_value: IAO:0000114 IAO:0000122
property_value: IAO:0000116 "2009-03-16: original definition when imported from OBI read: \"objective is an non realizable information entity which can serve as that  proper part of a plan towards which the realization of the plan is directed.\"" xsd:string
property_value: IAO:0000116 "2014-03-31: In the example of usage (\"In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction\") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that." xsd:string
property_value: IAO:0000116 "Answers the question, why did you do this experiment?" xsd:string
property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string
property_value: IAO:0000117 "PERSON: Barry Smith" xsd:string
property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string
property_value: IAO:0000117 "PERSON: Jennifer Fostel" xsd:string
property_value: IAO:0000118 "goal specification" xsd:string
property_value: IAO:0000119 "OBI Plan and Planned Process/Roles Branch" xsd:string
property_value: IAO:0000119 "OBI_0000217" xsd:string

[Term]
id: IAO:0000006
name: narrative object
def: "A narrative object is an information content entity that is a set of propositions." []
is_a: IAO:0000030 ! information content entity
property_value: IAO:0000111 "narrative object" xsd:string
property_value: IAO:0000112 "Examples of narrative objects are reports, journal  articles, and patents submission." xsd:string
property_value: IAO:0000114 IAO:0000123
property_value: IAO:0000116 "2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity' and 'figure'. Alan restored as there are OBI dependencies and this merits further discussion" xsd:string
property_value: IAO:0000116 "agree - DENRIE. Issue(alan) do we only mean text? What about a story told by mime. Does music count? (no) what about an oral report. Regarding definition, saying it is a set of propositions means we loose the idea that wording matters. Maybe adjust saying a narrative object has some relationshop to a set of propositions" xsd:string
property_value: IAO:0000117 "person:Chris Stoeckert" xsd:string
property_value: IAO:0000119 group:OBI xsd:string
property_value: IAO:0000119 "OBI_0000013" xsd:string

[Term]
id: IAO:0000007
name: action specification
def: "A directive information entity that describes an action the bearer will take." []
is_a: IAO:0000033 ! directive information entity
property_value: IAO:0000112 "Pour the contents of flask 1 into flask 2" xsd:string
property_value: IAO:0000114 IAO:0000122
property_value: IAO:0000117 "Alan Ruttenberg" xsd:string
property_value: IAO:0000119 "OBI Plan and Planned Process branch" xsd:string

[Term]
id: IAO:0000008
name: obsolete_artifact
is_a: ObsoleteClass ! Obsolete Class
property_value: IAO:0000231 IAO:0000103
is_obsolete: true

[Term]
id: IAO:0000009
name: datum label
def: "A label is a symbol that is part of some other datum and is used to either partially define  the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label" []
is_a: IAO:0000030 ! information content entity
property_value: IAO:0000111 "datum label" xsd:string
property_value: IAO:0000114 IAO:0000123
property_value: IAO:0000116 http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n xsd:string
property_value: IAO:0000117 "GROUP: IAO" xsd:string
property_value: IAO:0000232 "9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum. \n" xsd:string

[Term]
id: IAO:0000010
name: software
def: "Software is a plan specification composed of a series of instructions that can be \ninterpreted by or directly executed by a processing unit." []
is_a: IAO:0000104 ! plan specification
property_value: IAO:0000111 "software" xsd:string
property_value: IAO:0000114 IAO:0000120
property_value: IAO:0000116 "see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178" xsd:string
property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string
property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string
property_value: IAO:0000117 "PERSON: Chris Stoeckert" xsd:string
property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string
property_value: IAO:0000119 "GROUP: OBI" xsd:string

[Term]
id: IAO:0000012
name: obsolete2_digital entity
def: "A digital entity is an information entity which is a collection of bits that can be interpreted by a computer. Two digital entities are the same if they are bitwise identical." []
is_a: ObsoleteClass ! Obsolete Class
property_value: IAO:0000111 "obsolete_digital entity" xsd:string
property_value: IAO:0000116 "3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4\n\nSuperclass was 'digitial quality'" xsd:string
property_value: IAO:0000117 "person:Chris Stoeckert" xsd:string
property_value: IAO:0000119 group:OBI xsd:string
property_value: IAO:0000119 "OBI_0000261" xsd:string
property_value: IAO:0000231 IAO:0000103
is_obsolete: true

[Term]
id: IAO:0000013
name: journal article
def: "A report that is published in a journal." []
is_a: IAO:0000088 ! report
is_a: IAO:0000311 ! publication
relationship: OBI:0000312 IAO:0000444 ! is_specified_output_of publishing process
relationship: OBI:0000312 IAO:0000444 ! is_specified_output_of publishing process
property_value: IAO:0000111 "journal article" xsd:string
property_value: IAO:0000112 "Examples are articles published in the journals, Nature and Science. The content can often be cited by reference to a paper based encoding, e.g.  Authors, Title of article, Journal name, date or year of publication, volume and page number." xsd:string
property_value: IAO:0000114 IAO:0000120
property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string
property_value: IAO:0000117 "PERSON: Chris Stoeckert" xsd:string
property_value: IAO:0000119 group:OBI xsd:string
property_value: IAO:0000119 "OBI_0000159" xsd:string

[Term]
id: IAO:0000015
name: information carrier
def: "A quality of an information bearer that imparts the information content" []
is_a: BFO:0000019 ! quality
intersection_of: BFO:0000019 ! quality
intersection_of: RO:0000059 IAO:0000030 ! concretizes information content entity
relationship: RO:0000059 IAO:0000030 ! concretizes information content entity
property_value: IAO:0000111 "information carrier" xsd:string
property_value: IAO:0000112 "In the case of a printed paperback novel the physicality of the ink and of the paper form part of the information bearer. The qualities of appearing black and having a certain pattern for the ink and appearing white for the paper form part of the information carrier in this case." xsd:string
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000116 "12/15/09: There is a concern that some ways that carry information may be processes rather than qualities, such as in a 'delayed wave carrier'." xsd:string
property_value: IAO:0000116 "2014-03-10: We are not certain that all information carriers are qualities. There was a discussion of dropping it." xsd:string
property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string
property_value: IAO:0000119 "Smith, Ceusters, Ruttenberg, 2000 years of philosophy" xsd:string

[Term]
id: IAO:0000017
name: model number
def: "A model number is an information content entity specifically borne by catalogs, design specifications, advertising materials, inventory systems and similar  that is about manufactured objects of the same class. The model number is an alternative term for the class. The manufactered objects may or may not also bear the model number. Model numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots." []
is_a: IAO:0000028 ! symbol
property_value: IAO:0000111 "model number" xsd:string
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000116 "manufactered items may have more than one model number, sometimes by rebranding, or because companies are sold and the products issued new model numbers" xsd:string
property_value: IAO:0000117 "Person: Alan Ruttenberg" xsd:string

[Term]
id: IAO:0000018
name: obsolete_material_entity
is_a: ObsoleteClass ! Obsolete Class
property_value: IAO:0000231 IAO:0000226
is_obsolete: true

[Term]
id: IAO:0000019
name: obsolete2_binary digital entity
def: "A binary digital entity is a digital entity that is encoded in a way that is not easily human readable and that contains other than text characters." []
is_a: ObsoleteClass ! Obsolete Class
property_value: IAO:0000111 "binary digital entity" xsd:string
property_value: IAO:0000112 "MS Word document, ZIP file, DICOM file, JPEG file" xsd:string
property_value: IAO:0000116 "3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4\nSuperclass was 'digital entity'" xsd:string
property_value: IAO:0000116 "digital_entity" xsd:string
property_value: IAO:0000117 "person:Chris Stoeckert" xsd:string
property_value: IAO:0000119 group:OBI xsd:string
property_value: IAO:0000119 "OBI_0000244" xsd:string
property_value: IAO:0000231 IAO:0000103
is_obsolete: true

[Term]
id: IAO:0000024
name: obsolete_unit of measure
def: "a unit of measure is the quality of some material entity compared to which another quality is some multiple of." []
is_a: ObsoleteClass ! Obsolete Class
property_value: IAO:0000112 "The length of a ruler." xsd:string
property_value: IAO:0000117 "Alan Ruttenberg" xsd:string
property_value: IAO:0000119 "Smith, Ceusters, Ruttenberg, 2000 years of philosophy" xsd:string
property_value: IAO:0000231 IAO:0000103
is_obsolete: true

[Term]
id: IAO:0000025
name: programming language
def: "A language in which source code is written that is intended to be executed/run by a software interpreter. Programming languages are ways to write instructions that specify what to do, and sometimes, how to do it." []
is_a: IAO:0000104 ! plan specification
property_value: IAO:0000111 "programming language" xsd:string
property_value: IAO:0000112 "R, Perl, Java" xsd:string
property_value: IAO:0000114 IAO:0000120
property_value: IAO:0000117 "person:Alan Ruttenberg" xsd:string
property_value: IAO:0000117 "person:Chris Stoeckert" xsd:string
property_value: IAO:0000119 group:OBI xsd:string
property_value: IAO:0000119 "OBI_0000058" xsd:string

[Term]
id: IAO:0000027
name: data item
def: "An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements." []
is_a: IAO:0000030 ! information content entity
relationship: IAO:0000136 NCBITaxon:9606 ! is about Homo sapiens
property_value: IAO:0000111 "data item" xsd:string
property_value: IAO:0000112 "Data items include counts of things, analyte concentrations, and statistical summaries." xsd:string
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000116 "2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers." xsd:string
property_value: IAO:0000116 "2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum." xsd:string
property_value: IAO:0000116 "2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym." xsd:string
property_value: IAO:0000116 "2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/" xsd:string
property_value: IAO:0000116 "JAR: datum     -- well, this will be very tricky to define, but maybe some \ninformation-like stuff that might be put into a computer and that is \nmeant, by someone, to denote and/or to be interpreted by some \nprocess... I would include lists, tables, sentences... I think I might \ndefer to Barry, or to Brian Cantwell Smith\n\nJAR: A data item is an approximately justified approximately true approximate belief" xsd:string
property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string
property_value: IAO:0000117 "PERSON: Chris Stoeckert" xsd:string
property_value: IAO:0000117 "PERSON: Jonathan Rees" xsd:string
property_value: IAO:0000118 "data" xsd:string

[Term]
id: IAO:0000028
name: symbol
def: "An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity." []
is_a: IAO:0000030 ! information content entity
property_value: IAO:0000111 "symbol" xsd:string
property_value: IAO:0000112 "a serial number such as \"12324X\"" xsd:string
property_value: IAO:0000112 "a stop sign" xsd:string
property_value: IAO:0000112 "a written proper name such as \"OBI\"" xsd:string
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000116 "20091104, MC: this needs work and will most probably change" xsd:string
property_value: IAO:0000116 "2014-03-31: We would like to have a deeper analysis of 'mark' and 'sign' in the future (see https://github.com/information-artifact-ontology/IAO/issues/154)." xsd:string
property_value: IAO:0000117 "PERSON: James A. Overton" xsd:string
property_value: IAO:0000117 "PERSON: Jonathan Rees" xsd:string
property_value: IAO:0000119 "based on Oxford English Dictionary" xsd:string

[Term]
id: IAO:0000029
name: numeral
def: "A symbol that denotes a number." []
is_a: IAO:0000028 ! symbol
property_value: IAO:0000111 "numeral" xsd:string
property_value: IAO:0000114 IAO:0000123
property_value: IAO:0000117 "PERSON: Jonathan Rees" xsd:string

[Term]
id: IAO:0000030
name: information content entity
def: "A generically dependent continuant that is about some thing." []
is_a: BFO:0000031 ! generically dependent continuant
relationship: IAO:0000136 BFO:0000001 ! is about entity
property_value: IAO:0000111 "information content entity" xsd:string
property_value: IAO:0000112 "Examples of information content entites include journal articles, data, graphical layouts, and graphs." xsd:string
property_value: IAO:0000114 IAO:0000122
property_value: IAO:0000116 "2014-03-10: The use of \"thing\" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ)." xsd:string
property_value: IAO:0000116 "information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907).\n\nPrevious. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity." xsd:string
property_value: IAO:0000117 "PERSON: Chris Stoeckert" xsd:string
property_value: IAO:0000119 "OBI_0000142" xsd:string

[Term]
id: IAO:0000031
name: integer numeral
def: "A numeral that denotes an integer" []
is_a: IAO:0000029 ! numeral
property_value: IAO:0000111 "integer numeral" xsd:string
property_value: IAO:0000114 IAO:0000123
property_value: IAO:0000117 "PERSON: Jonathan Rees" xsd:string

[Term]
id: IAO:0000032
name: scalar measurement datum
def: "A scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label." []
is_a: IAO:0000109 ! measurement datum
property_value: IAO:0000112 "10 feet. 3 ml." xsd:string
property_value: IAO:0000114 IAO:0000120
property_value: IAO:0000116 "2009-03-16: we decided to keep datum singular in scalar measurement datum, as in\nthis case we explicitly refer to the singular form" xsd:string
property_value: IAO:0000116 "Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them." xsd:string
property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string
property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string

[Term]
id: IAO:0000033
name: directive information entity
def: "An information content entity whose concretizations indicate to their bearer how to realize them in a process." []
is_a: IAO:0000030 ! information content entity
relationship: IAO:0000136 BFO:0000017 ! is about realizable entity
property_value: IAO:0000114 IAO:0000122
property_value: IAO:0000116 "2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was  \"is the specification of a process that can be concretized and realized by an actor\" with alternative term  \"instruction\".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term." xsd:string
property_value: IAO:0000116 "2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it." xsd:string
property_value: IAO:0000116 "8/6/2009 Alan Ruttenberg: Changed label from \"information entity about a realizable\" after discussions at ICBO" xsd:string
property_value: IAO:0000116 "Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan" xsd:string
property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string
property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string

[Term]
id: IAO:0000034
name: time trigger
is_a: IAO:0000001 ! conditional specification
property_value: IAO:0000111 "time trigger" xsd:string
property_value: IAO:0000114 IAO:0000124
property_value: IAO:0000117 "PlanAndPlannedProcess Branch" xsd:string

[Term]
id: IAO:0000035
name: obsolete_study interpretation
def: "A study interpretation is a textual entity about the implications of a study result. Examples include discussion of whether a hypothesis is false, whether the study failed to address the hypothesis, and whether the study results have led to new hypotheses" []
is_a: ObsoleteClass ! Obsolete Class
property_value: IAO:0000111 "obsolete_study interpretation" xsd:string
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000116 "2009-03-16: definition was \"A conclusion is a narrative object which can be published in a paper summerizing and interpreting a protocol application.\"" xsd:string
property_value: IAO:0000116 "2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI." xsd:string
property_value: IAO:0000116 "The obsoleting of narrative object required a modest change in the definition of this term.  Circularity with \"interpretation... interprets\" has been removed, using \"about the implications\" instead." xsd:string
property_value: IAO:0000117 "Lawrence Hunter" xsd:string
property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string
property_value: IAO:0000117 "PERSON: Jennifer Fostel" xsd:string
property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string
property_value: IAO:0000118 "conclusion" xsd:string
property_value: IAO:0000119 "OBI_0000005" xsd:string
property_value: IAO:0000231 IAO:0000103
is_obsolete: true

[Term]
id: IAO:0000037
name: dot plot
def: "A dot plot is a report graph which is a graphical representation of data where each data point is represented by a single dot placed on coordinates corresponding to data point values in particular dimensions." []
is_a: IAO:0000038 ! graph
property_value: IAO:0000111 "dot plot" xsd:string
property_value: IAO:0000112 "Dot plot of SSC-H and FSC-H." xsd:string
property_value: IAO:0000114 IAO:0000002
property_value: IAO:0000117 "person:Allyson Lister" xsd:string
property_value: IAO:0000117 "person:Chris Stoeckert" xsd:string
property_value: IAO:0000119 group:OBI xsd:string
property_value: IAO:0000119 "OBI_0000123" xsd:string

[Term]
id: IAO:0000038
name: graph
def: "A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way." []
is_a: IAO:0000309 ! diagram
property_value: IAO:0000111 "graph" xsd:string
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string
property_value: IAO:0000117 "person:Alan Ruttenberg" xsd:string
property_value: IAO:0000117 "person:Allyson Lister" xsd:string
property_value: IAO:0000119 group:OBI xsd:string
property_value: IAO:0000119 "OBI_0000240" xsd:string

[Term]
id: IAO:0000047
name: obsolete2_text based digital entity
def: "A text based digital entity is a digital entity that is encoded so that it only contains text characters." []
is_a: ObsoleteClass ! Obsolete Class
property_value: IAO:0000111 "text based digital entity" xsd:string
property_value: IAO:0000112 "XML file, C++ source code file" xsd:string
property_value: IAO:0000116 "3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4\nsuperclass was 'digital document'" xsd:string
property_value: IAO:0000116 "digital_entity" xsd:string
property_value: IAO:0000117 "person:Chris Stoeckert" xsd:string
property_value: IAO:0000119 group:OBI xsd:string
property_value: IAO:0000119 "OBI_0000132" xsd:string
property_value: IAO:0000231 IAO:0000103
is_obsolete: true

[Term]
id: IAO:0000055
name: rule
def: "A rule is an executable which guides, defines, restricts actions." []
is_a: IAO:0000001 ! conditional specification
property_value: IAO:0000111 "rule" xsd:string
property_value: IAO:0000112 "example to be added" xsd:string
property_value: IAO:0000114 IAO:0000123
property_value: IAO:0000116 "MSI" xsd:string
property_value: IAO:0000117 "PRS" xsd:string
property_value: IAO:0000119 "OBI_0500021" xsd:string
property_value: IAO:0000119 "PRS" xsd:string

[Term]
id: IAO:0000057
name: contour plot
is_a: IAO:0000038 ! graph
property_value: IAO:0000111 "contour plot" xsd:string
property_value: IAO:0000112 "Contour plot of SSC-H, FSC-H, and FL1-H." xsd:string
property_value: IAO:0000114 IAO:0000002
property_value: IAO:0000116 "generically_dependent_continuants" xsd:string
property_value: IAO:0000117 "person:Allyson Lister" xsd:string
property_value: IAO:0000117 "person:Chris Stoeckert" xsd:string
property_value: IAO:0000119 "group:Flow Cytometry community" xsd:string
property_value: IAO:0000119 "OBI_0000246" xsd:string

[Term]
id: IAO:0000059
name: obsolete2_report figure
def: "A report figure is a report display element that has some aspect of illustration, but may be a composite of figures, images, and other elements" []
is_a: ObsoleteClass ! Obsolete Class
property_value: IAO:0000111 "report figure" xsd:string
property_value: IAO:0000114 IAO:0000124
property_value: IAO:0000116 "I prepended the 'report ' to make it clear that we mean parts of reports here. We may want a more generic version of 'figure', in which case this would become a defined class - figure and part_of some report" xsd:string
property_value: IAO:0000116 "Replaced by defined version of figure" xsd:string
property_value: IAO:0000117 "person:Alan Ruttenberg" xsd:string
property_value: IAO:0000117 "person:Allyson Lister" xsd:string
property_value: IAO:0000119 group:OBI xsd:string
property_value: IAO:0000119 "OBI_0000027" xsd:string
property_value: IAO:0000231 IAO:0000103
is_obsolete: true

[Term]
id: IAO:0000064
name: algorithm
def: "A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata." []
is_a: IAO:0000104 ! plan specification
property_value: IAO:0000111 "algorithm" xsd:string
property_value: IAO:0000112 "PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies." xsd:string
property_value: IAO:0000114 IAO:0000120
property_value: IAO:0000117 "Philippe Rocca-Serra" xsd:string
property_value: IAO:0000117 "PlanAndPlannedProcess Branch" xsd:string
property_value: IAO:0000119 "adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg)" xsd:string
property_value: IAO:0000119 "OBI_0000270" xsd:string

[Term]
id: IAO:0000065
name: software interpreter
def: "A software interpreter is a software application that executes some specified input software." []
is_a: IAO:0000064 ! algorithm
property_value: IAO:0000111 "software interpreter" xsd:string
property_value: IAO:0000112 "R program, Perl interpreter, Java virtual machine" xsd:string
property_value: IAO:0000114 IAO:0000120
property_value: IAO:0000116 "Do we care? Jennifer: Yes, there was a particular version of R that had a bug and it was fixed later. That would imply that we mean specific version of an interpreter. So an instance of this would be a particular version of the interpreter" xsd:string
property_value: IAO:0000117 "person:Alan Ruttenberg" xsd:string
property_value: IAO:0000117 "person:Chris Stoeckert" xsd:string
property_value: IAO:0000119 group:OBI xsd:string
property_value: IAO:0000119 "OBI_0000199" xsd:string

[Term]
id: IAO:0000078
name: curation status specification
def: "The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value." []
is_a: IAO:0000102 ! data about an ontology part
property_value: IAO:0000111 "curation status specification" xsd:string
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000116 "Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)" xsd:string
property_value: IAO:0000117 "PERSON:Bill Bug" xsd:string
property_value: IAO:0000119 GROUP:OBI:<http://purl.obolibrary.org/obo/obi> xsd:string
property_value: IAO:0000119 "OBI_0000266" xsd:string

[Term]
id: IAO:0000079
name: density plot
def: "A density plot is a report graph which is a graphical representation of data where the tint of a particular pixel corresponds to some kind of function corresponding the the amount of data points relativelly with their distance from the the pixel." []
is_a: IAO:0000038 ! graph
property_value: IAO:0000111 "density plot" xsd:string
property_value: IAO:0000112 "Density plot of SSC-H and FSC-H." xsd:string
property_value: IAO:0000114 IAO:0000002
property_value: IAO:0000117 "person:Allyson Lister" xsd:string
property_value: IAO:0000117 "person:Chris Stoeckert" xsd:string
property_value: IAO:0000119 "group:Flow Cytometry community" xsd:string
property_value: IAO:0000119 "OBI_0000179" xsd:string

[Term]
id: IAO:0000088
name: report
def: "A document assembled by an author for the purpose of providing information for the audience. A report is the output of a documenting process and has the objective to be consumed by a specific audience. Topic of the report is on something that has completed. A report is not a single figure. Examples of reports are journal article, patent application, grant progress report, case report (not patient record)." []
is_a: IAO:0000310 ! document
property_value: IAO:0000111 "report" xsd:string
property_value: IAO:0000112 "Examples of reports are gene lists and investigation reports. These are not published (journal) articles but may be included in a journal article." xsd:string
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000116 "2009-03-16: comment from Darren Natale: I am slightly uneasy with the sentence \"Topic of the report is on \nsomething that has completed.\"  Should it be restricted to those things \nthat are completed?  For example, a progress report is (usually) about \nsomething that definitely has *not* been completed, or may include \n(only) projections.  I think the definition would not suffer if the \nwhole sentence is deleted." xsd:string
property_value: IAO:0000116 "2009-03-16: this was report of results with definition: A report is a narrative object that is a formal statement of the results of an investigation, or of any matter on which definite information is required, made by some person or body instructed or required to do so." xsd:string
property_value: IAO:0000116 "2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI." xsd:string
property_value: IAO:0000116 "2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'document'. Alan restored as there are OBI dependencies and this merits further discussion" xsd:string
property_value: IAO:0000116 "disagreement about where reports go. alan: only some gene lists are reports. Is a report all the content of some document? The example of usage suggests that a report may be part of  some article. Term needs clarification" xsd:string
property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string
property_value: IAO:0000117 "PERSON: Chris Stoeckert" xsd:string
property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string
property_value: IAO:0000119 "GROUP: OBI" xsd:string
property_value: IAO:0000119 "OBI_0000099" xsd:string

[Term]
id: IAO:0000091
name: obsolete_report element
def: "A report element is a narrative object in which information is presented and consumed by a human being, and is part of a report. Examples of report elements are figure (dot plot), table, text portion (may include a movie or audio clip on a web page)." []
is_a: ObsoleteClass ! Obsolete Class
property_value: IAO:0000111 "report element" xsd:string
property_value: IAO:0000114 IAO:0000120
property_value: IAO:0000116 "2009-03-16: needs some more work (clarify relations)." xsd:string
property_value: IAO:0000116 "2009-03-16: was report display element with definition: A report display element is a narrative object that is part of a report. Report display elements are set off from the textual parts of a report and are typically given a label(e.g. Figure 2) which is used to refer to the element from the text. Typically the 2d layout is part of the identity of such elements." xsd:string
property_value: IAO:0000116 "2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI." xsd:string
property_value: IAO:0000116 "2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity' and 'figure'. Alan restored as there are OBI dependencies and this merits further discussion" xsd:string
property_value: IAO:0000116 "Replaced by textual entity and figure" xsd:string
property_value: IAO:0000116 "There will be some issue here about whether these are defined classes. As intended these are meant to denote the parts of the report that are not textual but are typically boxed and set within the text, labelled with some identifier, and referred to in the text" xsd:string
property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string
property_value: IAO:0000117 "PERSON: Allyson Lister" xsd:string
property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string
property_value: IAO:0000119 GROUP:OBI xsd:string
property_value: IAO:0000119 "OBI_0000001" xsd:string
property_value: IAO:0000231 IAO:0000103
is_obsolete: true

[Term]
id: IAO:0000093
name: obsolete2_binary executable
def: "Binary executable is a digital entity consisting of the binary representation of machine instructions of a specific processor or they may be binary pseudocode for a virtual machine. A non-source executable file is also called an object program. It is assumed that the binary executable file contains properly-formatted computer instructions.  (derived from Wikipedia, Nov 1, 2007)" []
is_a: ObsoleteClass ! Obsolete Class
property_value: IAO:0000111 "binary executable" xsd:string
property_value: IAO:0000116 "3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4\nsuperclass was 'digital entity'" xsd:string
property_value: IAO:0000117 "person:Jennifer Fostel" xsd:string
property_value: IAO:0000119 group:OBI xsd:string
property_value: IAO:0000119 "OBI_0000222" xsd:string
property_value: IAO:0000231 IAO:0000103
is_obsolete: true

[Term]
id: IAO:0000096
name: source code module
def: "A source code module is a directive information entity that specifies, using a programming language, some algorithm." []
is_a: IAO:0000033 ! directive information entity
property_value: IAO:0000111 "source code module" xsd:string
property_value: IAO:0000112 "The written source code that implements part of an algorithm. Test - if you know that it was written in a specific language, then it can be source code module. We mean here, roughly, the wording of a document such as a perl script." xsd:string
property_value: IAO:0000114 IAO:0000123
property_value: IAO:0000117 "person:Alan Ruttenberg" xsd:string
property_value: IAO:0000117 "person:Chris Stoeckert" xsd:string
property_value: IAO:0000119 group:OBI xsd:string
property_value: IAO:0000119 "OBI_0000039" xsd:string

[Term]
id: IAO:0000097
name: obsolete_report table
def: "A report table is a report display element consisting of a matrix of cells layed out in a grid, some set of which are filled with some information content" []
is_a: ObsoleteClass ! Obsolete Class
property_value: IAO:0000111 "report table" xsd:string
property_value: IAO:0000114 IAO:0000002
property_value: IAO:0000116 "2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity table'. Alan restored as there are OBI dependencies and this merits further discussion" xsd:string
property_value: IAO:0000117 "person:Alan Ruttenberg" xsd:string
property_value: IAO:0000117 "person:Allyson Lister" xsd:string
property_value: IAO:0000119 group:OBI xsd:string
property_value: IAO:0000119 "OBI_0000265" xsd:string
property_value: IAO:0000231 IAO:0000103
is_obsolete: true

[Term]
id: IAO:0000098
name: data format specification
def: "A data format specification is the information content borne by the document published defining the specification.\nExample: The ISO document specifying what encompasses an XML document; The instructions in a XSD file" []
is_a: IAO:0000033 ! directive information entity
property_value: IAO:0000111 "data format specification" xsd:string
property_value: IAO:0000114 IAO:0000123
property_value: IAO:0000116 "2009-03-16: provenance: term imported from OBI_0000187, which had original definition \"A data format specification is a plan which organizes\ninformation. Example: The ISO document specifying what encompasses an\nXML document; The instructions in a XSD file\"" xsd:string
property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string
property_value: IAO:0000117 "PlanAndPlannedProcess Branch" xsd:string
property_value: IAO:0000119 "OBI branch derived" xsd:string
property_value: IAO:0000119 "OBI_0000187" xsd:string

[Term]
id: IAO:0000100
name: data set
def: "A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets." []
is_a: IAO:0000027 ! data item
property_value: IAO:0000111 "data set" xsd:string
property_value: IAO:0000112 "Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves)." xsd:string
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000116 "2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type" xsd:string
property_value: IAO:0000116 "2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction." xsd:string
property_value: IAO:0000117 "person:Allyson Lister" xsd:string
property_value: IAO:0000117 "person:Chris Stoeckert" xsd:string
property_value: IAO:0000119 group:OBI xsd:string
property_value: IAO:0000119 "OBI_0000042" xsd:string

[Term]
id: IAO:0000101
name: image
def: "An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface." []
is_a: IAO:0000308 ! figure
property_value: IAO:0000111 "image" xsd:string
property_value: IAO:0000114 IAO:0000122
property_value: IAO:0000117 "person:Alan Ruttenberg" xsd:string
property_value: IAO:0000117 person:Allyson xsd:string
property_value: IAO:0000117 "person:Chris Stoeckert" xsd:string
property_value: IAO:0000119 group:OBI xsd:string
property_value: IAO:0000119 "OBI_0000030" xsd:string

[Term]
id: IAO:0000102
name: data about an ontology part
def: "Data about an ontology part is a data item about a part of an ontology, for example a term" []
is_a: IAO:0000027 ! data item
property_value: IAO:0000111 "data about an ontology part" xsd:string
property_value: IAO:0000117 "Person:Alan Ruttenberg" xsd:string

[Term]
id: IAO:0000104
name: plan specification
def: "A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified." []
comment: 2/3/2009 Comment from OBI review.\n\nAction specification not well enough specified.\nConditional specification not well enough specified.\nQuestion whether all plan specifications have objective specifications.\n\nRequest that IAO either clarify these or change definitions not to use them
is_a: IAO:0000033 ! directive information entity
relationship: BFO:0000051 IAO:0000005 ! has part objective specification
relationship: BFO:0000051 IAO:0000007 ! has part action specification
property_value: IAO:0000111 "plan specification" xsd:string
property_value: IAO:0000112 "PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice." xsd:string
property_value: IAO:0000114 IAO:0000122
property_value: IAO:0000116 "2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was \" a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan\". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term." xsd:string
property_value: IAO:0000116 "2014-03-31: A plan specification can have other parts, such as conditional specifications." xsd:string
property_value: IAO:0000116 "Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved" xsd:string
property_value: IAO:0000117 "Alan Ruttenberg" xsd:string
property_value: IAO:0000119 "OBI Plan and Planned Process branch" xsd:string
property_value: IAO:0000119 "OBI_0000344" xsd:string

[Term]
id: IAO:0000105
name: obsolete2_digital document
def: "A digital document is a digital entity consisting of an electronic file which can be rendered into human-readable form by one or more computational applications.  The digital document does not refer to the information content of the document but to an instance of the file." []
is_a: ObsoleteClass ! Obsolete Class
property_value: IAO:0000111 "digital document" xsd:string
property_value: IAO:0000116 "3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4\nsuperclass was 'digial entity'" xsd:string
property_value: IAO:0000117 "person:Jennifer Fostel" xsd:string
property_value: IAO:0000119 group:OBI xsd:string
property_value: IAO:0000119 "OBI_0000195" xsd:string
property_value: IAO:0000231 IAO:0000103
is_obsolete: true

[Term]
id: IAO:0000109
name: measurement datum
def: "A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device." []
is_a: IAO:0000027 ! data item
property_value: IAO:0000111 "measurement datum" xsd:string
property_value: IAO:0000112 "Examples of measurement data are the recoding of the weight of a mouse as {40,mass,\"grams\"}, the recording of an observation of the behavior of the mouse {,process,\"agitated\"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}." xsd:string
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000116 "2/2/2009 is_specified_output of some assay?" xsd:string
property_value: IAO:0000117 "person:Chris Stoeckert" xsd:string
property_value: IAO:0000119 group:OBI xsd:string
property_value: IAO:0000119 "OBI_0000305" xsd:string

[Term]
id: IAO:0000128
name: obsolete_identifier
is_a: ObsoleteClass ! Obsolete Class
property_value: IAO:0000114 IAO:0000121
property_value: IAO:0000116 "_identifier is a container under information content entity for collecting types of terms to indicate a specific instance or clas of what was used or participated in an investigation. Identifiers are borne by a product or its packaging, and can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots.\n\nNote: everybody agreed that identifier is probably a too general term. We however felt that it would be appropriate to group \"identifiying\" terms under some kind of umbrella. We therefore propose to use _identifier for that purpose. As per OBI conventions, the _ prefixing identifier indicates that this is a helper class and shouldn't be considered as final." xsd:string
property_value: IAO:0000231 IAO:0000226
is_obsolete: true

[Term]
id: IAO:0000129
name: version number
def: "A version number is an information content entity which is a sequence of characters borne by part of each of a class of manufactured products or its packaging and indicates its order within a set of other products having the same name." []
is_a: IAO:0000028 ! symbol
property_value: IAO:0000111 "version number" xsd:string
property_value: IAO:0000114 IAO:0000123
property_value: IAO:0000116 "Note: we feel that at the moment we are happy with a general version number, and that we will subclass as needed in the future. For example, see 7. genome sequence version" xsd:string
property_value: IAO:0000117 "GROUP: IAO" xsd:string

[Term]
id: IAO:0000131
name: serial number
def: "A serial number is an information content entity which is a unique sequence of characters borne by part of manufactured product or its packaging that is assigned to each individual in some class of products, and so can serve as a way to identify an individual product within the class. Serial numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots." []
is_a: IAO:0000028 ! symbol
property_value: IAO:0000111 "serial number" xsd:string
property_value: IAO:0000114 IAO:0000123
property_value: IAO:0000116 "Note: during the call there was some confusion between serial number and model number. We agreed that it would be very helpful for all those terms to have example of usages - please add if you have any :-)" xsd:string
property_value: IAO:0000117 "GROUP: IAO" xsd:string

[Term]
id: IAO:0000132
name: lot number
def: "A lot number is an information content entity which is an identical sequence of character borne by part of manufactured product or its packaging for each instances of a product class in a discrete batch of an item. Lot numbers are usually assigned to each separate production run of an item. Manufacturing as a lot might be due to a variety of reasons, for example,  a single process during which many individuals are made from the same portion of source material. Lot numbers can be encoded in a pattern  of other information objects, such as bar codes, numerals, or patterns of dots." []
is_a: IAO:0000028 ! symbol
property_value: IAO:0000111 "lot number" xsd:string
property_value: IAO:0000114 IAO:0000123
property_value: IAO:0000117 "GROUP: IAO" xsd:string
property_value: IAO:0000118 "batch number" xsd:string

[Term]
id: IAO:0000140
name: setting datum
def: "A settings datum is a datum that denotes some configuration of an instrument." []
is_a: IAO:0000027 ! data item
property_value: IAO:0000114 IAO:0000123
property_value: IAO:0000116 "2/3/2009 Feedback from OBI\n\nThis should be a \"setting specification\". There is a question of whether it is information about a realizable or not.\n\nPro other specification are about realizables.\nCons sometimes specifies a quality which is not a realizable." xsd:string
property_value: IAO:0000116 "Alan grouped these in placeholder for the moment. Name by analogy to measurement datum." xsd:string

[Term]
id: IAO:0000141
name: obsolete_digital quality
is_a: ObsoleteClass ! Obsolete Class
property_value: IAO:0000116 "3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4" xsd:string
property_value: IAO:0000116 "Need to rework digital entity. Digital quality was suggested by Barry." xsd:string
property_value: IAO:0000231 IAO:0000103
is_obsolete: true

[Term]
id: IAO:0000144
name: conclusion textual entity
def: "A textual entity that expresses the results of reasoning about a problem, for instance as typically found towards the end of scientific papers." []
is_a: IAO:0000300 ! textual entity
property_value: IAO:0000111 "conclusion textual entity" xsd:string
property_value: IAO:0000112 "that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660" xsd:string
property_value: IAO:0000114 IAO:0000120
property_value: IAO:0000116 "2009/09/28 Alan Ruttenberg. Fucoidan-use-case" xsd:string
property_value: IAO:0000116 "2009/10/23 Alan Ruttenberg: We need to work on the definition still" xsd:string
property_value: IAO:0000117 "Person:Alan Ruttenberg" xsd:string

[Term]
id: IAO:0000178
name: material information bearer
def: "A material entity in which a concretization of an information content entity inheres." []
is_a: BFO:0000040 ! material entity
property_value: IAO:0000111 "material information bearer" xsd:string
property_value: IAO:0000112 "a brain" xsd:string
property_value: IAO:0000112 "a hard drive" xsd:string
property_value: IAO:0000112 "A page of a paperback novel with writing on it. The paper itself is a material information bearer, the pattern of ink is the information carrier." xsd:string
property_value: IAO:0000114 IAO:0000122
property_value: IAO:0000117 "GROUP: IAO" xsd:string

[Term]
id: IAO:0000179
name: histogram
def: "A histogram is a report graph which is a statistical description of a\ndistribution in terms of occurrence frequencies of different event classes." []
is_a: IAO:0000038 ! graph
property_value: IAO:0000111 "histogram" xsd:string
property_value: IAO:0000114 IAO:0000122
property_value: IAO:0000117 "PERSON:Chris Stoeckert" xsd:string
property_value: IAO:0000117 "PERSON:James Malone" xsd:string
property_value: IAO:0000117 "PERSON:Melanie Courtot" xsd:string
property_value: IAO:0000119 GROUP:OBI xsd:string

[Term]
id: IAO:0000180
name: heatmap
def: "A heatmap is a report graph which is a graphical representation of data\nwhere the values taken by a variable(s) are shown as colors in a\ntwo-dimensional map." []
is_a: IAO:0000038 ! graph
property_value: IAO:0000111 "heatmap" xsd:string
property_value: IAO:0000114 IAO:0000122
property_value: IAO:0000117 "PERSON:Chris Stoeckert" xsd:string
property_value: IAO:0000117 "PERSON:James Malone" xsd:string
property_value: IAO:0000117 "PERSON:Melanie Courtot" xsd:string
property_value: IAO:0000119 GROUP:OBI xsd:string

[Term]
id: IAO:0000181
name: Venn diagram
def: "A Venn diagram is a report graph showing all hypothetically possible\nlogical relations between a finite collection of sets." []
is_a: IAO:0000038 ! graph
property_value: IAO:0000111 "Venn diagram" xsd:string
property_value: IAO:0000114 IAO:0000122
property_value: IAO:0000117 "PERSON:Chris Stoeckert" xsd:string
property_value: IAO:0000117 "PERSON:James Malone" xsd:string
property_value: IAO:0000117 "PERSON:Melanie Courtot" xsd:string
property_value: IAO:0000119 "WEB: http://en.wikipedia.org/wiki/Venn_diagram" xsd:string

[Term]
id: IAO:0000182
name: obsolete_survival curve
def: "A survival curve is a report graph which is a graphical representation of data where the percentage of survival is plotted as a function of time." []
is_a: ObsoleteClass ! Obsolete Class
property_value: IAO:0000111 "obsolete_survival curve" xsd:string
property_value: IAO:0000114 IAO:0000122
property_value: IAO:0000117 "PERSON:Chris Stoeckert" xsd:string
property_value: IAO:0000117 "PERSON:James Malone" xsd:string
property_value: IAO:0000117 "PERSON:Melanie Courtot" xsd:string
property_value: IAO:0000119 "WEB: http://www.graphpad.com/www/book/survive.htm" xsd:string
property_value: IAO:0000231 IAO:0000103
is_obsolete: true

[Term]
id: IAO:0000183
name: dendrogram
def: "A dendrogram is a report graph which is a tree diagram\nfrequently used to illustrate the arrangement of the clusters produced by a\nclustering algorithm." []
is_a: IAO:0000038 ! graph
property_value: IAO:0000111 "dendrogram" xsd:string
property_value: IAO:0000112 "Dendrograms are often used in computational biology to\nillustrate the clustering of genes." xsd:string
property_value: IAO:0000114 IAO:0000122
property_value: IAO:0000117 "PERSON:Chris Stoeckert" xsd:string
property_value: IAO:0000117 "PERSON:James Malone" xsd:string
property_value: IAO:0000117 "PERSON:Melanie Courtot" xsd:string
property_value: IAO:0000119 "WEB: http://en.wikipedia.org/wiki/Dendrogram" xsd:string

[Term]
id: IAO:0000184
name: scatter plot
def: "A scatterplot is a graph which uses Cartesian coordinates to display values for two variables for a set of data. The data is displayed as a collection of points, each having the value of one variable determining the position on the horizontal axis and the value of the other variable determining the position on the vertical axis." []
is_a: IAO:0000038 ! graph
property_value: IAO:0000111 "scatter plot" xsd:string
property_value: IAO:0000112 "Comparison of gene expression values in two samples can be displayed in a scatter plot" xsd:string
property_value: IAO:0000114 IAO:0000122
property_value: IAO:0000117 "PERSON:Chris Stoeckert" xsd:string
property_value: IAO:0000117 "PERSON:James Malone" xsd:string
property_value: IAO:0000117 "PERSON:Melanie Courtot" xsd:string
property_value: IAO:0000118 "scattergraph" xsd:string
property_value: IAO:0000119 "WEB: http://en.wikipedia.org/wiki/Scatterplot" xsd:string

[Term]
id: IAO:0000185
name: photograph
def: "A photograph is created by projecting an image onto a photosensitive surface such as a chemically treated plate or film, CCD receptor, etc." []
is_a: IAO:0000101 ! image
property_value: IAO:0000114 IAO:0000122
property_value: IAO:0000117 "PERSON:Alan Ruttenberg" xsd:string
property_value: IAO:0000117 "PERSON:Joanne Luciano" xsd:string
property_value: IAO:0000117 "PERSON:Melanie Courtot" xsd:string
property_value: IAO:0000119 "WEB: http://en.wiktionary.org/wiki/photograph" xsd:string

[Term]
id: IAO:0000186
name: photographic print
def: "A photographic print is a material entity upon which a photograph generically depends." []
is_a: IAO:0000178 ! material information bearer
property_value: IAO:0000111 "photographic print" xsd:string
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "PERSON:Alan Ruttenberg" xsd:string
property_value: IAO:0000117 "PERSON:Melanie Courtot" xsd:string

[Term]
id: IAO:0000225
name: obsolescence reason specification
def: "The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value." []
is_a: IAO:0000102 ! data about an ontology part
property_value: IAO:0000111 "obsolescence reason specification" xsd:string
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000116 "The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology." xsd:string
property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string
property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string

[Term]
id: IAO:0000300
name: textual entity
def: "A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc." []
is_a: IAO:0000030 ! information content entity
property_value: IAO:0000111 "textual entity" xsd:string
property_value: IAO:0000112 "Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities" xsd:string
property_value: IAO:0000114 IAO:0000123
property_value: IAO:0000116 "AR, (IAO call 2009-09-01): a document as a whole is not typically a textual entity, because it has pictures in it - rather there are parts of it that are textual entities. Examples: The title, paragraph 2 sentence 7, etc." xsd:string
property_value: IAO:0000116 "MC, 2009-09-14 (following IAO call 2009-09-01): textual entities live at the FRBR (http://en.wikipedia.org/wiki/Functional_Requirements_for_Bibliographic_Records) manifestation level. Everything is significant: line break, pdf and html versions of same document are different textual entities." xsd:string
property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string
property_value: IAO:0000118 "text" xsd:string

[Term]
id: IAO:0000301
name: citation
def: "A textual entity intended to identify a particular publication." []
is_a: IAO:0000300 ! textual entity
relationship: IAO:0000136 IAO:0000310 ! is about document
property_value: IAO:0000111 "citation" xsd:string
property_value: IAO:0000112 "Verspoor, K., Cohen, KB., Hunter, L. Textual characteristics of traditional and Open Access scientific journals are similar, BMC Bioinformatics 2009, 10:183." xsd:string
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string

[Term]
id: IAO:0000302
name: author identification
def: "A textual entity intended to identify a particular author" []
is_a: IAO:0000590 ! written name
property_value: IAO:0000111 "author identification" xsd:string
property_value: IAO:0000112 "L. Hunter" xsd:string
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string

[Term]
id: IAO:0000303
name: institutional identification
def: "A textual entity intended to identify a particular institution" []
is_a: IAO:0000300 ! textual entity
property_value: IAO:0000111 "institutional identification" xsd:string
property_value: IAO:0000112 "University of Colorado Denver School of Medicine" xsd:string
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string

[Term]
id: IAO:0000304
name: caption
def: "A textual entity that describes a figure" []
is_a: IAO:0000300 ! textual entity
relationship: IAO:0000136 IAO:0000308 ! is about figure
property_value: IAO:0000111 "caption" xsd:string
property_value: IAO:0000112 "Figure 1: A system diagram describing the modules of the Hanalyzer.  Reading methods (green) take external sources of knowledge (blue) and extract information from them, either by parsing structured data or biomedical language processing to extract information from unstructured data.  Reading modules are responsible for tracking the provenance of all knowledge.  Reasoning methods (yellow) enrich the knowledge that results from reading by, for example, noting two genes that are annotated to the same ontology term or database entry.  All knowledge sources, read or reasoned, are assigned a reliability score, and all are combined using that score into a knowledge network (orange) that represents the integration of all sorts of relationship between a pair of genes and a combined reliability score.  A data network (also orange) is created from experimental results to be analyzed.  The reporting modules (pink) integrate the data and knowledge networks, producing visualizations that can be queried with the associated drill-down tool." xsd:string
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string

[Term]
id: IAO:0000305
name: document title
def: "A textual entity that names a document" []
is_a: IAO:0000300 ! textual entity
property_value: IAO:0000111 "document title" xsd:string
property_value: IAO:0000112 "Textual characteristics of traditional and Open Access scientific journals are similar" xsd:string
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string

[Term]
id: IAO:0000306
name: table
def: "A textual entity that contains a two-dimensional arrangement of texts repeated at regular intervals across a spatial range, such that the spatial relationships among the constituent texts expresses propositions" []
is_a: IAO:0000300 ! textual entity
property_value: IAO:0000111 "table" xsd:string
property_value: IAO:0000112 "| T     F\n--+-----\nT   | T     F\nF   |  F    F" xsd:string
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string

[Term]
id: IAO:0000307
name: table of abbreviations
def: "A table where the constituent texts are abbreviations and their expansions" []
is_a: IAO:0000306 ! table
property_value: IAO:0000111 "table of abbreviations" xsd:string
property_value: IAO:0000112 "IAO  information artifact ontology\nOBI  ontology of biomedical investiations\nGO   gene ontology" xsd:string
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string

[Term]
id: IAO:0000308
name: figure
def: "An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something." []
is_a: IAO:0000030 ! information content entity
property_value: IAO:0000111 "figure" xsd:string
property_value: IAO:0000112 "Any picture, diagram or table" xsd:string
property_value: IAO:0000114 IAO:0000120
property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string

[Term]
id: IAO:0000309
name: diagram
def: "A figure that expresses one or more propositions" []
is_a: IAO:0000308 ! figure
property_value: IAO:0000111 "diagram" xsd:string
property_value: IAO:0000112 "A molecular structure ribbon cartoon showing helices, turns and sheets and their relations to each other in space." xsd:string
property_value: IAO:0000114 IAO:0000120
property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string

[Term]
id: IAO:0000310
name: document
def: "A collection of information content entities intended to be understood together as a whole" []
is_a: IAO:0000030 ! information content entity
property_value: IAO:0000111 "document" xsd:string
property_value: IAO:0000112 "A journal article, patent application, laboratory notebook, or a book" xsd:string
property_value: IAO:0000114 IAO:0000120
property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string

[Term]
id: IAO:0000311
name: publication
def: "A document that is the output of a publishing process." []
comment: Revisit the term in Octorber 2020. Improve the defintion.
is_a: IAO:0000310 ! document
intersection_of: IAO:0000310 ! document
intersection_of: OBI:0000312 IAO:0000444 {all_only="true"} ! is_specified_output_of publishing process
property_value: IAO:0000111 "publication" xsd:string
property_value: IAO:0000112 "journal article, newspaper story, book, etc." xsd:string
property_value: IAO:0000114 IAO:0000120
property_value: IAO:0000117 "PERSON: Chris Stoeckert" xsd:string
property_value: IAO:0000117 "PERSON: Jie Zheng" xsd:string
property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string
property_value: IAO:0000118 "published document" xsd:string
property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/232

[Term]
id: IAO:0000312
name: publication about an investigation
def: "A publication that is about an investigation" []
is_a: IAO:0000311 ! publication
relationship: IAO:0000136 OBI:0000066 ! is about investigation
property_value: IAO:0000111 "publication about an investigation" xsd:string
property_value: IAO:0000112 "Most scientific journal articles" xsd:string
property_value: IAO:0000114 IAO:0000120
property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string
property_value: IAO:0000118 "scientific publication" xsd:string

[Term]
id: IAO:0000313
name: patent
def: "A document that has been accepted by a patent authority" []
is_a: IAO:0000310 ! document
property_value: IAO:0000111 "patent" xsd:string
property_value: IAO:0000112 "US Patent 6,449,603" xsd:string
property_value: IAO:0000114 IAO:0000120
property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string

[Term]
id: IAO:0000314
name: document part
def: "An information content entity that is part of a document." []
is_a: IAO:0000030 ! information content entity
relationship: BFO:0000050 IAO:0000310 ! part of document
property_value: IAO:0000111 "document part" xsd:string
property_value: IAO:0000112 "An abstract, introduction, method or results section." xsd:string
property_value: IAO:0000114 IAO:0000120
property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string

[Term]
id: IAO:0000315
name: abstract
def: "A summary of the entire document that is substantially smaller than the document it summarizes.  It is about the document it summarizes." []
is_a: IAO:0000314 ! document part
relationship: IAO:0000136 IAO:0000310 ! is about document
property_value: IAO:0000111 "abstract" xsd:string
property_value: IAO:0000112 "The profusion of high-throughput instruments and the explosion of new results in the scientific literature, particularly in molecular biomedicine, is both a blessing and a curse to the bench researcher.   Even knowledgeable and experienced scientists can benefit from computational tools that help navigate this vast and rapidly evolving terrain. In this paper, we describe a novel computational approach to this challenge, a knowledge-based system that combines reading, reasoning and reporting methods to facilitate analysis of experimental data. Reading methods extract information from external resources, either by parsing structured data or biomedical language processing to extract information from unstructured data, and track knowledge provenance.  Reasoning methods enrich the knowledge that results from reading by, for example, noting two genes that are annotated to the same ontology term or database entry.  Reasoning is also used to combine all sources into a knowledge network that represents the integration of all sorts of relationships between a pair of genes, and to calculate a combined reliability score. Reporting methods combine the knowledge network with a congruent network constructed from experimental data and visualize the combined network in a tool that facilitates the knowledge-based analysis of that data." xsd:string
property_value: IAO:0000114 IAO:0000120
property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string
property_value: IAO:0000118 "precis" xsd:string
property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/234

[Term]
id: IAO:0000316
name: introduction to a publication about an investigation
def: "A part of a publication about an investigation that is about the objective specification (why the investigation is being done)" []
is_a: IAO:0000314 ! document part
relationship: IAO:0000136 IAO:0000005 ! is about objective specification
property_value: IAO:0000111 "introduction to a publication about an investigation" xsd:string
property_value: IAO:0000112 "Section labelled 'introduction' of a typical scientific journal article" xsd:string
property_value: IAO:0000114 IAO:0000120
property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string
property_value: IAO:0000118 "background" xsd:string
property_value: IAO:0000118 "introduction" xsd:string
property_value: IAO:0000118 "overview" xsd:string
property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/234

[Term]
id: IAO:0000317
name: methods section
def: "A part of a publication about an investigation that is about the study design of the investigation" []
is_a: IAO:0000314 ! document part
relationship: IAO:0000136 OBI:0500000 ! is about study design
property_value: IAO:0000111 "methods section" xsd:string
property_value: IAO:0000112 "The section labelled 'Methods' or 'Materials and Methods' in a typical scientific journal article." xsd:string
property_value: IAO:0000114 IAO:0000120
property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string
property_value: IAO:0000118 "experimental" xsd:string
property_value: IAO:0000118 "experimental methods" xsd:string
property_value: IAO:0000118 "experimental procedures" xsd:string
property_value: IAO:0000118 "experimental section" xsd:string
property_value: IAO:0000118 "method" xsd:string
property_value: IAO:0000118 "methodology" xsd:string
property_value: IAO:0000118 "methods" xsd:string
property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/234

[Term]
id: IAO:0000318
name: results section
def: "A part of a publication about an investigation that is about a study design execution" []
is_a: IAO:0000314 ! document part
relationship: IAO:0000136 OBI:0000471 ! is about study design execution
property_value: IAO:0000111 "results section" xsd:string
property_value: IAO:0000112 "The section labelled 'results' in a typical scientific journal article" xsd:string
property_value: IAO:0000114 IAO:0000120
property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string
property_value: IAO:0000118 "results" xsd:string

[Term]
id: IAO:0000319
name: discussion section of a publication about an investigation
def: "A part of a publication about an investigation that is about the study interpretation of the investigation" []
is_a: IAO:0000314 ! document part
property_value: IAO:0000111 "discussion section of a publication about an investigation" xsd:string
property_value: IAO:0000114 IAO:0000120
property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string
property_value: IAO:0000118 "discussion" xsd:string
property_value: IAO:0000118 "discussion section" xsd:string
property_value: IAO:0000118 "discussions" xsd:string
property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/234

[Term]
id: IAO:0000320
name: references section
def: "A part of a document that has citations as parts" []
is_a: IAO:0000314 ! document part
relationship: BFO:0000051 IAO:0000301 ! has part citation
property_value: IAO:0000111 "references section" xsd:string
property_value: IAO:0000112 "The list of citations found at the end of a scientific publication, grant proposal or patent application, sometimes called \"literature cited\" or \"bibliography\"" xsd:string
property_value: IAO:0000114 IAO:0000120
property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string
property_value: IAO:0000118 "literature cited" xsd:string
property_value: IAO:0000118 "reference" xsd:string
property_value: IAO:0000118 "reference list" xsd:string
property_value: IAO:0000118 "references" xsd:string
property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/234

[Term]
id: IAO:0000321
name: author list
def: "A part of a document that enumerates the authors of the document" []
is_a: IAO:0000314 ! document part
relationship: BFO:0000051 IAO:0000302 ! has part author identification
property_value: IAO:0000111 "author list" xsd:string
property_value: IAO:0000112 "Lawrence Hunter and Kevin Brettonel Cohen" xsd:string
property_value: IAO:0000114 IAO:0000120
property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string

[Term]
id: IAO:0000322
name: institution list
def: "A part of a document that has parts that are institution identifications associated with the authors of the document" []
is_a: IAO:0000314 ! document part
relationship: BFO:0000051 IAO:0000303 ! has part institutional identification
property_value: IAO:0000111 "institution list" xsd:string
property_value: IAO:0000112 "The University of Colorado Denver School of Medicine and the University of Colorado Boulder." xsd:string
property_value: IAO:0000114 IAO:0000120
property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string

[Term]
id: IAO:0000323
name: author contributions section
def: "A part of a publication that is about the specific contributions of each author" []
is_a: IAO:0000314 ! document part
property_value: IAO:0000111 "author contributions section" xsd:string
property_value: IAO:0000112 "LH conceived of the hypothesis, designed the study and contributed to the writing of the manuscript.  KBC executed the experiments, analyzed the data, and contributed to the writing of the manuscript." xsd:string
property_value: IAO:0000114 IAO:0000120
property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string
property_value: IAO:0000118 "author contributions" xsd:string
property_value: IAO:0000118 "authors' contribution" xsd:string
property_value: IAO:0000118 "authors' contributions" xsd:string
property_value: IAO:0000118 "authors' roles" xsd:string
property_value: IAO:0000118 "contributions by the authors" xsd:string
property_value: IAO:0000118 "contributorship" xsd:string
property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/234

[Term]
id: IAO:0000324
name: acknowledgements section
def: "Part of a publication that is about the contributions of people or institutions other than the authors." []
is_a: IAO:0000314 ! document part
property_value: IAO:0000111 "acknowledgements section" xsd:string
property_value: IAO:0000112 "The authors wish to thank Alan Ruttenberg for his constructive comments about an earlier draft of this manuscript" xsd:string
property_value: IAO:0000114 IAO:0000120
property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string
property_value: IAO:0000118 "acknowledgement" xsd:string
property_value: IAO:0000118 "acknowledgements" xsd:string
property_value: IAO:0000118 "acknowledgment" xsd:string
property_value: IAO:0000118 "acknowledgments" xsd:string
property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/234

[Term]
id: IAO:0000325
name: footnote
def: "A part of a document that is about a specific other part of the document.  Usually footnotes are spatially segregated from the rest of the document." []
is_a: IAO:0000314 ! document part
relationship: IAO:0000136 IAO:0000314 ! is about document part
property_value: IAO:0000111 "footnote" xsd:string
property_value: IAO:0000112 "The referent in the text is usually indicated by a special typographic character such as * or a superscripted number, which is also used to indicate the footnote that refers to that text." xsd:string
property_value: IAO:0000114 IAO:0000120
property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string
property_value: IAO:0000118 "endnote" xsd:string
property_value: IAO:0000118 "footnotes" xsd:string
property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/234

[Term]
id: IAO:0000326
name: supplementary material to a document
def: "A part of a document that is segregated from the rest of the document due to its size" []
is_a: IAO:0000314 ! document part
property_value: IAO:0000111 "supplementary material to a document" xsd:string
property_value: IAO:0000114 IAO:0000120
property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string
property_value: IAO:0000118 "additional file" xsd:string
property_value: IAO:0000118 "additional files" xsd:string
property_value: IAO:0000118 "additional information" xsd:string
property_value: IAO:0000118 "appendix" xsd:string
property_value: IAO:0000118 "electronic supplementary material" xsd:string
property_value: IAO:0000118 "electronic supplementary materials" xsd:string
property_value: IAO:0000118 "supplemental data" xsd:string
property_value: IAO:0000118 "supplemental information" xsd:string
property_value: IAO:0000118 "supplemental material" xsd:string
property_value: IAO:0000118 "supplementary data" xsd:string
property_value: IAO:0000118 "supplementary files" xsd:string
property_value: IAO:0000118 "supplementary information" xsd:string
property_value: IAO:0000118 "supplementary material" xsd:string
property_value: IAO:0000118 "supplementary materials" xsd:string
property_value: IAO:0000118 "supporting information" xsd:string
property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/234

[Term]
id: IAO:0000327
name: table of contents
def: "A table that relates document parts to specific locations in a document (usually page numbers).  This is also a document part (subsumption there should be inferred)." []
is_a: IAO:0000306 ! table
property_value: IAO:0000111 "table of contents" xsd:string
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string

[Term]
id: IAO:0000328
name: table of figures
def: "A table that relates figures in a document to specific locations in that document (usually page numbers).  This is also a document part (subsumption there should be inferred)." []
is_a: IAO:0000306 ! table
property_value: IAO:0000111 "table of figures" xsd:string
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string

[Term]
id: IAO:0000329
name: running title
def: "A shorter version of a document title" []
is_a: IAO:0000305 ! document title
property_value: IAO:0000111 "running title" xsd:string
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string

[Term]
id: IAO:0000330
name: copyright section
def: "A document part that describes  legal restrictions on making or distributing copies of the document" []
is_a: IAO:0000314 ! document part
property_value: IAO:0000111 "copyright section" xsd:string
property_value: IAO:0000112 "This work is licensed under a Creative Commons Attribution-Share Alike 3.0 United States License." xsd:string
property_value: IAO:0000114 IAO:0000120
property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string

[Term]
id: IAO:0000400
name: cartesian spatial coordinate datum
def: "A cartesian spatial coordinate datum is a representation of a point in a spatial region, in which equal changes in the magnitude of a coordinate value denote length qualities with the same magnitude" []
is_a: IAO:0000027 ! data item
relationship: IAO:0000219 BFO:0000018 ! denotes zero-dimensional spatial region
property_value: IAO:0000114 IAO:0000120
property_value: IAO:0000116 "2009-08-18 Alan Ruttenberg - question to BFO list about whether the BFO sense of the lower dimensional regions is that they are always part of actual space (the three dimensional sort) http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617" xsd:string
property_value: IAO:0000117 "Alan Ruttenberg" xsd:string
property_value: IAO:0000232 "AR notes: We need to discuss whether it should include site." xsd:string
property_value: seeAlso http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617 xsd:string

[Term]
id: IAO:0000401
name: one dimensional cartesian spatial coordinate datum
def: "A cartesion spatial coordinate datum that  uses one value to specify a position along a one dimensional spatial region" []
is_a: IAO:0000400 ! cartesian spatial coordinate datum
property_value: IAO:0000114 IAO:0000123
property_value: IAO:0000117 "Alan Ruttenberg" xsd:string

[Term]
id: IAO:0000402
name: two dimensional cartesian spatial coordinate datum
def: "A cartesion spatial coordinate datum that  uses two values to specify a position within a two dimensional spatial region" []
is_a: IAO:0000400 ! cartesian spatial coordinate datum
property_value: IAO:0000114 IAO:0000123
property_value: IAO:0000117 "Alan Ruttenberg" xsd:string

[Term]
id: IAO:0000403
name: three dimensional cartesian spatial coordinate datum
def: "A cartesion spatial coordinate datum that  uses three values to specify a position within a three dimensional spatial region" []
is_a: IAO:0000400 ! cartesian spatial coordinate datum
property_value: IAO:0000114 IAO:0000123
property_value: IAO:0000117 "Alan Ruttenberg" xsd:string

[Term]
id: IAO:0000408
name: length measurement datum
def: "A scalar measurement datum that is the result of measurement of length quality" []
is_a: IAO:0000032 ! scalar measurement datum
relationship: IAO:0000039 UO:0000001 ! has measurement unit label length unit
relationship: IAO:0000221 PATO:0000122 ! is quality measurement of length
property_value: IAO:0000114 IAO:0000123
property_value: IAO:0000117 "Alan Ruttenberg" xsd:string

[Term]
id: IAO:0000409
name: denotator type
def: "A denotator type indicates how a term should be interpreted from an ontological perspective." []
is_a: IAO:0000102 ! data about an ontology part
property_value: IAO:0000111 "denotator type" xsd:string
property_value: IAO:0000112 "The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are \"natural kinds\" and the latter arbitrary collections of entities." xsd:string
property_value: IAO:0000117 "Alan Ruttenberg" xsd:string
property_value: IAO:0000119 "Barry Smith, Werner Ceusters" xsd:string

[Term]
id: IAO:0000414
name: mass measurement datum
def: "A scalar measurement datum that is the result of measurement of mass quality" []
is_a: IAO:0000032 ! scalar measurement datum
relationship: IAO:0000039 UO:0000002 ! has measurement unit label mass unit
relationship: IAO:0000221 PATO:0000125 ! is quality measurement of mass
property_value: IAO:0000114 IAO:0000123
property_value: IAO:0000116 "2009/09/28 Alan Ruttenberg. Fucoidan-use-case" xsd:string
property_value: IAO:0000117 "Person:Alan Ruttenberg" xsd:string

[Term]
id: IAO:0000415
name: hypothesis textual entity
def: "A textual entity that expresses an assertion that is intended to be tested." []
is_a: IAO:0000300 ! textual entity
property_value: IAO:0000111 "hypothesis textual entity" xsd:string
property_value: IAO:0000112 "that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660" xsd:string
property_value: IAO:0000114 IAO:0000120
property_value: IAO:0000116 "2009/09/28 Alan Ruttenberg. Fucoidan-use-case" xsd:string
property_value: IAO:0000117 "Person:Alan Ruttenberg" xsd:string

[Term]
id: IAO:0000416
name: time measurement datum
def: "A scalar measurement datum that is the result of measuring a temporal interval" []
is_a: IAO:0000032 ! scalar measurement datum
relationship: IAO:0000039 UO:0000003 ! has measurement unit label time unit
relationship: IAO:0000413 BFO:0000015 ! is duration of process
property_value: IAO:0000114 IAO:0000123
property_value: IAO:0000116 "2009/09/28 Alan Ruttenberg. Fucoidan-use-case" xsd:string
property_value: IAO:0000117 "Person:Alan Ruttenberg" xsd:string

[Term]
id: IAO:0000422
name: postal address
def: "A textual entity that is used as directive to deliver something to a person, or organization" []
is_a: IAO:0000300 ! textual entity
relationship: IAO:0000136 GAZ:00000448 ! is about geographic location
property_value: IAO:0000114 IAO:0000123
property_value: IAO:0000116 "2010-05-24 Alan Ruttenberg. Use label for the string representation. See issue https://github.com/information-artifact-ontology/IAO/issues/59" xsd:string

[Term]
id: IAO:0000429
name: email address
is_a: IAO:0000030 ! information content entity
property_value: IAO:0000111 "email address" xsd:string
property_value: IAO:0000114 IAO:0000123
property_value: IAO:0000116 "Alan Ruttenberg 1/3/2012 - Provisional id, see issue at https://github.com/information-artifact-ontology/IAO/issues/130&thanks=130&ts=1325636583" xsd:string
property_value: IAO:0000117 "Person:Alan Ruttenberg" xsd:string
property_value: IAO:0000117 "Person:Chris Stoeckart" xsd:string

[Term]
id: IAO:0000442
name: author role
def: "A role inhering in a person or organization that is realized when the bearer participates in the work which is the basis of the document, in the writing of the document, and signs it with their name." []
is_a: BFO:0000023 ! role
property_value: IAO:0000111 "author role" xsd:string
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string
property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string

[Term]
id: IAO:0000443
name: data item extraction from journal article
def: "A planned process in which journal articles are read or processed and data items are extracted, typically for further analysis or indexing" []
is_a: OBI:0000011 ! planned process
relationship: OBI:0000293 IAO:0000013 ! has_specified_input journal article
relationship: OBI:0000299 IAO:0000027 ! has_specified_output data item
property_value: IAO:0000114 IAO:0000120
property_value: IAO:0000117 "Person:Alan Ruttenberg" xsd:string

[Term]
id: IAO:0000444
name: publishing process
def: "A planned process of making information, such as literature, music, and software etc., available to the public for sale or for free." []
is_a: OBI:0000011 ! planned process
property_value: IAO:0000114 IAO:0000120
property_value: IAO:0000117 "Person: Jie Zheng" xsd:string
property_value: IAO:0000119 https://en.wikipedia.org/wiki/Publishing xsd:string
property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/232
property_value: IAO:0000234 "VEuPathDB" xsd:string

[Term]
id: IAO:0000445
name: document in preparation for publication
def: "A document that is in preparation for submission to be published." []
is_a: IAO:0000310 ! document
property_value: IAO:0000114 IAO:0000120
property_value: IAO:0000117 "PERSON: Jie Zheng" xsd:string
property_value: IAO:0000119 "EFO_0001795 in preparation" xsd:string
property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/232
property_value: IAO:0000234 "VEuPathDB" xsd:string

[Term]
id: IAO:0000572
name: documenting
def: "A planned process in which a document is created or added to by including the specified input in it." []
is_a: OBI:0000011 ! planned process
relationship: OBI:0000293 IAO:0000030 ! has_specified_input information content entity
relationship: OBI:0000299 IAO:0000310 ! has_specified_output document
property_value: IAO:0000112 "Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database." xsd:string
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000116 "6/11/9: Edited at OBI workshop. We need to be able identify a child form of information artifact which corresponds to something enduring (not brain like). This used to be restricted to physical document or digital entity as the output, but that excludes e.g. an audio cassette tape" xsd:string
property_value: IAO:0000117 "Bjoern Peters" xsd:string
property_value: IAO:0000119 "wikipedia http://en.wikipedia.org/wiki/Documenting" xsd:string

[Term]
id: IAO:0000573
name: line graph
def: "A line graph is a type of graph created by connecting a series of data\npoints together with a line." []
is_a: IAO:0000038 ! graph
property_value: IAO:0000111 "line graph" xsd:string
property_value: IAO:0000114 IAO:0000122
property_value: IAO:0000117 "PERSON:Chris Stoeckert" xsd:string
property_value: IAO:0000117 "PERSON:Melanie Courtot" xsd:string
property_value: IAO:0000118 "line chart" xsd:string
property_value: IAO:0000119 GROUP:OBI xsd:string
property_value: IAO:0000119 "WEB: http://en.wikipedia.org/wiki/Line_chart" xsd:string

[Term]
id: IAO:0000574
name: assigning a centrally registered identifier
def: "A planned process in which a new CRID is created, associated with an entity, and stored in the CRID registry thereby registering it as being associated with some entity" []
is_a: OBI:0000011 ! planned process
relationship: OBI:0000299 IAO:0000577 ! has_specified_output centrally registered identifier symbol
relationship: RO:0000057 IAO:0000579 ! has_participant centrally registered identifier registry
property_value: IAO:0000112 "A new pubmed ID being created for a journal article, and the associated pubmed record containing information to the journal article. A license plate number registered at the DMV to be belonging to a specific vehicle and owner. Placing a barcode on a product and entering information in a database that this barcode is assigned." xsd:string
property_value: IAO:0000114 IAO:0000120
property_value: IAO:0000116 "2014-05-05: It is the CRID registry that assigns CRIDs, not the users of the registry." xsd:string
property_value: IAO:0000117 "Person:Alan Ruttenberg" xsd:string
property_value: IAO:0000117 "Person:Bjoern Peters" xsd:string
property_value: IAO:0000117 "Person:Melanie Courtot" xsd:string
property_value: IAO:0000118 "assigning a CRID" xsd:string

[Term]
id: IAO:0000575
name: associating information with a centrally registered identifier in its registry
def: "A planned process in which a CRID registry associates an information content entity with a CRID symbol" []
is_a: OBI:0000011 ! planned process
relationship: OBI:0000293 IAO:0000577 ! has_specified_input centrally registered identifier symbol
relationship: RO:0000057 IAO:0000579 ! has_participant centrally registered identifier registry
property_value: IAO:0000112 "Articles in Pubmed are reviewed by curators who add MESH terms to the Pubmed records in order to categorize them better and improve the ability to search for them. " xsd:string
property_value: IAO:0000114 IAO:0000120
property_value: IAO:0000117 "PERSON:Alan Ruttenberg" xsd:string
property_value: IAO:0000118 "associating information with a CRID in the CRID registry" xsd:string

[Term]
id: IAO:0000576
name: obsolete_establishing a CRID registry
def: "a planned process with the objective to establish a system that allows to refer to specific entities of a certain kind and store information about them, by establishing a CRID registry and plan specifications for the process of 1) assigning a CRID and 2) looking up a CRID." []
is_a: ObsoleteClass ! Obsolete Class
property_value: IAO:0000116 "MC, 20101124: deprecated following discussion at IAO call 20101124. Term was deemed not necessary - no use case for now." xsd:string
property_value: IAO:0000231 IAO:0000103
is_obsolete: true

[Term]
id: IAO:0000577
name: centrally registered identifier symbol
def: "A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry." []
is_a: IAO:0000028 ! symbol
relationship: BFO:0000050 IAO:0000578 ! part of centrally registered identifier
property_value: IAO:0000112 "The sentence \"The article has Pubmed ID 12345.\" contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed." xsd:string
property_value: IAO:0000114 IAO:0000120
property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string
property_value: IAO:0000117 "PERSON: Bill Hogan" xsd:string
property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string
property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string
property_value: IAO:0000118 "CRID symbol" xsd:string
property_value: IAO:0000119 "Original proposal from Bjoern, discussions at IAO calls" xsd:string

[Term]
id: IAO:0000578
name: centrally registered identifier
def: "An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs." []
is_a: IAO:0020000 ! identifier
relationship: BFO:0000051 IAO:0000577 ! has part centrally registered identifier symbol
property_value: IAO:0000112 "The sentence \"The article has Pubmed ID 12345.\" contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed." xsd:string
property_value: IAO:0000114 IAO:0000120
property_value: IAO:0000116 "2014-05-05: In defining this term we take no position on what the CRID denotes. In particular do not assume it denotes a *record* in the CRID registry (since the registry might not have 'records')." xsd:string
property_value: IAO:0000116 "Alan, IAO call 20101124: potentially the CRID denotes the instance it was associated with during creation." xsd:string
property_value: IAO:0000116 "Note, IAO call 20101124: URIs are not always CRID, as not centrally registered. We acknowledge that CRID is a subset of a larger identifier class, but this subset fulfills our current needs. OBI PURLs are CRID as they are registered with OCLC. UPCs (Universal Product Codes from AC Nielsen)are not CRID as they are not centrally registered." xsd:string
property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string
property_value: IAO:0000117 "PERSON: Bill Hogan" xsd:string
property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string
property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string
property_value: IAO:0000118 "CRID" xsd:string
property_value: IAO:0000119 "Original proposal from Bjoern, discussions at IAO calls" xsd:string

[Term]
id: IAO:0000579
name: centrally registered identifier registry
def: "A CRID registry is a dataset of CRID records, each consisting of a CRID symbol and additional information which was recorded in the dataset through a assigning a centrally registered identifier process." []
is_a: IAO:0000100 ! data set
property_value: IAO:0000112 "PubMed is a CRID registry. It has a dataset of PubMed identifiers associated with journal articles. " xsd:string
property_value: IAO:0000114 IAO:0000120
property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string
property_value: IAO:0000117 "PERSON: Bill Hogan" xsd:string
property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string
property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string
property_value: IAO:0000118 "CRID registry" xsd:string
property_value: IAO:0000119 "Original proposal from Bjoern, discussions at IAO calls" xsd:string

[Term]
id: IAO:0000580
name: looking up a centrally registered identifier
def: "A planned process in which a request to a CRID registry is made to return the information associated with a CRID symbol" []
is_a: OBI:0000011 ! planned process
relationship: OBI:0000293 IAO:0000577 ! has_specified_input centrally registered identifier symbol
relationship: OBI:0000299 IAO:0000030 ! has_specified_output information content entity
relationship: RO:0000057 IAO:0000579 ! has_participant centrally registered identifier registry
property_value: IAO:0000112 "Going to the PubMed website and entering a PubMed ID in order to retrieve the Pubmed information associated with that ID. " xsd:string
property_value: IAO:0000114 IAO:0000120
property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string
property_value: IAO:0000117 "PERSON: Bill Hogan" xsd:string
property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string
property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string
property_value: IAO:0000118 "looking up a CRID" xsd:string

[Term]
id: IAO:0000582
name: time stamped measurement datum
is_a: IAO:0000109 ! measurement datum
relationship: IAO:0000581 IAO:0000416 ! has time stamp time measurement datum
relationship: IAO:0000583 IAO:0000109 ! has measurement datum measurement datum
property_value: IAO:0000114 IAO:0000123

[Term]
id: IAO:0000584
name: time sampled measurement data set
def: "A data set that is an aggregate of data recording some measurement at a number of time points. The time series data set is an ordered list of pairs of time measurement data and the corresponding measurement data acquired at that time." []
is_a: IAO:0000100 ! data set
relationship: BFO:0000051 IAO:0000582 ! has part time stamped measurement datum
property_value: IAO:0000112 "pmid:20604925 - time-lapse live cell microscopy" xsd:string
property_value: IAO:0000114 IAO:0000120
property_value: IAO:0000117 "Alan Ruttenberg" xsd:string
property_value: IAO:0000118 "experimental time series" xsd:string

[Term]
id: IAO:0000590
name: written name
def: "A textual entity that denotes a particular in reality." []
is_a: IAO:0000300 ! textual entity
property_value: IAO:0000111 "written name" xsd:string
property_value: IAO:0000112 "\"Bill Clinton\"" xsd:string
property_value: IAO:0000112 "\"The Eiffel Tower\"" xsd:string
property_value: IAO:0000112 "\"United States of America\"" xsd:string
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "PERSON: Bill Hogan" xsd:string
property_value: IAO:0000119 https://github.com/information-artifact-ontology/IAO/issues/114 xsd:string
property_value: IAO:0000232 "The qualifier \"written\" is to set it apart from spoken names.  Also, note the restrictions to particulars.  We are not naming universals.   We could however, be naming, attributive collections which are particulars, so \"All people located in the boundaries of the city of Little Rock, AR on June 18, 2011 at 9:50a CDT\" would be a name." xsd:string

[Term]
id: IAO:0000591
name: software method
def: "A software method (also called subroutine, subprogram, procedure, method, function, or routine) is software designed to execute a specific task." []
is_a: IAO:0000010 ! software
property_value: IAO:0000114 IAO:0000123
property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string
property_value: IAO:0000117 "PERSON: Michel Dumontier" xsd:string
property_value: IAO:0000119 https://github.com/information-artifact-ontology/IAO/issues/80 xsd:string

[Term]
id: IAO:0000592
name: software module
def: "A software module is software composed of a collection of software methods." []
is_a: IAO:0000010 ! software
property_value: IAO:0000114 IAO:0000123
property_value: IAO:0000117 "PERSON: Melanei Courtot" xsd:string
property_value: IAO:0000117 "PERSON: Michel Dumontier" xsd:string
property_value: IAO:0000119 https://github.com/information-artifact-ontology/IAO/issues/80 xsd:string

[Term]
id: IAO:0000593
name: software library
def: "A software library is software composed of a collection of software modules and/or software methods in a form that can be statically or dynamically linked to some software application." []
is_a: IAO:0000010 ! software
property_value: IAO:0000114 IAO:0000123
property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string
property_value: IAO:0000117 "PERSON: Michel Dumontier" xsd:string
property_value: IAO:0000119 https://github.com/information-artifact-ontology/IAO/issues/80 xsd:string

[Term]
id: IAO:0000594
name: software application
def: "A software application is software that can be directly executed by some processing unit." []
is_a: IAO:0000010 ! software
property_value: IAO:0000114 IAO:0000123
property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string
property_value: IAO:0000117 "PERSON: Michel Dumontier" xsd:string
property_value: IAO:0000119 https://github.com/information-artifact-ontology/IAO/issues/80 xsd:string

[Term]
id: IAO:0000595
name: software script
def: "A software script is software whose instructions can be executed using a software interpreter." []
is_a: IAO:0000010 ! software
property_value: IAO:0000114 IAO:0000123
property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string
property_value: IAO:0000117 "PERSON: Michel Dumontier" xsd:string
property_value: IAO:0000119 https://github.com/information-artifact-ontology/IAO/issues/80 xsd:string

[Term]
id: IAO:0000605
name: abbreviation textual entity
def: "A textual entity listing abbreviations and their expansions that are used in a document." []
is_a: IAO:0000300 ! textual entity
property_value: IAO:0000111 "abbreviation textual entity" xsd:string
property_value: IAO:0000112 "From Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/):\n\nBAC: Bacterial artificial chromosome; CR: Calretinin; GFAP: Glial fibrillary acidic protein; MAP: Microtubule-associated protein; MRI: Magnetic resonance imaging; NSC: Neural stem cell; PDA: Patent ductus arteriosus; PMG: Polymicrogyria; PNH: Periventricular nodular heterotopia; VSD: Ventricular septal defect." xsd:string
property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string
property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183

[Term]
id: IAO:0000606
name: abbreviations section
def: "A part of a document where abbreviations and their long-forms used within the document are listed." []
is_a: IAO:0000314 ! document part
relationship: BFO:0000051 IAO:0000605 ! has part abbreviation textual entity
property_value: IAO:0000111 "abbreviations section" xsd:string
property_value: IAO:0000112 "The section labelled 'abbreviations' in a typical scientific journal article." xsd:string
property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string
property_value: IAO:0000118 "abbreviation and acronyms" xsd:string
property_value: IAO:0000118 "abbreviation list" xsd:string
property_value: IAO:0000118 "abbreviations" xsd:string
property_value: IAO:0000118 "abbreviations and acronyms" xsd:string
property_value: IAO:0000118 "abbreviations list" xsd:string
property_value: IAO:0000118 "abbreviations used" xsd:string
property_value: IAO:0000118 "definitions for abbreviations" xsd:string
property_value: IAO:0000118 "list of abbreviations" xsd:string
property_value: IAO:0000118 "list of abbreviations used" xsd:string
property_value: IAO:0000118 "non-standard abbreviations" xsd:string
property_value: IAO:0000118 "nonstandard abbreviations" xsd:string
property_value: IAO:0000118 "nonstandard abbreviations and acronyms" xsd:string
property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183
property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/234

[Term]
id: IAO:0000607
name: author information section
def: "A part of a document about the authors that provides biographical information and may discuss how the authors' professional experiences are relevant to the work described in the document." []
is_a: IAO:0000314 ! document part
relationship: BFO:0000051 IAO:0000608 ! has part author information textual entity
property_value: IAO:0000111 "author information section" xsd:string
property_value: IAO:0000112 "The section labelled 'author information' in a typical scientific journal article, e.g. in Takon. Ann Gen Psychiatry. 2011; 10: 25. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3204268/)" xsd:string
property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string
property_value: IAO:0000118 "author information" xsd:string
property_value: IAO:0000118 "authors’ information" xsd:string
property_value: IAO:0000118 "biographies" xsd:string
property_value: IAO:0000118 "contributor information" xsd:string
property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183
property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/234

[Term]
id: IAO:0000608
name: author information textual entity
def: "A textual entity expression information about an author of a document. This information may include biographical information and may discuss how the authors' professional experiences are relevant to the work described in the document." []
is_a: IAO:0000300 ! textual entity
property_value: IAO:0000111 "author information textual entity" xsd:string
property_value: IAO:0000112 "From Takon. Ann Gen Psychiatry. 2011; 10: 25. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3204268/):\n\nIT [the author] is the lead paediatrician for ADHD services in East Hertfordshire, UK, where she runs a weekly joint ADHD clinic with the Child and Adolescent psychiatrist and works within an ADHD specialist team. IT also sees children with other neurodisability issues who may have comorbid ADHD, where the presentation may be more complex and challenging to manage. IT has vast experience in managing children with complex ADHD. She has 18 years of experience in paediatrics and also has extensive experience in the use of psychopharmacologic agents in managing children with ADHD." xsd:string
property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string
property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183

[Term]
id: IAO:0000609
name: author summary section
def: "A part of a document, distinct from the abstract, that describes the significance and broader context of the document content. The author summary is often written in a non-technical manner and is aimed at both scientists and non-scientist readers." []
is_a: IAO:0000314 ! document part
relationship: BFO:0000051 IAO:0000610 ! has part author summary textual entity
property_value: IAO:0000111 "author summary section" xsd:string
property_value: IAO:0000112 "The section labelled 'synopsis' in a typical scientific journal article, e.g. in Pendse et al. BMC Genomics. 2013; 14: 136. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3608171/)" xsd:string
property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string
property_value: IAO:0000118 "author summary" xsd:string
property_value: IAO:0000118 "summary" xsd:string
property_value: IAO:0000118 "synopsis" xsd:string
property_value: IAO:0000119 "Article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines)" xsd:string
property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183

[Term]
id: IAO:0000610
name: author summary textual entity
def: "A textual entity, distinct from the abstract, that describes the significance and broader context of the document content. The author summary is often written in a non-technical manner and is aimed at both scientists and non-scientist readers, e.g as described in the article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines)." []
is_a: IAO:0000300 ! textual entity
property_value: IAO:0000111 "author summary textual entity" xsd:string
property_value: IAO:0000112 "From Pendse et al. BMC Genomics. 2013; 14: 136. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3608171/):\n\n\nThe search for genetic risk factors for common human diseases often relies on the use of linkage and association studies to establish correlation between genomic markers and disease risk. These studies require additional functional evaluation of candidate genes, including their possible interaction with diet and environment. The number of candidate genes is typically large and the development of appropriate genetic tools in mammalian systems is slow. By contrast, large-scale genetic screens, using widely available genetic tools, are routinely conducted in the fruit fly Drosophila melanogaster. In this study, we used Drosophila to screen candidate genes identified in human genome-wide scans as associated with risk of metabolic abnormalities such as type 2 diabetes. We show that a number of human candidate genes have fly orthologs that play an important role in Drosophila tolerance to high dietary sucrose. We further explored some of the specific metabolic abnormalities that can result when these genes’ activities are reduced in flies, focusing on a gene we call dHHEX (CG7056), the fly ortholog of human HHEX." xsd:string
property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string
property_value: IAO:0000119 "Article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines)." xsd:string
property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183

[Term]
id: IAO:0000611
name: availability section
def: "A part of a document about a resource described in the document, e.g. software, that describes where and/or how that resource can be obtained." []
is_a: IAO:0000314 ! document part
relationship: BFO:0000051 IAO:0000612 ! has part availability textual entity
property_value: IAO:0000111 "availability section" xsd:string
property_value: IAO:0000112 "The section labelled 'availability and requirements' in a typical scientific journal article, e.g. Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/)." xsd:string
property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string
property_value: IAO:0000118 "availability" xsd:string
property_value: IAO:0000118 "availability of data" xsd:string
property_value: IAO:0000118 "data archiving" xsd:string
property_value: IAO:0000118 "data availability" xsd:string
property_value: IAO:0000118 "data availability statement" xsd:string
property_value: IAO:0000118 "data sharing statement" xsd:string
property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183
property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/234

[Term]
id: IAO:0000612
name: availability textual entity
def: "A textual entity expressing the location of a resource, e.g. software, or the manner in which a resource can be obtained." []
is_a: IAO:0000300 ! textual entity
property_value: IAO:0000111 "availability textual entity" xsd:string
property_value: IAO:0000112 "From Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/):\n\nProject home page:http://krux.googlecode.com" xsd:string
property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string
property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183

[Term]
id: IAO:0000613
name: case report section
def: "A part of a document about the medical history of a specific patient as it relates to the topic of the document." []
is_a: IAO:0000314 ! document part
relationship: BFO:0000051 IAO:0000614 ! has part case report textual entity
property_value: IAO:0000111 "case report section" xsd:string
property_value: IAO:0000112 "The section labelled 'case report' in a typical scientific journal article, e.g. in Taglia et al. Acta Myol. 2012 Dec; 31(3): 201–203. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631801/)" xsd:string
property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string
property_value: IAO:0000118 "case presentation" xsd:string
property_value: IAO:0000118 "case report" xsd:string
property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183

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name: case report textual entity
def: "A textual entity that expresses a detailed account of a portion of the medical history for a specific patient." []
is_a: IAO:0000300 ! textual entity
property_value: IAO:0000111 "case report textual entity" xsd:string
property_value: IAO:0000112 "Excerpt from Taglia et al. Acta Myol. 2012 Dec; 31(3): 201–203. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631801/):\n\nThe patient is a 50-year-old man. His medical history was not contributory. At the age of 37 years, he complained of persistent fatigue and dyspnoea even for modest efforts and oedema of lower limbs. The patient was examined at the department of internal medicine of the local hospital, and hospitalised with a diagnosis of dilated cardiomyopathy probably consequence of a myocarditis process. Soon after he was transferred to the cardiologic department of the regional hospital, and pharmacologically treated for heart failure and pulmonary hypertension." xsd:string
property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string
property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183

[Term]
id: IAO:0000615
name: conclusion section
def: "A part of a document used to summarize the findings discussed in the document. The conclusion section is typically found near the end of a document." []
is_a: IAO:0000314 ! document part
relationship: BFO:0000051 IAO:0000144 ! has part conclusion textual entity
property_value: IAO:0000111 "conclusion section" xsd:string
property_value: IAO:0000112 "The section labelled 'conclusion' in a typical scientific journal article." xsd:string
property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string
property_value: IAO:0000118 "concluding remarks" xsd:string
property_value: IAO:0000118 "conclusion" xsd:string
property_value: IAO:0000118 "conclusions" xsd:string
property_value: IAO:0000118 "findings" xsd:string
property_value: IAO:0000118 "summary" xsd:string
property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183

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id: IAO:0000616
name: conflict of interest section
def: "A part of a document used to declare any competing interests regarding the authors and/or funding organization for the work described in the document." []
is_a: IAO:0000314 ! document part
relationship: BFO:0000051 IAO:0000617 ! has part conflict of interest textual entity
property_value: IAO:0000111 "conflict of interest section" xsd:string
property_value: IAO:0000112 "The section labelled 'conflict of interest statement' in a typical scientific journal article." xsd:string
property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string
property_value: IAO:0000118 "authors' disclosures of potential conflicts of interest" xsd:string
property_value: IAO:0000118 "competing financial interests" xsd:string
property_value: IAO:0000118 "competing interests" xsd:string
property_value: IAO:0000118 "conflict of interest" xsd:string
property_value: IAO:0000118 "conflict of interest statement" xsd:string
property_value: IAO:0000118 "conflict of interests" xsd:string
property_value: IAO:0000118 "conflicts of interest" xsd:string
property_value: IAO:0000118 "declaration of competing interest" xsd:string
property_value: IAO:0000118 "declaration of competing interests" xsd:string
property_value: IAO:0000118 "declaration of interest" xsd:string
property_value: IAO:0000118 "declaration of interests" xsd:string
property_value: IAO:0000118 "disclosure of conflict of interest" xsd:string
property_value: IAO:0000118 "disclosure of potential conflicts of interest" xsd:string
property_value: IAO:0000118 "duality of interest" xsd:string
property_value: IAO:0000118 "statement of interest" xsd:string
property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183
property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/234

[Term]
id: IAO:0000617
name: conflict of interest textual entity
def: "A textual entity that expresses a situation involving one or more of the authors, or the funding source of a document whereby the authors or funding source stand to potentially gain (typically financially) from the results reported in the document." []
is_a: IAO:0000300 ! textual entity
property_value: IAO:0000111 "conflict of interest statement" xsd:string
property_value: IAO:0000112 "SD [an author] is a Merck employee and Merck is the sponsor of this study. [Taken from 'Effects of obstructive sleep apnoea risk on postoperative respiratory complications: protocol for a hospital-based registry study' Shin et al. 2016  (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4735131/)] " xsd:string
property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string
property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183

[Term]
id: IAO:0000618
name: consent section
def: "A part of a document about the consent process that was used to enroll patients in a study." []
is_a: IAO:0000314 ! document part
relationship: BFO:0000051 IAO:0000619 ! has part consent textual entity
property_value: IAO:0000111 "consent section" xsd:string
property_value: IAO:0000112 "The section labelled 'consent' in a typical scientific journal article, e.g. Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/)" xsd:string
property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string
property_value: IAO:0000118 "consent" xsd:string
property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183

[Term]
id: IAO:0000619
name: consent textual entity
def: "A textual entity that documents the consenting process used to enroll patients in a study." []
is_a: IAO:0000300 ! textual entity
property_value: IAO:0000111 "consent textual entity" xsd:string
property_value: IAO:0000112 "From Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/):\n\nWritten informed consent was obtained from the patient’s parents for publication of this Case report and any accompanying images. A copy of the written consent is available for review by the Editor-in chief of this journal." xsd:string
property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string
property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183

[Term]
id: IAO:0000620
name: ethical approval section
def: "A part of a document about the governance body responsible for approving the work discussed in a document on an ethical basis." []
is_a: IAO:0000314 ! document part
relationship: BFO:0000051 IAO:0000621 ! has part ethical approval textual entity
property_value: IAO:0000111 "ethical approval section" xsd:string
property_value: IAO:0000112 "The section labelled 'ethical approval' in a typical scientific journal article." xsd:string
property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string
property_value: IAO:0000118 "ethical approval" xsd:string
property_value: IAO:0000118 "ethical requirements" xsd:string
property_value: IAO:0000118 "ethics" xsd:string
property_value: IAO:0000118 "ethics statement" xsd:string
property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183
property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/234

[Term]
id: IAO:0000621
name: ethical approval textual entity
def: "A textual entity that documents the ethical approval of some study design." []
is_a: IAO:0000300 ! textual entity
relationship: IAO:0000136 OBI:0500000 ! is about study design
property_value: IAO:0000111 "ethical approval textual entity" xsd:string
property_value: IAO:0000112 "From McLean et al. Br J Gen Pract. 2014 Jul; 64(624): e440–e447 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4073730/):\n\nThe NHS National Research Ethics Service had previously approved the use of these anonymised data for research purposes and this analysis did not require independent review." xsd:string
property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string
property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183

[Term]
id: IAO:0000622
name: figures section
def: "A part of a document that contains one or more figures." []
is_a: IAO:0000314 ! document part
relationship: BFO:0000051 IAO:0000308 ! has part figure
property_value: IAO:0000111 "figures section" xsd:string
property_value: IAO:0000112 "The section labelled 'figures' in a typical scientific journal article." xsd:string
property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string
property_value: IAO:0000118 "figures" xsd:string
property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183

[Term]
id: IAO:0000623
name: funding source declaration section
def: "A part of a document used to detail information regarding the source of funding used in support of the generation of the document content." []
is_a: IAO:0000314 ! document part
relationship: BFO:0000051 IAO:0000624 ! has part funding source declaration textual entity
property_value: IAO:0000111 "funding source declaration section" xsd:string
property_value: IAO:0000112 "The section labelled 'funding' in a typical scientific journal article." xsd:string
property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string
property_value: IAO:0000118 "financial support" xsd:string
property_value: IAO:0000118 "funding" xsd:string
property_value: IAO:0000118 "funding information" xsd:string
property_value: IAO:0000118 "funding sources" xsd:string
property_value: IAO:0000118 "funding statement" xsd:string
property_value: IAO:0000118 "funding/support" xsd:string
property_value: IAO:0000118 "grants" xsd:string
property_value: IAO:0000118 "role of the funding source" xsd:string
property_value: IAO:0000118 "source of funding" xsd:string
property_value: IAO:0000118 "sources of funding" xsd:string
property_value: IAO:0000118 "study funding" xsd:string
property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183
property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/234

[Term]
id: IAO:0000624
name: funding source declaration textual entity
def: "A textual entity documenting the source of funding that supported some study." []
is_a: IAO:0000300 ! textual entity
property_value: IAO:0000111 "funding souce declaration textual entity" xsd:string
property_value: IAO:0000112 "From Stephan et al. Accid Anal Prev. 2011 May; 43(3): 1062–1067. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3062852/):\n\nThis study was supported by the International Collaborative Research Grants Scheme with joint grants from the Wellcome Trust UK (GR071587MA) and the Australian NHMRC (268055). The funding sources played no role in study design, data collection, analysis or interpretation, writing the report, or the decision to submit the paper for publication." xsd:string
property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string
property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183

[Term]
id: IAO:0000625
name: future directions section
def: "A part of a document detailing extensions of the described work that may be implemented at some future point in time." []
is_a: IAO:0000314 ! document part
relationship: BFO:0000051 IAO:0000626 ! has part future directions textual entity
property_value: IAO:0000111 "future directions section" xsd:string
property_value: IAO:0000112 "The section labelled 'future directions' in a typical scientific journal article." xsd:string
property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string
property_value: IAO:0000118 "future challenges" xsd:string
property_value: IAO:0000118 "future considerations" xsd:string
property_value: IAO:0000118 "future developments" xsd:string
property_value: IAO:0000118 "future directions" xsd:string
property_value: IAO:0000118 "future outlook" xsd:string
property_value: IAO:0000118 "future perspectives" xsd:string
property_value: IAO:0000118 "future plans" xsd:string
property_value: IAO:0000118 "future prospects" xsd:string
property_value: IAO:0000118 "future research" xsd:string
property_value: IAO:0000118 "future research directions" xsd:string
property_value: IAO:0000118 "future studies" xsd:string
property_value: IAO:0000118 "future work" xsd:string
property_value: IAO:0000118 "outlook" xsd:string
property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183
property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/234

[Term]
id: IAO:0000626
name: future directions textual entity
def: "A textual entity expressing ideas regarding future work relevant to work described in a document that could be done." []
is_a: IAO:0000300 ! textual entity
property_value: IAO:0000111 "future directions textual entity" xsd:string
property_value: IAO:0000112 "Excerpt from Wang and Li. Acta Pharmacol Sin. 2016 Jan; 37(1): 25–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4722976/):\n\nIn the future, several questions will need to be resolved regarding the physiological assembly of KCNQ channels and their functional implications in complex neural circuits. First, we still lack sufficiently selective inhibitors and activators among the KCNQ family members." xsd:string
property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string
property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183

[Term]
id: IAO:0000627
name: genome announcement section
def: "A document part announcing the publication of a novel draft genome sequence." []
is_a: IAO:0000314 ! document part
relationship: BFO:0000051 IAO:0000628 ! has part genome announcement textual entity
property_value: IAO:0000111 "genome announcement section" xsd:string
property_value: IAO:0000112 "The section labelled 'genome announcement' in a typical scientific journal article, e.g. in Kim et al. J Bacteriol. 2011 Oct; 193(19): 5537. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187466/)" xsd:string
property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string
property_value: IAO:0000118 "genome announcement" xsd:string
property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183

[Term]
id: IAO:0000628
name: genome announcement textual entity
def: "A textual entity that describes the generation and public release of a novel, draft genome sequence." []
is_a: IAO:0000300 ! textual entity
property_value: IAO:0000111 "genome announcement textual entity" xsd:string
property_value: IAO:0000112 "Excerpt from Kim et al. J Bacteriol. 2011 Oct; 193(19): 5537. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187466/):\n\nHere we report the genome sequence of Lactobacillus malefermentans KCTC 3548, which we obtained using a whole-genome shotgun strategy (4) with Roche 454 GS (FLX Titanium) pyrosequencing (257,559 reads totaling ∼89.8 Mb; ∼45-fold coverage of the genome) at the Genome Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB)." xsd:string
property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string
property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183

[Term]
id: IAO:0000629
name: keyword textual entity
def: "A textual entity listing keywords indicating the major theme(s) of a document." []
is_a: IAO:0000300 ! textual entity
property_value: IAO:0000111 "keyword textual entity" xsd:string
property_value: IAO:0000112 "From: Fu and Lin. Identification of gene-oriented exon orthology between human and mouse. BMC Genomics. 2012; 13(Suppl 1): S10. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3303729/):\n\nExon orthology; alternative splicing; exon duplication; intron-exon structure." xsd:string
property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string
property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183

[Term]
id: IAO:0000630
name: keywords section
def: "A part of a document where keywords selected by the author to categorize the major theme(s) of a document are listed." []
is_a: IAO:0000314 ! document part
relationship: BFO:0000051 IAO:0000629 ! has part keyword textual entity
property_value: IAO:0000111 "keywords section" xsd:string
property_value: IAO:0000112 "The section labelled 'keywords' in a typical scientific journal article." xsd:string
property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string
property_value: IAO:0000118 "keywords" xsd:string
property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183

[Term]
id: IAO:0000631
name: study limitations section
def: "A part of a document about biases or short comings related to the study design and execution." []
is_a: IAO:0000314 ! document part
relationship: BFO:0000051 IAO:0000632 ! has part study limitations textual entity
relationship: IAO:0000136 OBI:0500000 ! is about study design
property_value: IAO:0000111 "study limitations section" xsd:string
property_value: IAO:0000112 "The section labelled 'limitations' in a typical scientific journal article." xsd:string
property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string
property_value: IAO:0000118 "limitations" xsd:string
property_value: IAO:0000118 "study limitations" xsd:string
property_value: IAO:0000119 "Author guidelines published by The Society for Academic Emergency Medicine. (http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1553-2712/homepage/ForAuthors.html)" xsd:string
property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183

[Term]
id: IAO:0000632
name: study limitations textual entity
def: "A textual entity addressing a shortcoming or bias of a study design or execution." []
is_a: IAO:0000300 ! textual entity
property_value: IAO:0000111 "study limitations textual entity" xsd:string
property_value: IAO:0000112 "Excerpt from the Limitations section of Fermann et al 2015, Acad Emerg Med. 2015 Mar; 22(3): 299–307 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4405051/). \n\nOwing to the nature of a post hoc study, any significant values must be interpreted with caution. In the current analysis, no multiple testing was conducted and p-values remain unadjusted. Moreover, a selection bias arising from the randomized open-label design of the original EINSTEIN PE study cannot be ruled out." xsd:string
property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string
property_value: IAO:0000119 "Author guidelines published by The Society for Academic Emergency Medicine. (http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1553-2712/homepage/ForAuthors.html)" xsd:string
property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183

[Term]
id: IAO:0000633
name: materials section
def: "A part of a document about the materials required to reproduce the content of the document." []
is_a: IAO:0000314 ! document part
property_value: IAO:0000111 "materials section" xsd:string
property_value: IAO:0000112 "The section labelled 'materials' in a typical scientific journal article, e.g. Nguyen et al. BMC Bioinformatics. 2010; 11: 279. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2889936/)" xsd:string
property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string
property_value: IAO:0000118 "materials" xsd:string
property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183

[Term]
id: IAO:0000634
name: notes section
def: "A part of a document containing typically short notes about the document itself and/or the authors. Often the notes section contains subsections related to funding, competing interests, ethical approval, etc." []
is_a: IAO:0000314 ! document part
property_value: IAO:0000111 "notes section" xsd:string
property_value: IAO:0000112 "The section labelled 'notes' in a typical scientific journal article, e.g. McLean et al. Br J Gen Pract. 2014 Jul; 64(624): e440–e447 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4073730/):" xsd:string
property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string
property_value: IAO:0000118 "notes" xsd:string
property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183

[Term]
id: IAO:0000635
name: patients section
def: "A part of a document about the patients that participated in a study." []
is_a: IAO:0000314 ! document part
relationship: BFO:0000051 IAO:0000636 ! has part patients textual entity
property_value: IAO:0000111 "patients section" xsd:string
property_value: IAO:0000112 "The section labelled 'patients' in a typical scientific journal article, e.g. in Citak et al. Acta Orthop. 2013 Jun; 84(3): 326–327. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3715825/)" xsd:string
property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string
property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183

[Term]
id: IAO:0000636
name: patients textual entity
def: "A textual entity expressing information regarding the patients used in a study." []
is_a: IAO:0000300 ! textual entity
property_value: IAO:0000111 "patients textual entity" xsd:string
property_value: IAO:0000112 "Excerpt from Citak et al. Acta Orthop. 2013 Jun; 84(3): 326–327. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3715825/):\n\nBetween January 1996 and February 2012, we treated 4 patients with interprosthetic femoral fractures (3 of them women) (Figure 2) using a custom-made interposition device (Waldemar Link GmbH, Hamburg, Germany) (Figure 1). Mean age was 74 (59–86) years. The fractures occurred mean 18 (13–28) years after primary THA and mean 14 (10–17) years after primary TKA. At the latest follow-up, after mean 8 (0.5–16) years, revision surgery with a total femur replacement was required in 1 case due to aseptic loosening. No other complications requiring revision surgery occurred." xsd:string
property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string
property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183

[Term]
id: IAO:0000637
name: pre-publication history section
def: "A part of the document about the publication history of a document. This section typically details dates of document submission to a journal and dates of any re-submissions as well as reviewer comments and responses to reviewers by the authors." []
is_a: IAO:0000314 ! document part
relationship: BFO:0000051 IAO:0000638 ! has part pre-publication history textual entity
property_value: IAO:0000111 "pre-publication history section" xsd:string
property_value: IAO:0000112 "The section labelled 'pre-publication history' in a typical scientific journal article, e.g. in Xiao et al. BMC Anesthesiol. 2013; 13: 33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4016475/)" xsd:string
property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string
property_value: IAO:0000118 "notice of republication" xsd:string
property_value: IAO:0000118 "pre-publication history" xsd:string
property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183

[Term]
id: IAO:0000638
name: pre-publication history textual entity
def: "A textual entity that expresses the pre-publication history (submission dates, reviewer comments, etc) for a document, often including a hyperlink to a web page detailing the information." []
is_a: IAO:0000300 ! textual entity
property_value: IAO:0000111 "pre-publication history textual entity" xsd:string
property_value: IAO:0000112 "From Xiao et al. BMC Anesthesiol. 2013; 13: 33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4016475/):\n\nThe pre-publication history for this paper can be accessed here:\nhttp://www.biomedcentral.com/1471-2253/13/33/prepub" xsd:string
property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string
property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183

[Term]
id: IAO:0000639
name: related work section
def: "A part of a document about work in other publications that is relevant to the content of the document." []
is_a: IAO:0000314 ! document part
relationship: BFO:0000051 IAO:0000640 ! has part related work textual entity
property_value: IAO:0000111 "related work section" xsd:string
property_value: IAO:0000112 "The section labelled 'related work' in a typical scientific journal article, e.g. Žitnik and Zupan. Bioinformatics. 2015 Jun 15; 31(12): i230–i239. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4542780/)" xsd:string
property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string
property_value: IAO:0000118 "related literature" xsd:string
property_value: IAO:0000118 "related work" xsd:string
property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183

[Term]
id: IAO:0000640
name: related work textual entity
def: "A textual entity that discusses work from other publications and expresses their relevancy to the content of a document." []
is_a: IAO:0000300 ! textual entity
property_value: IAO:0000111 "related work textual entity" xsd:string
property_value: IAO:0000112 "Excerpt from Žitnik and Zupan. Bioinformatics. 2015 Jun 15; 31(12): i230–i239. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4542780/):\n\nOur work presented here is similar in spirit to our recently developed methodology for data fusion via collective matrix factorization (Žitnik and Zupan, 2015).\n\n" xsd:string
property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string
property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183

[Term]
id: IAO:0000641
name: requirements section
def: "A part of a document about a resource described in the document, e.g. software, that describes the requirements necessary to use the resource, e.g. operating systems, hardware, etc. in the case of a software resource." []
is_a: IAO:0000314 ! document part
relationship: BFO:0000051 IAO:0000642 ! has part requirements textual entity
property_value: IAO:0000111 "requirements section" xsd:string
property_value: IAO:0000112 "The section labelled 'availability and requirements' in a typical scientific journal article, e.g. Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/)." xsd:string
property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string
property_value: IAO:0000118 "requirements" xsd:string
property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183

[Term]
id: IAO:0000642
name: requirements textual entity
def: "A textual entity that expresses the requirements necessary to use a resource, e.g. software." []
is_a: IAO:0000300 ! textual entity
property_value: IAO:0000111 "requirements textual entity" xsd:string
property_value: IAO:0000112 "From Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/):\n\n• Operating systems: Platform independent\n\n• Programming language: Matlab, R, Python\n\n• Other requirements: None\n\n• License: GNU GPL v3\n\n• Any restrictions to use by non-academics: None" xsd:string
property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string
property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183

[Term]
id: IAO:0000643
name: statistical analysis textual entity
def: "A textual entity documenting statistical analysis tools and techniques employed." []
is_a: IAO:0000300 ! textual entity
property_value: IAO:0000111 "statistical analysis textual entity" xsd:string
property_value: IAO:0000112 "From Mondo et al. Cardiovasc J Afr. 2013 Mar; 24(2): 28–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3734881/):\n\nData were captured into EPI-DATA (version 3.1), cleaned and then exported to Stata version 10 for analysis. Continuous variables were summarised as mean (± standard deviation) and median (inter-quartile range), and presented in the tables. Categorical data were analysed using frequency and percentages, and results are presented in frequency tables and bar charts. Test of significance (p-value) was determined using the chi-square test. A p-value of less than 0.05 was considered significant." xsd:string
property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string
property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183

[Term]
id: IAO:0000644
name: statistical analysis section
def: "A part of the document used to describe the statistical methodologies employed in the work presented in the document." []
is_a: IAO:0000314 ! document part
relationship: BFO:0000051 IAO:0000643 ! has part statistical analysis textual entity
property_value: IAO:0000111 "statistical analysis section" xsd:string
property_value: IAO:0000112 "The section labelled 'statistical analysis' in a typical scientific journal article, e.g. Mondo et al. Cardiovasc J Afr. 2013 Mar; 24(2): 28–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3734881/)" xsd:string
property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string
property_value: IAO:0000118 "statistical analysis" xsd:string
property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183

[Term]
id: IAO:0000645
name: tables section
def: "A part of a document that contains one or more tables." []
is_a: IAO:0000314 ! document part
relationship: BFO:0000051 IAO:0000306 ! has part table
property_value: IAO:0000111 "tables section" xsd:string
property_value: IAO:0000112 "The section labelled 'tables' in a typical scientific journal article." xsd:string
property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string
property_value: IAO:0000118 "tables" xsd:string
property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183

[Term]
id: IAO:0000646
name: postal code
def: "An identifier that denotes some postal delivery route, some aggregate of postal delivery routes or a geographical region and was created for the purpose of sorting and delivering mail." []
is_a: IAO:0020000 ! identifier
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string

[Term]
id: IAO:0000647
name: Postal delivery route
def: "A plan specification that if realized, is realized by the delivery of mail to some facility or mailbox within some geographical region." []
is_a: IAO:0000104 ! plan specification
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string

[Term]
id: IAO:0000648
name: zone improvement plan code
def: "A postal code that is used in the United States for the purpose of sorting and delivering mail, and that denotes some postal delivery route or some aggregate of postal delivery routes." []
is_a: IAO:0000646 ! postal code
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
property_value: IAO:0000118 "ZIP code" xsd:string

[Term]
id: IAO:0000650
name: database extract, transform, and load process
def: "A planned process which takes as input a database and fills another database by extracting concretizations of information entities from the first, transforming them, and loading the transformed concretizations into the second." []
is_a: OBI:0000011 ! planned process
relationship: OBI:0000293 IAO:0000030 ! has_specified_input information content entity
relationship: OBI:0000299 IAO:0000030 ! has_specified_output information content entity
property_value: http://xmlns.com/foaf/0.1/page https://en.wikipedia.org/wiki/Extract,_transform,_load
property_value: IAO:0000111 "database extract, transform, and load process" xsd:string
property_value: IAO:0000116 "Alan Ruttenberg 12/21/16: Maybe this definition instead: A planned process which takes as input a database and copies concretizations from the first, optionally transforms then copies the result to the second" xsd:string
property_value: IAO:0000116 "Alan Ruttenberg 12/21/16: We don't define database in IAO, currently, as the bare word is ambiguous. Reasonable interpretations of the word might be the material entity, an information structure, an information content entity. However this definition commits, at least, to there being some material thing which bear concretizations of information entities and that there are new concretizations created during the process.  We consider the ETL process in terms of information entities rather than the concretizations. No committment is made as to whether the specified output." xsd:string
property_value: IAO:0000117 "PERSON:Alan Ruttenberg" xsd:string
property_value: IAO:0000118 "ETL" xsd:string
property_value: IAO:0000119 WEB:https://en.wikipedia.org/wiki/Extract,_transform,_load xsd:string
property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/187
property_value: isDefinedBy https://github.com/information-artifact-ontology/IAO

[Term]
id: IAO:0000701
name: descriptive data section
def: "A document part that lists and defines data variables, describes data characteristics (e.g. missing data information) and any assumptions and simplifications made." []
is_a: IAO:0000314 ! document part
property_value: IAO:0000111 "descriptive data section" xsd:string
property_value: IAO:0000114 IAO:0000120
property_value: IAO:0000117 "PERSON: Chen Yang" xsd:string
property_value: IAO:0000117 "PERSON: Jie Zheng" xsd:string
property_value: IAO:0000119 https://www.equator-network.org/reporting-guidelines/prisma/ xsd:string
property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/235
property_value: IAO:0000234 "ONE ontology" xsd:string

[Term]
id: IAO:0000702
name: additional results section
def: "A results section that reports analyses other than main results of the study (e.g. subgroups analyses, adjusted analyses, sensitivity analyses, etc.)" []
is_a: IAO:0000318 ! results section
property_value: IAO:0000111 "additional results section" xsd:string
property_value: IAO:0000114 IAO:0000120
property_value: IAO:0000117 "PERSON: Chen Yang" xsd:string
property_value: IAO:0000117 "PERSON: Jie Zheng" xsd:string
property_value: IAO:0000119 https://www.equator-network.org/reporting-guidelines/consort/ xsd:string
property_value: IAO:0000119 https://www.equator-network.org/reporting-guidelines/prisma/ xsd:string
property_value: IAO:0000119 https://www.equator-network.org/reporting-guidelines/strobe/ xsd:string
property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/235
property_value: IAO:0000234 "ONE ontology" xsd:string

[Term]
id: IAO:0000703
name: research participants section
def: "A document part that describes human subject(s) that participated in a study (e.g. inclusion & exclusion criteria, recruitment methods, reasons for non-participation, grouping and randomisation, methods of follow-up, etc.)." []
is_a: IAO:0000314 ! document part
property_value: IAO:0000111 "research participants section" xsd:string
property_value: IAO:0000114 IAO:0000120
property_value: IAO:0000117 "PERSON: Chen Yang" xsd:string
property_value: IAO:0000117 "PERSON: Jie Zheng" xsd:string
property_value: IAO:0000119 https://www.equator-network.org/reporting-guidelines/consort/ xsd:string
property_value: IAO:0000119 https://www.equator-network.org/reporting-guidelines/prisma/ xsd:string
property_value: IAO:0000119 https://www.equator-network.org/reporting-guidelines/strobe-nut/ xsd:string
property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/235
property_value: IAO:0000234 "ONE ontology" xsd:string

[Term]
id: IAO:0000704
name: measurement methods section
def: "A methods section that describes details of data assessment methods (data measurement)." []
is_a: IAO:0000317 ! methods section
property_value: IAO:0000111 "measurement methods section" xsd:string
property_value: IAO:0000114 IAO:0000120
property_value: IAO:0000117 "PERSON: Chen Yang" xsd:string
property_value: IAO:0000117 "PERSON: Jie Zheng" xsd:string
property_value: IAO:0000119 https://www.equator-network.org/reporting-guidelines/strobe/ xsd:string
property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/235
property_value: IAO:0000234 "ONE ontology" xsd:string

[Term]
id: IAO:0000705
name: research settings section
def: "A document part that describes the physical/social/cultural conditions around a research trial." []
is_a: IAO:0000314 ! document part
property_value: IAO:0000111 "research settings section" xsd:string
property_value: IAO:0000114 IAO:0000120
property_value: IAO:0000117 "PERSON: Chen Yang" xsd:string
property_value: IAO:0000117 "PERSON: Jie Zheng" xsd:string
property_value: IAO:0000119 https://www.ncbi.nlm.nih.gov/books/NBK262175/ xsd:string
property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/235
property_value: IAO:0000234 "ONE ontology" xsd:string

[Term]
id: IAO:0000706
name: study bias section
def: "A study limitations section that describes systematic error introduced into sampling or testing by selecting or encouraging one outcome or answer over others." []
is_a: IAO:0000631 ! study limitations section
property_value: IAO:0000111 "study bias section" xsd:string
property_value: IAO:0000114 IAO:0000120
property_value: IAO:0000117 "PERSON: Chen Yang" xsd:string
property_value: IAO:0000117 "PERSON: Jie Zheng" xsd:string
property_value: IAO:0000119 "DOI: 10.1097/PRS.0b013e3181de24bc" xsd:string
property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/235
property_value: IAO:0000234 "ONE ontology" xsd:string

[Term]
id: IAO:0000707
name: graphical abstract
def: "An abstract that is pictorial summary of the main findings described in the document." []
is_a: IAO:0000315 ! abstract
property_value: IAO:0000111 "graphical abstract" xsd:string
property_value: IAO:0000114 IAO:0000120
property_value: IAO:0000117 "PERSON: Jie Zheng" xsd:string
property_value: IAO:0000117 "PERSON: Tim Beck" xsd:string
property_value: IAO:0000118 "visual abstract" xsd:string
property_value: IAO:0000119 https://www.elsevier.com/authors/journal-authors/graphical-abstract xsd:string
property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/234
property_value: IAO:0000234 "Biomedical literature NLP project" xsd:string

[Term]
id: IAO:0020000
name: identifier
def: "An identifier is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity." []
comment: Sep 29, 2016: The current definition has been amended from the previous version: "A proper name is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity." to more accuratly reflect the necessary and sufficient condition on the class. (MB)
is_a: IAO:0000030 ! information content entity
intersection_of: IAO:0000219 BFO:0000001 ! denotes entity
intersection_of: OBI:0000312 IAO:0020010 {all_only="true"} ! is_specified_output_of dubbing process
relationship: IAO:0000219 BFO:0000001 ! denotes entity
property_value: http://purl.org/dc/elements/1.1/creator "Mathias Brochhausen" xsd:string
property_value: IAO:0000111 "identifier" xsd:string
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
property_value: IAO:0000118 "proper name" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/iao/pno.owl

[Term]
id: IAO:0020001
name: grapheme
def: "A grapheme  is an information content entity that is a fundamental unit in a written language. " []
is_a: IAO:0000030 ! information content entity
property_value: http://purl.org/dc/elements/1.1/creator "Mathias Brochhausen" xsd:string
property_value: IAO:0000112 "alphabetic letters, Chinese characters, numerical digits, punctuation marks, and the individual symbols of any of the world's writing systems" xsd:string
property_value: IAO:0000119 http://en.wikipedia.org/wiki/Grapheme xsd:string

[Term]
id: IAO:0020002
name: utterance
def: "An utterance is an information content entity that is a complete unit of speech in spoken language. " []
is_a: IAO:0000030 ! information content entity
property_value: http://purl.org/dc/elements/1.1/creator "Mathias Brochhausen" xsd:string
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
property_value: IAO:0000119 "Wikipedia: http://en.wikipedia.org/wiki/Utterance" xsd:string

[Term]
id: IAO:0020003
name: mechanical wave quality
def: "An attributive collection of qualities inhering in energy when transported through a medium in a wave." []
is_a: BFO:0000019 ! quality
property_value: http://purl.org/dc/elements/1.1/creator "Mathias Brochhausen" xsd:string

[Term]
id: IAO:0020004
name: writing quality
def: "is a quality that is the concretization of graphemes and inheres in a material object." []
is_a: BFO:0000019 ! quality
property_value: http://purl.org/dc/elements/1.1/creator "Mathias Brochhausen" xsd:string
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string

[Term]
id: IAO:0020005
name: writing bearer
def: "is a material information bearer that bears the concretization of graphemes." []
is_a: IAO:0000178 ! material information bearer
property_value: http://purl.org/dc/elements/1.1/creator "Mathias Brochhausen" xsd:string
property_value: IAO:0000112 "pieces of paper, tables, walls, floors, driveways, highway signs, computer screens, skin, tablets of clay, rocks, sheets of metal (license plates), sheets of papyrus, etc.   clouds of smoke in skywriting," xsd:string
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string

[Term]
id: IAO:0020006
name: portion of energy
is_a: BFO:0000004 ! independent continuant

[Term]
id: IAO:0020007
name: sound energy
def: "Energy that is transported in a sound wave." []
is_a: IAO:0020006 ! portion of energy
relationship: RO:0000053 IAO:0020003 ! bearer of mechanical wave quality
property_value: http://purl.org/dc/elements/1.1/creator "Mathias Brochhausen" xsd:string

[Term]
id: IAO:0020008
name: utterance energy
def: "Sound energy bearing the concretization of an utterance and being the output of an uttering process. " []
is_a: IAO:0020007 ! sound energy

[Term]
id: IAO:0020009
name: oscillating
def: "Oscillating is a processual that shows repetitive variation, typically in time, of some measured quality about a central value (often a point of equilibrium) or between two or more different states." []
is_a: BFO:0000015 ! process
property_value: http://purl.org/dc/elements/1.1/creator "Mathias Brochhausen" xsd:string
property_value: IAO:0000119 http://en.wikipedia.org/wiki/Oscillation xsd:string

[Term]
id: IAO:0020010
name: dubbing process
def: "A dubbing process is a planned process that provides a reference to an individual entity shared by a group of subscribers to refer to that individual entity." []
is_a: OBI:0000011 ! planned process
relationship: OBI:0000299 IAO:0020000 ! has_specified_output identifier
property_value: http://purl.org/dc/elements/1.1/creator "Mathias Brochhausen" xsd:string
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string

[Term]
id: IAO:0020011
name: utterance process
def: "is a planned process of making speech sounds which may or may not have an actual language involved. " []
is_a: OBI:0000011 ! planned process
relationship: OBI:0000299 IAO:0020008 ! has_specified_output utterance energy
property_value: http://purl.org/dc/elements/1.1/creator "Mathias Brochhausen" xsd:string
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
property_value: IAO:0000119 http://en.wiktionary.org/wiki/utter xsd:string

[Term]
id: IAO:0020015
name: personal name
def: "A personal name is a proper name identifying an individual person." []
comment: Personal names "today usually comprises a given name bestowed at birth or at a young age plus a surname. It is nearly universal for a human to have a name; except in rare cases, for example feral children growing up in isolation, or infants orphaned by natural disaster for whom no written record survives.[citation needed] The Convention on the Rights of the Child specifies that a child has the right from birth to a name. Certain isolated tribes, such as the Machiguenga of the Amazon, also lack personal names." (http://en.wikipedia.org/wiki/Personal_name)
comment: Sep 29, 2016: The comment that including the wikipedia definition of personal name is not to be interpreted in a way that restricts this class to only contain strings of letters. A numerical or alphanumerical identifier that denotes a human is being is a personal name, too. (MB)
is_a: IAO:0020000 ! identifier
intersection_of: IAO:0020000 ! identifier
intersection_of: IAO:0000219 NCBITaxon:9606 {all_only="true"} ! denotes Homo sapiens
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
property_value: IAO:0000119 http://en.wikipedia.org/wiki/Personal_name xsd:string

[Term]
id: IAO:0020016
name: given name
def: "A given name, in Western contexts often referred to as a first name, is a personal name that specifies and differentiates between members of a group of individuals, especially in a family, all of whose members usually share the same family name (surname). A given name is purposefully given, usually by a child's parents at or near birth, in contrast to an inherited one such as a family name" []
is_a: IAO:0020015 ! personal name
relationship: BFO:0000050 IAO:0020015 ! part of personal name
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
property_value: IAO:0000119 http://en.wikipedia.org/wiki/Given_name xsd:string

[Term]
id: IAO:0020017
name: family name
def: "A family name (in Western contexts often referred to as a surname or last name) is typically a part of a person's name which has been passed, according to law or custom, from one or both parents to their children." []
is_a: IAO:0020015 ! personal name
relationship: BFO:0000050 IAO:0020015 ! part of personal name
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
property_value: IAO:0000119 http://en.wikipedia.org/wiki/Family_name xsd:string

[Term]
id: IAO:0020020
name: code set
def: "A document that is a collection of identifiers that has been created to identify and annotate core ideas of a specified domain, and where the intention of its creators is that the identifiers have a one-to-one correspondence with entities in reality outside the aggregate." []
comment: Does not imply absence vs. presence of any taxonomy.
comment: Does not imply that identifiers denote particulars, universals, or defined classes (a.k.a. attributive collections) or even that they denote only one of these three types of entities (e.g., SNOMED and even various OBO ontologies have identifiers that identify entities in all three categories).
comment: Each identifier is often (but not necessarily) associated with a text string—variously called a “description,” “name,” “title,” or “label”—that helps humans reach the target of denotation.\n\nWhen there is no such string, it is almost always because the identifiers take the form of human language words. For example, a “sex” or “gender” code set could have identifiers “MALE” and “FEMALE,” or even “M” and “F” (by convention, we understand what these mean).
comment: For each given domain, there can potentially exist multiple code sets. The multiplicity of code sets is partially due to the different specific purposes of those code sets.
comment: For National Drug Codes (NDCs) and similar code sets, there doesn’t even have to be a single, fully-concretized copy somewhere (for example, for NDCs there is no centralized database or repository where they all live as one instance of concretization of code set). The code set can be “distributively” concretized. This seems like an unusual exception, but it also likely applies to Universal Product Codes (UPCs) and their follow on Global Trade Item Numbers (GTINs).
comment: Many code sets are created for a specific purpose in addition to merely identifying and annotating core ideas of a specified domain.
comment: The identifiers do not denote each other.
is_a: IAO:0000310 ! document
relationship: BFO:0000051 IAO:0020000 ! has part identifier
property_value: http://purl.org/dc/elements/1.1/contributor "Clint Dowland" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Matt Diller" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Sarah Bost" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
property_value: IAO:0000118 "code system" xsd:string
property_value: IAO:0000118 "codeset" xsd:string
property_value: IAO:0000118 "coding system" xsd:string
property_value: IAO:0000118 "controlled vocabulary" xsd:string

[Term]
id: IAO:0020021
name: identity document
def: "A document that denotes some identity and is concretized by the bearer of some credential role." []
is_a: IAO:0000310 ! document
relationship: IAO:0000136 IAO:0020022 ! is about documented identity
property_value: IAO:0000117 "Amanda Hicks" xsd:string

[Term]
id: IAO:0020022
name: documented identity
def: "A documented identity is the aggregate of all data items about an entity.  Notice that a documented identity is not itself a document since a document is intended to be understood as a whole and data items about an individual are usually scattered across different documents." []
comment: is an aggregate of ICEs also an ICE? yes\nIs part_of the appropriate relation to use for data items and documented identities?
is_a: IAO:0000030 ! information content entity
property_value: IAO:0000117 "Amanda Hicks" xsd:string

[Term]
id: IAO:0020023
name: authentication
def: "Authentication is the act of checking or verifying an identity claim (that is either tacit or explicit).\n" []
is_a: BFO:0000015 ! process
property_value: IAO:0000112 " I order a beer and the bartender authenticates my age by looking at my DOB on my driver's license.  I sign into my email account, and the system authenticates my permission to read the email by checking the password I enter against my password listed in the database." xsd:string
property_value: IAO:0000117 "Amanda Hicks" xsd:string

[Term]
id: IAO:0020024
name: credential role
def: "A role that inheres in a concretization of an identity document and is realized by an authentication process." []
is_a: BFO:0000023 ! role
relationship: BFO:0000054 IAO:0020023 ! realized in authentication
property_value: IAO:0000117 "Amanda Hicks" xsd:string

[Term]
id: IAO:0020025
name: obligor role
def: "A role that is the specified output of an obligation generating social act and that is realized by it's bearer being the providing part of a process that fulfills the previously agreed upon requirements." []
is_a: IAO:0021008 ! deontic role
property_value: IAO:0000111 "obligor role" xsd:string
property_value: IAO:0000112 "Sam's obligor role realized by him taking Nigel to lunch after promising to do so; Sarah's obligor role realized by paying the purchase price to Layla after signing the contract specifying that she is buying a piece of land from Layla." xsd:string
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
property_value: IAO:0000117 "Sarah Bost" xsd:string

[Term]
id: IAO:0020026
name: obligee role
def: "A role that is the specified output of an obligation generating social act and that is realized by it's bearer being the receiving part of a process that fulfills the previously agreed upon requirements." []
is_a: IAO:0021008 ! deontic role
property_value: IAO:0000111 "obligee role" xsd:string
property_value: IAO:0000112 "Nigel's obligee role realized by Sam taking him out for lunch after Sam so promised; Layla's obligee role realized by receiving the money after signing a contract in which Sarah obtained a piece of land in exchange for a specified sum of money." xsd:string
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
property_value: IAO:0000117 "Sarah Bost" xsd:string

[Term]
id: IAO:0020027
name: owner role
def: "A role in a human social process that is based on a social act and whose bearer exercises exclusive control over a property, where this control is permitted by one or more deontic roles, which are parts of the owner role." []
is_a: OMRSE:00000024 ! role in human social processes
property_value: IAO:0000112 "Tammy's owner role with regards to the house on 234 Evergreen Terrace; Walter's owner role with regards to the intellectual property on his movie script" xsd:string
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
property_value: IAO:0000119 https://github.com/d-acts/d-acts/issues/29 xsd:string
property_value: IAO:0000119 "OBIB/ICO community" xsd:string

[Term]
id: IAO:0021000
name: obsolete_claim
is_a: ObsoleteClass ! Obsolete Class
property_value: IAO:0000231 IAO:0000226
is_obsolete: true

[Term]
id: IAO:0021001
name: deontic document act
name: obsolete_deontic document act
def: "A deontic declaration creating or revoking a deontic role by lawfully manipulating (signing, stamping, publishing) a document." []
is_a: IAO:0021009 ! deontic declaration
is_a: ObsoleteClass ! Obsolete Class
intersection_of: IAO:0021009 ! deontic declaration
intersection_of: OBI:0000293 IAO:0021007 ! has_specified_input document act input document
intersection_of: OBI:0000299 IAO:0000310 ! has_specified_output document
relationship: OBI:0000293 IAO:0021007 ! has_specified_input document act input document
relationship: OBI:0000299 IAO:0000310 ! has_specified_output document
property_value: IAO:0000112 "my filling in an immigration form, a judge's signing and stamping a court order" xsd:string
property_value: IAO:0000112 "my filling in an immigration form, a judge's signing and stamping a court order" xsd:string
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
property_value: IAO:0000231 IAO:0000226
is_obsolete: true

[Term]
id: IAO:0021002
name: obsolete_document act
def: "A social act creating, revoking or transferring a socio-legal generically dependent continuant or a role by validating (signing, stamping, publishing) a document." []
is_a: ObsoleteClass ! Obsolete Class
property_value: IAO:0000112 "my filling in an immigration form, a judge's signing and stamping a court order" xsd:string
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
property_value: IAO:0000231 IAO:0000103
is_obsolete: true
replaced_by: IAO:0021001

[Term]
id: IAO:0021003
name: social act
def: "A planned process that is carried out by a conscious being or an organization, and is self-generated, directed towards another conscious being or an aggregate of conscious beings, an organization or an aggregate of organizations, and that is in need of being perceived." []
comment: The phrase "in need of being perceived" does not imply that only planned processes that are in fact perceived can be social acts. Reinach clarifies that by exemplifying these matters for commands: "The command is according to its essence in need of being heard (vernehmungsbedürtig". It can of course happen that commands are given without being heard. Then they fail to fulfil their purpose. They are like thrown spears which fall to the ground without hitting their target." (A. Reinach: The Apriori Foundations of the Civil Law." Edited by J. Crosby, Heusenstamm: ontos Verlag, 2012).\nReinach clearly does not imply that a command that does not fulfill its prupose would not be a command.\nThanks to W.R. Hogan for finding the Reinach quote.
is_a: OBI:0000011 ! planned process
property_value: IAO:0000112 "Colonel Klink giving Sergeant Schultz an order, Jake promising Jill to take her to the junior prom" xsd:string
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string

[Term]
id: IAO:0021004
name: obsolete_socio-legal generically dependent continuant
def: "Socio-legal generically dependent continuants are generically dependent continuants that come into existence through social acts and that if they get concretized are concretized as realizable entities." []
is_a: ObsoleteClass ! Obsolete Class
property_value: IAO:0000112 "the claim of a piece of land, the obligation to pay rent to the owner of a rental property" xsd:string
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
is_obsolete: true

[Term]
id: IAO:0021005
name: obsolete_deontic declaration
def: "A social act that brings about, transfers or revokes a socio-legal generically dependent continuant or brings about or transforms a role. Declarations do not depend on words spoken or written, but sometimes are merely actions, for instance the signing of a document." []
is_a: ObsoleteClass ! Obsolete Class
property_value: IAO:0000111 "deontic declaration" xsd:string
property_value: IAO:0000112 "my consenting verbally to buy a used TV set for $ 500, John Robie's taking of Mrs. Steven's jewels, Jane Doe's revoking of informed consent over the phone, John Doe signing an employment contract." xsd:string
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
property_value: IAO:0000118 "declaration" xsd:string
property_value: IAO:0000118 "status function declaration" xsd:string
property_value: IAO:0000231 IAO:0000103
is_obsolete: true

[Term]
id: IAO:0021006
name: obsolete obligee role
def: "A role that is either the specified output of an obligation generating social act or the concretization of a transferable obligation and that is realized by it's bearer being the providing part of a process that fulfills the previously agreed upon requirements." []
is_a: ObsoleteClass ! Obsolete Class
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
is_obsolete: true

[Term]
id: IAO:0021007
name: document act input document
def: "A document that is intended to be the specified input in a document act. It has a plan specification as a part that specifies the intended socio-legal entities that are created through the document (objective specification) and the way in which the document act is to be performed (by signing, by stamping, etc.) (action specification)." []
is_a: IAO:0000310 ! document
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string

[Term]
id: IAO:0021008
name: deontic role
def: "A role that inheres in an agent and which is externally grounded in the normative expectations that other agents within a social context have concerning how that agent should behave." []
is_a: BFO:0000023 ! role
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
property_value: IAO:0000117 "Neil Otte" xsd:string

[Term]
id: IAO:0021009
name: deontic declaration
def: "A social act that creates or revokes a deontic role." []
is_a: IAO:0021003 ! social act
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string

[Term]
id: IAO:0021010
name: obsolete_obligation
is_a: ObsoleteClass ! Obsolete Class
property_value: IAO:0000231 IAO:0000226
is_obsolete: true

[Term]
id: IAO:0021014
name: obsolete_declaration executive role
def: "The role borne by a human being, an organization or an aggregate of either of both that is realized by being the active participant in a declaration." []
is_a: ObsoleteClass ! Obsolete Class
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
property_value: IAO:0000231 IAO:0000226
is_obsolete: true

[Term]
id: IAO:0021015
name: obsolete_document template creator role
def: "The role of a human being or an aggregate of human beings preparing the initial document to undergo a document act, thus creating a socio-legal generically dependent continuant." []
comment: not that the "template" does not need to be a template at all. It can be a document that is getting stamped and signed and by these acts creating some socio-legal generically dependent continuants.
is_a: ObsoleteClass ! Obsolete Class
property_value: IAO:0000112 "the role borne by the US Citizen and Immigration Service realized by providing the template form for entering the US as a non-resident alien, the role of a guideline committee in putting together a clinical guideline" xsd:string
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
property_value: IAO:0000231 IAO:0000226
is_obsolete: true

[Term]
id: IAO:0021017
name: obsolete_claimant role
def: "The role of a human being or an aggregate of human beings concretizing a claim." []
is_a: ObsoleteClass ! Obsolete Class
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
property_value: IAO:0000231 IAO:0000226
is_obsolete: true

[Term]
id: IAO:0021018
name: obsolete_obligator role
def: "The role of a human being or an aggregate of human beings  concretizing an obligation." []
is_a: ObsoleteClass ! Obsolete Class
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
property_value: IAO:0000231 IAO:0000226
is_obsolete: true

[Term]
id: IAO:0021020
name: obsolete_declaration target
def: "The human being or organization or aggregate of any of the aforementioned that is the bearer of a concretization of a socio-legal generically dependent continuant brought about by or transferred in a specific document act." []
is_a: ObsoleteClass ! Obsolete Class
property_value: IAO:0000112 "me as a bearer of a spouse role, which participates in a document act, John Doe as bearer of a debtor role, which participates in a document act" xsd:string
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
property_value: IAO:0000231 IAO:0000103
is_obsolete: true

[Term]
id: IAO:0021021
name: document act template creator role
def: "A role that inheres in a human being or organization or aggregate of any of the aforementioned that prepares a document that is the specified input to a document act and is the input document of a document act." []
is_a: BFO:0000023 ! role
property_value: IAO:0000112 "The role of the U.S. Citizenship and Immigration Service realized by the creation of an immigration form that is being filled in, the role of a national professional association realized by the creation of a clinical guideline that is to be certified" xsd:string
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string

[Term]
id: IAO:0021022
name: deontic declaration performer role
def: "A role inhering in a human being or an organization or an aggregate of any of the aforementioned that is realized by the bearer being the agent in a declaration." []
is_a: BFO:0000023 ! role
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
property_value: IAO:0000118 "declaration performer role" xsd:string

[Term]
id: IAO:0021030
name: obsoleted_document act target
def: "The human being or organization or aggregate of any of the aforementioned that is the bearer of a concretization of a socio-legal generically dependent continuant brought about by or transferred in a specific document act." []
is_a: ObsoleteClass ! Obsolete Class
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
is_obsolete: true

[Term]
id: IAO:0021031
name: document act performer role
def: "A role inhering in a human being or an organization or an aggregate of any of the aforementioned that is realized by the bearer being the agent in a document act." []
is_a: BFO:0000023 ! role
property_value: IAO:0000112 "a judge's role of signing a court order" xsd:string
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string

[Term]
id: IAO:0021032
name: obsolete_obligee role
def: "A role that is either the specified output of an obligation generating social act or the concretization of a transferable obligation and that is realized by it's bearer being the receiving part of a process that fulfills the previously agreed upon requirements." []
is_a: ObsoleteClass ! Obsolete Class
property_value: IAO:0000117 "Sarah Bost" xsd:string
property_value: IAO:0000231 IAO:0000103
is_obsolete: true

[Term]
id: IAO:0021033
name: obsolete_obligor role
def: "A role that is either the specified output of an obligation generating social act or the concretization of a transferable obligation and that is realized by it's bearer being the providing part of a process that fulfills the previously agreed upon requirements." []
is_a: ObsoleteClass ! Obsolete Class
property_value: IAO:0000117 "Sarah Bost" xsd:string
property_value: IAO:0000231 IAO:0000103
is_obsolete: true

[Term]
id: IAO:0021102
name: standing declaration
def: "A social act that postulates a socio-legal fact for a specified group of people or organizations." []
is_a: IAO:0021003 ! social act
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
property_value: IAO:0000118 "enactment" xsd:string

[Term]
id: IAO:0021300
name: obsolete obligor role
def: "A role that is either the specified output of an obligation generating social act or the concretization of a transferable obligation and that is realized by it's bearer being the receiving part of a process that fulfills the previously agreed upon requirements." []
is_a: ObsoleteClass ! Obsolete Class
property_value: IAO:0000117 "John Judkins" xsd:string
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
is_obsolete: true

[Term]
id: IAO:8000000
name: ontology module
is_a: IAO:0000102 ! data about an ontology part
property_value: IAO:0000111 "ontology module" xsd:string
property_value: IAO:0000116 "I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it." xsd:string
property_value: IAO:0000118 "ontology file" xsd:string
property_value: IAO:0000232 "This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology." xsd:string

[Term]
id: IAO:8000001
name: base ontology module
def: "An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies." []
is_a: IAO:8000000 ! ontology module
property_value: IAO:0000111 "base ontology module" xsd:string
property_value: seeAlso https://github.com/INCATools/ontology-starter-kit/issues/50

[Term]
id: IAO:8000002
name: editors ontology module
def: "An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users." []
is_a: IAO:8000000 ! ontology module
property_value: IAO:0000111 "editors ontology module" xsd:string
property_value: IAO:0000118 "source ontology module" xsd:string

[Term]
id: IAO:8000003
name: main release ontology module
def: "An ontology module that is intended to be the primary release product and the one consumed by the majority of tools." []
is_a: IAO:8000000 ! ontology module
property_value: IAO:0000111 "main release ontology module" xsd:string
property_value: IAO:0000116 "TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module" xsd:string

[Term]
id: IAO:8000004
name: bridge ontology module
def: "An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module." []
is_a: IAO:8000000 ! ontology module
property_value: IAO:0000111 "bridge ontology module" xsd:string
property_value: seeAlso https://github.com/obophenotype/uberon/wiki/inter-anatomy-ontology-bridge-ontologies

[Term]
id: IAO:8000005
name: import ontology module
def: "A subset ontology module that is intended to be imported from another ontology." []
is_a: IAO:8000006 ! subset ontology module
property_value: IAO:0000111 "import ontology module" xsd:string
property_value: IAO:0000116 "TODO: add axioms that indicate this is the output of a module extraction process." xsd:string
property_value: IAO:0000118 "import file" xsd:string
property_value: seeAlso http://robot.obolibrary.org/extract

[Term]
id: IAO:8000006
name: subset ontology module
def: "An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms." []
is_a: IAO:8000000 ! ontology module
property_value: IAO:0000111 "subset ontology module" xsd:string
property_value: IAO:0000118 "ontology slim" xsd:string
property_value: IAO:0000118 "subset ontology" xsd:string
property_value: seeAlso http://robot.obolibrary.org/filter
property_value: seeAlso http://www.geneontology.org/page/go-slim-and-subset-guide

[Term]
id: IAO:8000007
name: curation subset ontology module
def: "A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation." []
is_a: IAO:8000006 ! subset ontology module
property_value: IAO:0000111 "curation subset ontology module" xsd:string

[Term]
id: IAO:8000008
name: analysis subset ontology module
def: "An ontology module that is intended for usage in analysis or discovery applications." []
is_a: IAO:8000006 ! subset ontology module
property_value: IAO:0000111 "analysis ontology module" xsd:string

[Term]
id: IAO:8000009
name: single layer subset ontology module
def: "A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint." []
is_a: IAO:8000006 ! subset ontology module
property_value: IAO:0000111 "single layer ontology module" xsd:string
property_value: IAO:0000118 "ribbon subset" xsd:string

[Term]
id: IAO:8000010
name: exclusion subset ontology module
def: "A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes." []
is_a: IAO:8000006 ! subset ontology module
property_value: IAO:0000111 "exclusion subset ontology module" xsd:string
property_value: IAO:0000118 "antislim" xsd:string

[Term]
id: IAO:8000011
name: external import ontology module
def: "An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach." []
is_a: IAO:8000005 ! import ontology module
property_value: IAO:0000111 "external import ontology module" xsd:string
property_value: IAO:0000118 "external import" xsd:string

[Term]
id: IAO:8000012
name: species subset ontology module
def: "A subset ontology that is crafted to either include or exclude a taxonomic grouping of species." []
is_a: IAO:8000006 ! subset ontology module
property_value: IAO:0000111 "species subset ontology module" xsd:string
property_value: IAO:0000118 "taxon subset" xsd:string
property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints

[Term]
id: IAO:8000013
name: reasoned ontology module
def: "An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available." []
is_a: IAO:8000000 ! ontology module
property_value: IAO:0000111 "reasoned ontology module" xsd:string
property_value: seeAlso http://robot.obolibrary.org/reason

[Term]
id: IAO:8000014
name: generated ontology module
def: "An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV." []
is_a: IAO:8000000 ! ontology module
property_value: IAO:0000111 "generated ontology module" xsd:string
property_value: IAO:0000116 "TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process" xsd:string

[Term]
id: IAO:8000015
name: template generated ontology module
def: "An ontology module that is automatically generated from a template specification and fillers for slots in that template." []
is_a: IAO:8000014 ! generated ontology module
property_value: IAO:0000111 "template generated ontology module" xsd:string
property_value: seeAlso http://robot.obolibrary.org/template
property_value: seeAlso https://doi.org/10.1186/s13326-017-0126-0
property_value: seeAlso https://github.com/dosumis/dead_simple_owl_design_patterns/

[Term]
id: IAO:8000016
name: taxonomic bridge ontology module
is_a: IAO:8000004 ! bridge ontology module
property_value: IAO:0000111 "taxonomic bridge ontology module" xsd:string

[Term]
id: IAO:8000017
name: ontology module subsetted by expressivity
is_a: IAO:8000006 ! subset ontology module
property_value: IAO:0000111 "ontology module subsetted by expressivity" xsd:string

[Term]
id: IAO:8000018
name: obo basic subset ontology module
def: "A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools.\n\nExamples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses).\n\nAn ontology is OBO Basic if and only if it has the following characteristics:\nDAG\nUnidirectional\nNo Dangling Clauses\nFully Asserted\nFully Labeled\nNo equivalence axioms\nSingly labeled edges\nNo qualifier lists\nNo disjointness axioms\nNo owl-axioms header\nNo imports" []
is_a: IAO:8000017 ! ontology module subsetted by expressivity
property_value: IAO:0000111 "obo basic subset ontology module" xsd:string
property_value: seeAlso "6.2"

[Term]
id: IAO:8000019
name: ontology module subsetted by OWL profile
is_a: IAO:8000017 ! ontology module subsetted by expressivity
property_value: IAO:0000111 "ontology module subsetted by OWL profile" xsd:string

[Term]
id: IAO:8000020
name: EL++ ontology module
is_a: IAO:8000019 ! ontology module subsetted by OWL profile
property_value: IAO:0000111 "EL++ ontology module" xsd:string

[Term]
id: NCBITaxon:9606
name: Homo sapiens
is_a: OBI:0100026 ! organism
property_value: IAO:0000111 "Homo sapiens" xsd:string
property_value: IAO:0000118 "human being" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/ncbitaxon.owl

[Term]
id: NCIT:C53489
name: obsolete Systematized Nomenclature of Medicine
is_a: IAO:0020020 ! code set
is_obsolete: true

[Term]
id: OAE:0000002
name: medical intervention
def: "medical intervention is a planned process that has the goal of diagnosing, preventing or relieving illness or injury. " []
is_a: OBI:0000011 ! planned process
property_value: IAO:0000116 "The act of intervening, interfering or interceding with the intent of modifying the outcome. In medicine, an intervention is usually undertaken to help treat or cure a condition. For example, \"Acupuncture as a therapeutic intervention is widely practiced in the United States,\" \nReference:\nhttp://www.medterms.com/script/main/art.asp?articlekey=34214 . Some interventions can be used for diagnosis. " xsd:string
property_value: IAO:0000117 "YH" xsd:string
property_value: IAO:0000119 "WEB: http://wiki.answers.com/Q/What_is_medical_intervention" xsd:string

[Term]
id: OAE:0000067
name: surgery
def: "Surgery is a medical procedure that uses operative manual and instrumental techniques on a patient to investigate and/or treat a pathological condition such as disease or injury, to help improve bodily function or appearance. The key difference between a surgery and a general procedure is the need for an incision. Making an incision, or cutting into the skin to gain access to the body’s deeper tissues or organs, is a defining characteristic of surgery." []
is_a: OAE:0002807 ! medical procedure
property_value: IAO:0000117 "YH, SS" xsd:string
property_value: IAO:0000118 "surgical procedure" xsd:string
property_value: IAO:0000119 "WEB: http://en.wikipedia.org/wiki/Surgery" xsd:string
property_value: IAO:0000119 "WEB: http://www.wisegeekhealth.com/what-is-the-difference-between-a-surgery-and-a-procedure.htm" xsd:string
property_value: OAE:0004334 "10042609" xsd:string

[Term]
id: OAE:0002807
name: medical procedure
def: "a medical intervention that refers to any series of pre-defined steps that should be followed to achieve a desired result." []
is_a: OAE:0000002 ! medical intervention
property_value: IAO:0000117 "YH, SS" xsd:string
property_value: IAO:0000119 "WEB: http://www.wisegeekhealth.com/what-is-the-difference-between-a-surgery-and-a-procedure.htm" xsd:string

[Term]
id: OBI:0000011
name: planned process
def: "A process that realizes a plan which is the concretization of a plan specification." []
def: "A processual entity that realizes a plan which is the concretization of a plan specification." []
is_a: BFO:0000015 ! process
property_value: IAO:0000111 "planned process" xsd:string
property_value: IAO:0000111 "planned process" xsd:string
property_value: IAO:0000112 "Injecting mice with a vaccine in order to test its efficacy" xsd:string
property_value: IAO:0000114 IAO:0000122
property_value: IAO:0000116 "'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)" xsd:string
property_value: IAO:0000116 "We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some \nobjectives is a planned process." xsd:string
property_value: IAO:0000117 "Bjoern Peters" xsd:string
property_value: IAO:0000119 "branch derived" xsd:string
property_value: IAO:0000232 "6/11/9: Edited at workshop. Used to include: is initiated by an agent" xsd:string
property_value: IAO:0000232 "This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0000066
name: investigation
def: "a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s)." []
is_a: OBI:0000011 ! planned process
property_value: IAO:0000111 "investigation" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0000245
name: organization
def: "An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members." []
def: "An organization is a continuant entity which can play roles,  has members, and has a set of organization rules.  Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members." []
is_a: BFO:0000040 ! material entity
property_value: IAO:0000111 "organization" xsd:string
property_value: IAO:0000112 "PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods." xsd:string
property_value: IAO:0000114 IAO:0000122
property_value: IAO:0000116 "BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that.  The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based:\n\n1) there are organization_member_roles (president, treasurer, branch\neditor), with individual persons as bearers\n\n2) there are organization_roles (employer, owner, vendor, patent holder)\n\n3) an organization has a charter / rules / bylaws, which specify what roles\nthere are, how they should be realized, and how to modify the\ncharter/rules/bylaws themselves.\n\nIt is debatable what the organization itself is (some kind of dependent\ncontinuant or an aggregate of people). This also determines who/what the\nbearer of organization_roles' are. My personal favorite is still to define\norganization as a kind of 'legal entity', but thinking it through leads to\nall kinds of questions that are clearly outside the scope of OBI.\n\nInterestingly enough, it does not seem to matter much where we place\norganization itself, as long as we can subclass it (University, Corporation,\nGovernment Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO,\nW3C, University of Oklahoma), and have it play roles.\n\nThis leads to my proposal: We define organization through the statements 1 -\n3 above, but without an 'is a' statement for now. We can leave it in its\ncurrent place in the is_a hierarchy (material entity) or move it up to\n'continuant'. We leave further clarifications to BFO, and close this issue\nfor now." xsd:string
property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string
property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string
property_value: IAO:0000117 "PERSON: Philippe Rocca-Serra" xsd:string
property_value: IAO:0000117 "PERSON: Susanna Sansone" xsd:string
property_value: IAO:0000119 "GROUP: OBI" xsd:string

[Term]
id: OBI:0000471
name: study design execution
def: "a planned process that carries out a study design" []
is_a: OBI:0000011 ! planned process
property_value: IAO:0000111 "study design execution" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0100026
name: organism
def: "A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs." []
is_a: BFO:0000040 ! material entity
property_value: IAO:0000111 "organism" xsd:string
property_value: IAO:0000112 "animal" xsd:string
property_value: IAO:0000112 "fungus" xsd:string
property_value: IAO:0000112 "plant" xsd:string
property_value: IAO:0000112 "virus" xsd:string
property_value: IAO:0000114 IAO:0000121
property_value: IAO:0000114 IAO:0000122
property_value: IAO:0000116 "10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms')" xsd:string
property_value: IAO:0000116 "13-02-2009:\nOBI doesn't take position as to  when an organism starts or ends being an organism - e.g. sperm, foetus.\nThis issue is outside the scope of OBI." xsd:string
property_value: IAO:0000117 "GROUP: OBI Biomaterial Branch" xsd:string
property_value: IAO:0000119 "WEB: http://en.wikipedia.org/wiki/Organism" xsd:string

[Term]
id: OBI:0200000
name: data transformation
def: "A planned process that produces output data from input data." []
is_a: OBI:0000011 ! planned process
property_value: IAO:0000111 "data transformation" xsd:string
property_value: IAO:0000112 "The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value." xsd:string
property_value: IAO:0000114 IAO:0000122
property_value: IAO:0000117 "Elisabetta Manduchi" xsd:string
property_value: IAO:0000117 "Helen Parkinson" xsd:string
property_value: IAO:0000117 "James Malone" xsd:string
property_value: IAO:0000117 "Melanie Courtot" xsd:string
property_value: IAO:0000117 "Philippe Rocca-Serra" xsd:string
property_value: IAO:0000117 "Richard Scheuermann" xsd:string
property_value: IAO:0000117 "Ryan Brinkman" xsd:string
property_value: IAO:0000117 "Tina Hernandez-Boussard" xsd:string
property_value: IAO:0000118 "data analysis" xsd:string
property_value: IAO:0000118 "data processing" xsd:string
property_value: IAO:0000119 "Branch editors" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0500000
name: study design
def: "A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution." []
is_a: IAO:0000104 ! plan specification
property_value: IAO:0000111 "study design" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0600052
name: dialysis
def: "a protocol application that uses diffusion through a semi-permeable membrane to separate an input material into two fractions of different composition" []
is_a: OBI:0000011 ! planned process
relationship: OBI:0000299 BFO:0000040 ! has_specified_output material entity
property_value: IAO:0000111 "dialysis" xsd:string
property_value: IAO:0000112 "the use of a dialysis bag of select pore size to remove salt from collagen isolated from mouse cartilage" xsd:string
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "PERSON:Kevin Clancy" xsd:string
property_value: IAO:0000119 "OBI branch derived" xsd:string

[Term]
id: OGMS:0000031
name: disease
def: "A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism." []
is_a: BFO:0000016 ! disposition
property_value: IAO:0000117 "Albert Goldfain" xsd:string
property_value: IAO:0000119 http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf xsd:string
property_value: IAO:0000232 "creation date: 2009-06-23T11:21:20Z" xsd:string
property_value: IAO:0000412 https://github.com/OGMS/ogms/releases/tag/v2019-04-30 xsd:string

[Term]
id: OGMS:0000073
name: diagnosis
def: "The representation of a conclusion of a diagnostic process." []
is_a: OGMS:0000123 ! clinical data item
relationship: OBI:0000312 OGMS:0000104 ! is_specified_output_of diagnostic process
property_value: IAO:0000117 "Albert Goldfain" xsd:string
property_value: IAO:0000119 http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf xsd:string
property_value: IAO:0000232 "creation date: 2009-06-23T12:42:23Z" xsd:string
property_value: IAO:0000412 https://github.com/OGMS/ogms/releases/tag/v2019-04-30 xsd:string

[Term]
id: OGMS:0000096
name: health care process
def: "A planned process with the objective to improve the health status of a patient that directly involves the treatment, diagnosis, or prevention of disease or injury of a patient" []
is_a: OBI:0000011 ! planned process
property_value: IAO:0000117 "Albert Goldfain\nSagar Jain" xsd:string
property_value: IAO:0000119 http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6 xsd:string
property_value: IAO:0000232 "creation date: 2011-02-21T09:57:44Z\neditor date: 2017-04-18\n" xsd:string
property_value: IAO:0000412 https://github.com/OGMS/ogms/releases/tag/v2019-04-30 xsd:string

[Term]
id: OGMS:0000097
name: health care encounter
def: "A temporally-connected health care process that has as participants an organization or person realizing the health care provider role and a person realizing the patient role.  The health care provider role and patient are realized during the health care encounter" []
is_a: OBI:0000011 ! planned process
property_value: IAO:0000117 "Albert Goldfain" xsd:string
property_value: IAO:0000119 http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6 xsd:string
property_value: IAO:0000232 "creation date: 2011-02-21T09:57:44Z" xsd:string

[Term]
id: OGMS:0000099
name: outpatient encounter
def: "TODO" []
is_a: OGMS:0000097 ! health care encounter
property_value: IAO:0000117 "Albert Goldfain" xsd:string
property_value: IAO:0000119 http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6 xsd:string
property_value: IAO:0000232 "creation date: 2011-02-21T09:57:44Z" xsd:string
property_value: IAO:0000412 https://github.com/OGMS/ogms/releases/tag/v2019-04-30 xsd:string

[Term]
id: OGMS:0000100
name: inpatient encounter
def: "TODO" []
is_a: OGMS:0000097 ! health care encounter
property_value: IAO:0000117 "Albert Goldfain" xsd:string
property_value: IAO:0000119 http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6 xsd:string
property_value: IAO:0000232 "creation date: 2011-02-21T09:57:44Z" xsd:string
property_value: IAO:0000412 https://github.com/OGMS/ogms/releases/tag/v2019-04-30 xsd:string

[Term]
id: OGMS:0000102
name: injury
def: "A disorder that involves some structural damage that is immediately caused by a catastrophic external force." []
is_a: BFO:0000040 ! material entity
property_value: IAO:0000116 "At the scale of organism (as opposed to the cellular scale or the population scale), an injury is typically the result of a catastrophic event. Consider the implications of making 'injury' a subtype of 'disorder'.\n\nNote: Adopted subtype of disorder, and injury can occur at the scale of organism down to cellular level." xsd:string
property_value: IAO:0000117 "Albert Goldfain\nSagar Jain" xsd:string
property_value: IAO:0000119 "http://groups.google.com/group/ogms-discuss/browse_thread/thread/ca0ad373f27774c5\n\nOGMS call adoption- 16 SEPT 2015\nhttps://docs.google.com/document/d/1iiV1-fTS7BUUSzDw3N_Afx42698YWf54-FOTY2NkAxo/edit" xsd:string
property_value: IAO:0000232 "creation date: 2011-09-20T09:57:44Z\nedited date: 30 SEPT 2015" xsd:string

[Term]
id: OGMS:0000104
name: diagnostic process
def: "A health care process that involves the interpretation of a clinical picture from a given patient (input) and the assertion to the effect that the patient has a disease, disorder, or syndrome of a certain type, or none of these (output)." []
is_a: OGMS:0000096 ! health care process
property_value: IAO:0000117 "Albert Goldfain" xsd:string
property_value: IAO:0000119 http://groups.google.com/group/ogms-discuss/browse_thread/thread/2a7008f311fac766/e7de486c94dfd82e xsd:string
property_value: IAO:0000232 "creation date: 2011-09-20T09:57:44Z" xsd:string
property_value: IAO:0000412 https://github.com/OGMS/ogms/releases/tag/v2019-04-30 xsd:string

[Term]
id: OGMS:0000123
name: clinical data item
def: "a data item that is about a patient and is the specified output of a health care process assay or diagnostic process" []
is_a: IAO:0000027 ! data item
property_value: IAO:0000232 "creation date: 2018-11-27" xsd:string
property_value: IAO:0000412 https://github.com/OGMS/ogms/releases/tag/v2019-04-30 xsd:string

[Term]
id: OMIABIS:0000060
name: survey data
def: "A data item that contains the outcome of a survey." []
is_a: IAO:0000027 ! data item
property_value: IAO:0000117 "Alice Nzinga" xsd:string
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string

[Term]
id: OMIABIS:0001025
name: survey plan specification
def: "A plan specification that is realized by  process of gathering information (e.g. by asking questions)." []
is_a: IAO:0000104 ! plan specification
property_value: IAO:0000117 "Alice Nzinga" xsd:string
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string

[Term]
id: OMIABIS:0001035
name: survey execution
def: "A planned process that realizes the concretization of a survey to generate an output(survey data.)" []
is_a: OBI:0000011 ! planned process

[Term]
id: OMRSE:00000000
name: social security number
def: "Social Security Number(SSN) is a Centrally Registered IDentifier that is a nine-digit number issued to U.S. citizens, permanent residents, and temporary (working) residents under section 205(c) of the Social Security Act, codified as 42 U.S.C. § 405(c). The number is issued to an individual by the Social Security Administration, an independent agency of the United States government. Its primary purpose is to track individuals for Social Security purposes." []
is_a: IAO:0000578 ! centrally registered identifier
property_value: http://purl.org/dc/elements/1.1/creator "Cheng Chen(cxchen1@ualr.edu)" xsd:string
property_value: IAO:0000118 "SSN" xsd:string
property_value: IAO:0000119 http://en.wikipedia.org/wiki/Social_Security_number xsd:string

[Term]
id: OMRSE:00000001
name: human social role
def: "A social role inhering in a human being." []
is_a: OMRSE:00000026 ! organism social role
is_a: OMRSE:00000050 ! Homo sapiens role
property_value: IAO:0000117 "Mathias Brochhausen\n" xsd:string
property_value: IAO:0000117 "William R. Hogan" xsd:string

[Term]
id: OMRSE:00000002
name: party to a legal entity
is_a: OMRSE:00000024 ! role in human social processes

[Term]
id: OMRSE:00000003
name: party to a legal proceeding
is_a: OMRSE:00000002 ! party to a legal entity

[Term]
id: OMRSE:00000004
name: party to a legal agreement
is_a: OMRSE:00000002 ! party to a legal entity

[Term]
id: OMRSE:00000005
name: party to a marriage contract
is_a: OMRSE:00000004 ! party to a legal agreement
is_a: OMRSE:00000050 ! Homo sapiens role

[Term]
id: OMRSE:00000006
name: party to a power of attorney
is_a: OMRSE:00000002 ! party to a legal entity

[Term]
id: OMRSE:00000007
name: gender role
def: "A human social role borne by a human being being realized in behaviour which is considered socially appropriate for individuals of a specific sex in the context of a specific culture." []
is_a: OMRSE:00000049 ! organism role
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
property_value: IAO:0000119 http://en.wikipedia.org/wiki/Gender_role xsd:string

[Term]
id: OMRSE:00000008
name: male gender role
def: "A gender role borne by a human being that is realized in behaviour which is considered socially appropriate for individuals of the male sex in the context of the culture in question." []
is_a: OMRSE:00000007 ! gender role
relationship: RO:0000052 OBI:0100026 ! inheres in organism
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
property_value: IAO:0000118 "male gender" xsd:string

[Term]
id: OMRSE:00000009
name: female gender role
def: "A gender role borne by a human being that is realized in behaviour which is considered socially appropriate for individuals of the female sex in the context of the culture in question." []
is_a: OMRSE:00000007 ! gender role
relationship: RO:0000052 OBI:0100026 ! inheres in organism
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
property_value: IAO:0000118 "female gender" xsd:string

[Term]
id: OMRSE:00000010
name: human health care role
def: "A role in human social processes that is realized by health care processes such as seeking or providing treatment for disease and injury, diagnosing disease and injury, or undergoing diagnosis. " []
comment: Mathias Brochhausen
is_a: OMRSE:00000024 ! role in human social processes
relationship: BFO:0000054 OGMS:0000097 ! realized in health care encounter
property_value: IAO:0000117 "William R. Hogan" xsd:string
property_value: IAO:0000118 "health care role" xsd:string

[Term]
id: OMRSE:00000011
name: patient role
def: "A role borne by an organism and that is realized by presenting to a health care provider in a clinical encounter." []
comment: In order to avoid the presumption of the formal structures and institutions of Western civilization, bearing a patient role does not entail that the organism presents at an official place of business, with an organization formally and legally registered with various gov't entities, with a person endowed by the gov't with certain certifications.
is_a: OMRSE:00000010 ! human health care role
is_a: OMRSE:00000049 ! organism role
property_value: IAO:0000117 "Amanda Hicks" xsd:string
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
property_value: IAO:0000118 "patient" xsd:string
property_value: IAO:0000119 "CAFE domain expert working group." xsd:string

[Term]
id: OMRSE:00000012
name: health care provider role
def: "A human health care role inhering in an organization or human being that is realized by a process of providing health care services to an organism." []
comment: William R. Hogan
is_a: OMRSE:00000010 ! human health care role
property_value: IAO:0000117 "Mathias Brochhausen\n" xsd:string

[Term]
id: OMRSE:00000013
name: physician role
def: "A health care role borne by a human being and realized by promoting, maintaining or restoring human health through the study, diagnosis, and treatment of disease, injury and other physical and mental impairments." []
is_a: OMRSE:00000012 ! health care provider role
is_a: OMRSE:00000050 ! Homo sapiens role
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
property_value: IAO:0000118 "physician" xsd:string
property_value: IAO:0000119 http://en.wikipedia.org/wiki/Physician xsd:string

[Term]
id: OMRSE:00000014
name: nurse role
def: "A health care role borne by a human being and realized by the care of individuals, families, and communities so they may attain, maintain, or recover optimal health and quality of life." []
is_a: OMRSE:00000012 ! health care provider role
is_a: OMRSE:00000050 ! Homo sapiens role
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
property_value: IAO:0000118 "nurse" xsd:string
property_value: IAO:0000119 "based on: http://en.wikipedia.org/wiki/Nursing" xsd:string

[Term]
id: OMRSE:00000015
name: health care provider organization role
def: "A role that inheres in an organization and that is realized by the providing of services in a health care encounter." []
is_a: OMRSE:00000027 ! organization health care role
relationship: BFO:0000054 OGMS:0000097 ! realized in health care encounter
property_value: http://purl.org/dc/elements/1.1/contributor "Mathias Brochhausen" xsd:string
property_value: http://purl.org/dc/elements/1.1/creator "Amanda Hicks" xsd:string

[Term]
id: OMRSE:00000016
name: person health care provider role
is_a: OMRSE:00000001 ! human social role

[Term]
id: OMRSE:00000017
name: physician practice
def: "A health care provider organization role that inheres in an organization consisting of two or more physicians." []
is_a: OMRSE:00000015 ! health care provider organization role
property_value: IAO:0000117 "Amanda Hicks" xsd:string

[Term]
id: OMRSE:00000018
name: obsolete_hospital role
def: "A role borne by an organization and realized by providing healthcare services by healthcare professionals of multiple different disciplines of medicine and enabling stationary treatment." []
is_a: ObsoleteClass ! Obsolete Class
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
property_value: IAO:0000118 "hospital" xsd:string
is_obsolete: true

[Term]
id: OMRSE:00000019
name: integrated delivery network
def: "A health care provider organization role that inheres in an organization that is comprised of other organizations." []
is_a: OMRSE:00000015 ! health care provider organization role
property_value: IAO:0000117 "Amanda Hicks" xsd:string

[Term]
id: OMRSE:00000022
name: aggregate of objectual organisms
def: "An object aggregate of objectual organisms." []
comment: Any arbitrary collection of organisms.  They need not be of the same taxonomic class.  
is_a: BFO:0000027 ! object aggregate
property_value: IAO:0000412 http://purl.obolibrary.org/obo/omrse.owl xsd:string

[Term]
id: OMRSE:00000023
name: collection of humans
def: "An object aggregate all of whose components are human beings." []
is_a: OMRSE:00000022 ! aggregate of objectual organisms
relationship: RO:0002351 NCBITaxon:9606 ! has member Homo sapiens
property_value: IAO:0000412 http://purl.obolibrary.org/obo/omrse.owl xsd:string

[Term]
id: OMRSE:00000024
name: role in human social processes
def: "A role inhering in an entity realized by social interactions in human society." []
comment: Previous definition: A role played by an entity in human social processes.
is_a: BFO:0000023 ! role
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/omrse.owl xsd:string

[Term]
id: OMRSE:00000025
name: organization social role
def: "A role in human social processes that inheres in an organization." []
comment: Defined class that we will ultimately move to an application ontology.  We are leaving here for now until we determine which application ontology: it is likely going to be an ontology that does not currently (2012-06-05) exist.\n\nDitto for its current descendants.
is_a: OMRSE:00000024 ! role in human social processes
is_a: OMRSE:00000051 ! organization role
property_value: IAO:0000117 "William R. Hogan" xsd:string

[Term]
id: OMRSE:00000026
name: organism social role
def: "A role in human social processes that inheres in an organism." []
comment: Defined class that we will ultimately move to an application ontology.  We are leaving here for now until we determine which application ontology: it is likely going to be an ontology that does not currently (2012-06-05) exist.\n\nDitto for its current descendants.
comment: Includes animals as well as humans.  For example, pet, assistance animal, animal grown for food, work animal, domesticated animal, K-9, etc.  Human roles include gender role, party to legal entities, health care provider roles like doctor, nurse, etc.
comment: Previous definition: A role in human social processes played by an organism.
is_a: OMRSE:00000024 ! role in human social processes
is_a: OMRSE:00000049 ! organism role
property_value: IAO:0000117 "William R. Hogan\nMathias Brochhausen" xsd:string

[Term]
id: OMRSE:00000027
name: organization health care role
def: "An organization social role that, if realized, is realized by either a health care process or an ancillary health care process" []
comment: Previous definition: An organization social role played by an organization in health care processes.
is_a: OMRSE:00000025 ! organization social role

[Term]
id: OMRSE:00000028
name: obsolete geopolitical organization
def: "An organization that governs the people living in a particular geographical region or aggregate of geographical regions.  The geographical region it governs can change over time (such as the westward expansion of the United States and the addition of Hawaii)." []
is_a: ObsoleteClass ! Obsolete Class
property_value: IAO:0000117 "William R. Hogan" xsd:string
property_value: IAO:0000118 "geopolitical organization" xsd:string
is_obsolete: true

[Term]
id: OMRSE:00000029
name: obsolete geopoli organization
is_a: ObsoleteClass ! Obsolete Class
property_value: IAO:0000118 "geopoli organization" xsd:string
is_obsolete: true

[Term]
id: OMRSE:00000030
name: human patient role
def: "A patient role that inheres in a human being." []
is_a: OMRSE:00000011 ! patient role
is_a: OMRSE:00000050 ! Homo sapiens role
intersection_of: OMRSE:00000011 ! patient role
intersection_of: RO:0000052 NCBITaxon:9606 ! inheres in Homo sapiens

[Term]
id: OMRSE:00000031
name: obsolete major administrative subdivision
def: "A subnational entity that is the primary organizational member of a nation, is subject to the full set of laws of the nation, enjoys all the privileges established under the laws of the nation, is not a member of any other geopolitical entity, and itself governs a part of the geographical region governed by the nation." []
comment: example: Northern Ireland
is_a: ObsoleteClass ! Obsolete Class
property_value: IAO:0000118 "major administrative subdivision" xsd:string
is_obsolete: true

[Term]
id: OMRSE:00000032
name: obsolete geopolitical dependency
def: "A subnational entity that does not possess full political independence or sovereignty as a sovereign state, but remains politically outside of the controlling state and controls a geographical region that is outside the controlling state's integral region." []
comment: Typically, the common feature is that the dependency does not conduct foreign affairs, and relegates this authority to the sovereign state.  BUt otherwise, it is largely or completely autonomous relative to the administrative subdivisions.  Examples include Puerto Rico (U.S.), Guam (U.S.), Greenland (Denmark), French Polynesia (France), and Falkland Islands (United Kingdom). 
is_a: ObsoleteClass ! Obsolete Class
property_value: IAO:0000118 "geopolitical dependency" xsd:string
is_obsolete: true

[Term]
id: OMRSE:00000033
name: aggregate of organizations
def: "An aggregate of organizations that have some feature in common, but is not itself an organization." []
def: "An object aggregate that is not itself an organization and whose members are only organizations that have some feature in common" []
comment: It is often convenient to group organizations together that otherwise might not even interact with one another. 
is_a: BFO:0000040 ! material entity
relationship: RO:0002351 OBI:0000245 ! has member organization
property_value: IAO:0000117 "William R. Hogan" xsd:string
property_value: IAO:0000117 "William R. Hogan\nAmanda Hicks" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/omrse.owl xsd:string

[Term]
id: OMRSE:00000034
name: obsolete aggregate of sovereign states
def: "An aggregate of sovereign states that share some feature in common, but is not an organization nor necessarily the outcome of some treaty among them." []
is_a: ObsoleteClass ! Obsolete Class
property_value: IAO:0000117 "An aggregate of geopoli organizations that is not itself a sovereign state and whose members are only sovereign states that have some feature in common" xsd:string
property_value: IAO:0000117 "William R. Hogan" xsd:string
property_value: IAO:0000118 "aggregate of sovereign states" xsd:string
is_obsolete: true

[Term]
id: OMRSE:00000035
name: obsolete aggregate of geopoli organizations
def: "An object aggregate that is not itself a geopolitical organization and whose members are only geopolitical organizations that have some feature in common" []
is_a: ObsoleteClass ! Obsolete Class
property_value: IAO:0000117 "Amanda Hicks" xsd:string
property_value: IAO:0000117 "William R. Hogan\n" xsd:string
property_value: IAO:0000118 "aggregate of geopoli organizations" xsd:string
is_obsolete: true

[Term]
id: OMRSE:00000036
name: obsolete aggregate of dependencies
def: "An aggregate of geopoli organizations that is not itself a geopolitical dependency and whose members are only geopolitical dependencies that have some feature in common." []
is_a: ObsoleteClass ! Obsolete Class
property_value: IAO:0000117 "Amanda Hicks" xsd:string
property_value: IAO:0000118 "aggregate of dependencies" xsd:string
is_obsolete: true

[Term]
id: OMRSE:00000037
name: obsolete aggregate of major administrative subdivisions
def: "An aggregate of geopoli organizations that is not itself a major administrative subdivision and whose members are only major administrative subdivisions that have some feature in common" []
is_a: ObsoleteClass ! Obsolete Class
property_value: IAO:0000117 "Amanda Hicks" xsd:string
property_value: IAO:0000118 "aggregate of major administrative subdivisions" xsd:string
is_obsolete: true

[Term]
id: OMRSE:00000038
name: legal person role
def: "A role borne by a human individual or by a collection of humans regarded as possessing rights and duties enforeable at law." []
comment: We are aware of the fact that Wikipedia's definition differs from ours by saying that "Legal personality (...) is the characteristic of a non-living entity regarded by law to have the status of personhood" (http://en.wikipedia.org/wiki/Legal_personality) \nHowever, Shaw explicates:\n"In any legal system, certain entities, whether they be individuals or companies, will be regarded as possessing rights and duties enforceable at law. Thus an individual may prosecute or be prosecuted for assault and a company can sue for breach of contract. They are able to do this because the law recognises them as 'legal persons' possessing the capacity to have and to maintain certain rights, and being subject to perform specific duties. (...) In municipal law individuals, limited companies and public corporations are recognized as each possessing a distinct legal personality, the terms of which are circumscribed by the relevant legislation" (Shaw MN: International Law. Sixth Edition. Cambridge University Press, Cambridge, 2008).                We hold that Shaw's position is ontological more prolific since it not only allows to explain how groups of individuals become recognized as unities at law, but also how different individuals can hold different legal personality roles (always against the context of one legal system). The latter will proof useful when dealing with the representing comatous patients or minorsat law in ontologies.
is_a: OMRSE:00000024 ! role in human social processes
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
property_value: IAO:0000119 "Malcolm N. Shaw: International Law. Cambridge University Press, Cambridge, 2008." xsd:string

[Term]
id: OMRSE:00000039
name: smoker role
def: "A role that inheres in an organism and is realized by habitually smoking tobacco products." []
is_a: OMRSE:00000050 ! Homo sapiens role

[Term]
id: OMRSE:00000040
name: intravenous drug user
is_a: OMRSE:00000050 ! Homo sapiens role

[Term]
id: OMRSE:00000041
name: obsolete intergovernmental organization
def: "an intergovernmental organization that has at least three member states, that has activies in at least three states, and that is unified by some formal intergovernmental agreement" []
comment: examples:\nNorth American Free Trade Argreement [NAFTA] , Universal Postal Union [UPU], Oragnaization of American States [OAS], World Bank), Organization of Petroleum exporting countries [OPEC] United Nations [UN[, The World Trade Organization [WTO], The World Health Organization [WHO], UNICEF
is_a: ObsoleteClass ! Obsolete Class
property_value: http://purl.org/dc/elements/1.1/contributor "Katrina Donovan" xsd:string
property_value: IAO:0000117 "Amanda Hicks" xsd:string
property_value: IAO:0000118 "intergovernmental organization" xsd:string
property_value: IAO:0000119 "\"IGOs are organizations whose memebers include at lesat three states, that have activities in several states, and whose members are held together by a formal intergovernmental agreement ... These organizations range in size from three members (North American Free Trade Argreement [NAFTA]) to more than 190 memembers (Universal Postal Union (UPU)].  Memebers may come from primarily one georgraphic regioni (Oragnaization of American States [OAS]) or from all geographic regions (World Bank).  although soem IGOs are designed to achieve a single purpose (Organization of Petroleum exporting countries [OPEC]), others have been developed for multiple tasks (United Nations [UN}).  ... IGOs are recognized subjects of international law with separate standing fromt heir member states.\" Karns and Mingst I(2004) p. 7" xsd:string
is_obsolete: true

[Term]
id: OMRSE:00000042
name: obsolete nongovernmental organization
def: "a geopolitical organization that is voluntary and private, whose members are individual persons or organizations that come together to acheive a common purpose." []
comment: Examples:\nInternaltion Federation of Red Cross and Red Crescent Societies, Oxfam, CARE, Doctors Without Borders, World Wildlife Fund, Transparency International, Human Rights Watch, Amnesty International, and Save the Children.
is_a: ObsoleteClass ! Obsolete Class
property_value: http://purl.org/dc/elements/1.1/contributor "Katrina Donovan" xsd:string
property_value: IAO:0000118 "nongovernmental organizations" xsd:string
property_value: IAO:0000119 "NGOs are private voluntary organizations whose members are individuals or associations that come together to acheive a common purpose.  Some organizations are formed to advocate a particular cause such as human rights, peace, or envirnomental projetion.  Others are established to provide services such as disaster relief, humantarian aid in war-torn socieities, or development assistance.  ... National level groups are often called interest or pressure groups, and many of them are now linked to counterpart groups in other countries through transnational networks or federations.  International NGOs, like IGOs, may draw their members from one region or several regions, and they may have very specific functions or be multi-functional.\n\nKarns and Mingst (2004) p. 10f." xsd:string
is_obsolete: true

[Term]
id: OMRSE:00000043
name: obsolete private governance organizations
comment: Examples: private bond-rating agencies such as Moody's Investors Service, International Chamber of Commerce, Worldwide Responsible Apparel Manufacturing Principles, Forest Stewardship
is_a: ObsoleteClass ! Obsolete Class
property_value: http://purl.org/dc/elements/1.1/contributor "Katrina Donovan" xsd:string
property_value: IAO:0000117 "Amanda Hicks" xsd:string
property_value: IAO:0000118 "private governance organizations" xsd:string
property_value: IAO:0000119 "\"Although the very meaning of the term is controversial, it involves authoritative decsionmaking in areas that once were part of national legal frameworks, the government, the sovereign state, or the public sector.\"\n\nKarns and Mingst (2004) p. 14." xsd:string
is_obsolete: true

[Term]
id: OMRSE:00000044
name: obsolete governmental organization
def: "An organization that governs the people living in a particular geographical region or aggregate of geographical regions.  The geographical region it governs can change over time (such as the westward expansion of the United States and the addition of Hawaii). \n\nNote: this definition was taken over from \"geopolitical organization\"." []
comment: IMPORTANT: The label "geopolitical organization" was previously used for OMRSE_00000044 (governmental organization).  "geopoli organization" is a label for a new and different class.
is_a: ObsoleteClass ! Obsolete Class
property_value: IAO:0000117 "Amanda Hicks" xsd:string
property_value: IAO:0000118 "governmental organization" xsd:string
is_obsolete: true

[Term]
id: OMRSE:00000045
name: obsolete sovereign state
def: "A governmental organization with a defined territory on which it exercises internal and external sovereignty, a permanent population, a government, and the capacity to enter into relations with other sovereign states." []
comment: Per Wikipedia, the word 'nation' does not always refer to soverign states.  For example, the "nation of Islam".
is_a: ObsoleteClass ! Obsolete Class
property_value: IAO:0000117 "William R. Hogan" xsd:string
property_value: IAO:0000118 "nation" xsd:string
property_value: IAO:0000118 "nation state" xsd:string
property_value: IAO:0000118 "sovereign state" xsd:string
property_value: IAO:0000119 http://en.wikipedia.org/wiki/Sovereign_state xsd:string
is_obsolete: true

[Term]
id: OMRSE:00000046
name: obsolete subnational entity
def: "a governmental organization that has a local, regional, or territorial government that recognizes a sovereign state as its higher political authority" []
is_a: ObsoleteClass ! Obsolete Class
property_value: IAO:0000117 "Amanda Hicks" xsd:string
property_value: IAO:0000117 "William R. Hogan" xsd:string
property_value: IAO:0000118 "subnational entity" xsd:string
is_obsolete: true

[Term]
id: OMRSE:00000047
name: obsolete supranational entity
comment: e.g., the EU
is_a: ObsoleteClass ! Obsolete Class
property_value: IAO:0000117 "Amanda Hicks" xsd:string
property_value: IAO:0000118 "supranational entity" xsd:string
is_obsolete: true

[Term]
id: OMRSE:00000048
name: material entity role
is_a: BFO:0000023 ! role
intersection_of: BFO:0000023 ! role
intersection_of: RO:0000052 BFO:0000040 ! inheres in material entity
relationship: RO:0000052 BFO:0000040 ! inheres in material entity
relationship: RO:0000052 BFO:0000040 ! inheres in material entity

[Term]
id: OMRSE:00000049
name: organism role
is_a: OMRSE:00000048 ! material entity role
intersection_of: OMRSE:00000048 ! material entity role
intersection_of: RO:0000052 OBI:0100026 ! inheres in organism
relationship: RO:0000052 OBI:0100026 ! inheres in organism
relationship: RO:0000052 OBI:0100026 ! inheres in organism

[Term]
id: OMRSE:00000050
name: Homo sapiens role
is_a: OMRSE:00000049 ! organism role
intersection_of: OMRSE:00000049 ! organism role
intersection_of: RO:0000052 NCBITaxon:9606 ! inheres in Homo sapiens
relationship: RO:0000052 NCBITaxon:9606 ! inheres in Homo sapiens
relationship: RO:0000052 NCBITaxon:9606 ! inheres in Homo sapiens

[Term]
id: OMRSE:00000051
name: organization role
is_a: OMRSE:00000048 ! material entity role
intersection_of: BFO:0000023 ! role
intersection_of: RO:0000052 OBI:0000245 ! inheres in organization
relationship: RO:0000052 OBI:0000245 ! inheres in organization
relationship: RO:0000052 OBI:0000245 ! inheres in organization

[Term]
id: OMRSE:00000052
name: hospital function
def: "A function inhering in a material entity that, if realized, is realized by the material entity being the site at which inpatient and outpatient healthcare is provided to a patient population." []
is_a: BFO:0000034 ! function
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string

[Term]
id: OMRSE:00000053
name: school function
def: "A function inhering in a material entity that, if realized, is realized by that material entity being the site at which formal education is provided to a student population." []
is_a: BFO:0000034 ! function
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string

[Term]
id: OMRSE:00000054
name: hospital role
def: "A healthcare provider role that inheres in an organization and is realized by providing inpatient and outpatient care." []
is_a: OMRSE:00000015 ! health care provider organization role
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string

[Term]
id: OMRSE:00000055
name: school role
is_a: OMRSE:00000025 ! organization social role
property_value: IAO:0000117 "An organization social role that inheres in an organization and is realized by providing formal education to students." xsd:string
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string

[Term]
id: OMRSE:00000056
name: hospital organization
def: "An organization that is the bearer of a hospital role." []
is_a: OBI:0000245 ! organization
intersection_of: OBI:0000245 ! organization
intersection_of: RO:0000053 OMRSE:00000054 ! bearer of hospital role
relationship: RO:0000053 OMRSE:00000054 ! bearer of hospital role
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string

[Term]
id: OMRSE:00000057
name: school organization
def: "An organization that is the bearer of a school role." []
is_a: OBI:0000245 ! organization
intersection_of: OBI:0000245 ! organization
intersection_of: RO:0000053 OMRSE:00000055 ! bearer of school role
relationship: RO:0000053 OMRSE:00000055 ! bearer of school role
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string

[Term]
id: OMRSE:00000058
name: student role
def: "A human social role that, if realized, is realized by the process of formal education that the bearer undergoes." []
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string

[Term]
id: OMRSE:00000059
name: nursery school role
is_a: OMRSE:00000055 ! school role
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string

[Term]
id: OMRSE:00000060
name: primary school role
is_a: OMRSE:00000055 ! school role
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string

[Term]
id: OMRSE:00000061
name: architectural structure
def: "A material entity that is a human made strcuture with firm connection between its foundation and the ground." []
comment: "Building" is a subclass of this. 
comment: This type of entity is referred to as "Bauwerk" or "Bauliche Anlage".
is_a: BFO:0000040 ! material entity
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
property_value: IAO:0000119 http://de.wikipedia.org/wiki/Bauwerk xsd:string

[Term]
id: OMRSE:00000062
name: facility
def: "An architectural structure that bears some function." []
is_a: OMRSE:00000061 ! architectural structure
intersection_of: OMRSE:00000061 ! architectural structure
intersection_of: RO:0000053 BFO:0000034 ! bearer of function
relationship: OMRSE:00000068 OBI:0000245 {http://www.w3.org/2002/07/owl#versionInfo="09/09/2017"} ! is administered by organization
relationship: RO:0000053 BFO:0000034 ! bearer of function
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string

[Term]
id: OMRSE:00000063
name: hospital facility
def: "A health care facility that bears the function to provide acute and intensive healthcare services and that is run by a hospital organization and is the bearer of a hospital function." []
is_a: OMRSE:00000102 ! health care facility
relationship: BFO:0000067 OMRSE:00000160 ! contains process acute care encounter
relationship: RO:0000053 OMRSE:00000052 ! bearer of hospital function
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
property_value: IAO:0000117 "William Hogan" xsd:string

[Term]
id: OMRSE:00000064
name: school facility
def: "A facility that is run by a school organization and is the bearer of a school function." []
is_a: OMRSE:00000062 ! facility
relationship: RO:0000053 OMRSE:00000053 ! bearer of school function
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string

[Term]
id: OMRSE:00000065
name: secondary school role
is_a: OMRSE:00000055 ! school role
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string

[Term]
id: OMRSE:00000066
name: pediatric trauma patient role
def: "A trauma patient role that inheres in a homo sapiens who is under the age of 15 years." []
is_a: OMRSE:00000030 ! human patient role
property_value: IAO:0000117 "Amanda Hicks" xsd:string
property_value: IAO:0000118 "pediatric trauma patient" xsd:string
property_value: IAO:0000119 "The following definition for 'pediatric trauma patient' was approved by the CAFE team of domain experts (experts in trauma care) May 29, 2015.\n\n\"A trauma patient who is under the age of 15 years.\"" xsd:string

[Term]
id: OMRSE:00000067
name: injured patient role
def: "A patient role that inheres an organism suffering one or more injuries." []
is_a: OMRSE:00000011 ! patient role
property_value: IAO:0000117 "Amanda Hicks" xsd:string
property_value: IAO:0000118 "injured patient" xsd:string
property_value: IAO:0000119 "The following definition for 'injured patient' was approved by the CAFE team of domain experts (experts in trauma care) May 29, 2015.\n\nA patient suffering one or more injuries." xsd:string

[Term]
id: OMRSE:00000069
name: burn patient role
def: "A patient role that inheres in an organism suffering a thermal, electrical, chemical or radiation burn." []
is_a: OMRSE:00000067 ! injured patient role
property_value: IAO:0000117 "Amanda Hicks" xsd:string
property_value: IAO:0000117 "burn patient" xsd:string
property_value: IAO:0000117 "The following definition for 'burn  patient' was approved by the CAFE team of domain experts (experts in trauma care) May 29, 2015.\n\nA patient suffering a thermal, electrical, chemical or radiation burn." xsd:string

[Term]
id: OMRSE:00000072
name: physiatrist role
def: "A physician role that is created by training and certification in rehabilitation/physical medicine and that is realized by the provision of or supervising of the provision of rehabilitation or physical therapy to a patient." []
comment: Definition updated May 5, 2016. Original definitions was, a health care role borne by a human being and realized by training and certification in rehabilitation medicine.
is_a: OMRSE:00000013 ! physician role
property_value: IAO:0000117 "Amanda Hicks" xsd:string
property_value: IAO:0000118 "physiatrist" xsd:string
property_value: IAO:0000119 "The following definition for 'physiatrist' was approved by the CAFE team of domain experts (experts in trauma care) May 29, 2015.\n\nA physician with training and certification in rehabilitation/physical medicine." xsd:string

[Term]
id: OMRSE:00000073
name: trauma patient role
def: "A patient role that inheres in an organism with some non-superficial traumatic injury.  The role is realized by admision to a hospital, transfer from one hospital to another for the purpose of trauma care, or has death as a result of the traumatic injury." []
is_a: OMRSE:00000011 ! patient role
property_value: IAO:0000117 "Amanda Hicks" xsd:string
property_value: IAO:0000118 "trauma patient" xsd:string
property_value: IAO:0000119 "The following definition for 'trauma  patient' was approved by the CAFE team of domain experts (experts in trauma care) May 29, 2015.\n\nA patient sustaining an injury who has been admitted to the hospital, transferred from one hospital to another for the purpose of trauma care, or has died as a result of the traumatic injury." xsd:string

[Term]
id: OMRSE:00000074
name: housing unit
def: "A material entity that has as parts one or more sites large enough to contain humans, has as part one or more material entities that separates it from other sites, and bears a residence function." []
comment: Housing units are individuated by their residence functions.
property_value: IAO:0000117 "Amanda Hicks" xsd:string
property_value: IAO:0000119 https://github.com/ufbmi/OMRSE/wiki/Housing-unit-and-Household xsd:string

[Term]
id: OMRSE:00000075
name: residence function
def: "A function that inheres in a material entity and, if realized, is realized by protecting persons and their possessions from weather and by some person or group of persons habitually sleeping in at least one site that is contained by that material entity." []
is_a: BFO:0000034 ! function
property_value: IAO:0000117 "Amanda Hicks" xsd:string

[Term]
id: OMRSE:00000076
name: household
def: "A human or collection of humans that occupies a housing unit by storing their possessions there and habitually sleeping there thereby participating in the realization of that housing unit's residence function." []
comment: Note in OMRSE it is the housing unit, not the people living there, that are the bearers of a "residence function".  Note the distinction between being a residence and a resident.
comment: Note that it is not possible in OWL 2, at least that we have yet found, to say that the housing unit in which the process occurs is the same one that is the bearer of the residence function (that the process realizes).
is_a: BFO:0000040 ! material entity
property_value: IAO:0000117 "Amanda Hicks" xsd:string

[Term]
id: OMRSE:00000077
name: job role
def: "A role in human social processes that, if realized, is realized when the bearer provides labor or services in exchange for a wage or salary as specified by some deontic declaration." []
relationship: BFO:0000054 OMRSE:00000146 ! realized in employment process
property_value: IAO:0000117 "Amanda hicks" xsd:string
property_value: IAO:0000118 "employee" xsd:string

[Term]
id: OMRSE:00000078
name: workplace facility
is_a: OMRSE:00000062 ! facility
relationship: RO:0000053 OMRSE:00000079 ! bearer of workplace function
property_value: IAO:0000117 "Amanda Hicks" xsd:string

[Term]
id: OMRSE:00000079
name: workplace function
def: "a function inhering in a material entity that, if realized, is realized by that material entity being the site where the work of some organization is carried out" []
is_a: BFO:0000034 ! function
property_value: IAO:0000117 "Amanda Hicks" xsd:string

[Term]
id: OMRSE:00000081
name: US census householder role
def: "A US Census householder role is a human social role that, if realized, is realized by that person being a member of a household and either owning or renting the housing unit in which that household resides and being designated as the householder. If there is only one member of the household who owns or rents the housing unit, that person is designated the householder by default." []
is_a: OMRSE:00000001 ! human social role
property_value: IAO:0000117 "Amanda Hicks" xsd:string
property_value: IAO:0000119 "http://www.census.gov/cps/about/cpsdef.html\n\nlast accessed on June 30, 2015" xsd:string

[Term]
id: OMRSE:00000082
name: US Census reference person role
def: "A US cenus reference person role is a human social role that inheres in a Homo sapiens who is a member of a household and is realized by other persons in the household being recorded in the US census in relation to that person." []
is_a: OMRSE:00000001 ! human social role
relationship: BFO:0000054 IAO:0000572 ! realized in documenting
property_value: IAO:0000117 "Amanda Hicks" xsd:string
property_value: IAO:0000119 "http://www.census.gov/cps/about/cpsdef.html\n\nlast accessed June 30, 2015" xsd:string

[Term]
id: OMRSE:00000083
name: obsolete OMB ethnic identity datum
def: "An ethnic identity datum that is the output of an ethnic identification process that uses OMB terminology for ethnicity or terminology that is mapped the OMB ethnicity terms." []
is_a: OMRSE:00000100 ! obsolete ethnic identity datum
property_value: IAO:0000117 "Amanda Hicks" xsd:string
is_obsolete: true
replaced_by: OMB ethnic identity information content entity

[Term]
id: OMRSE:00000084
name: enrollment end date
is_a: BFO:0000038 ! one-dimensional temporal region

[Term]
id: OMRSE:00000085
name: obsolete socio-legal human social role
is_a: ObsoleteClass ! Obsolete Class
is_a: OMRSE:00000001 ! human social role
property_value: IAO:0000117 "A role that concretizes a socio-lega generically dependent continuant" xsd:string
property_value: IAO:0000117 "Amanda Hicks" xsd:string
is_obsolete: true

[Term]
id: OMRSE:00000086
name: human role within an organization
def: "A human social role that is created by a deontic declaration performed by an organization." []
property_value: IAO:0000117 "Amanda Hicks" xsd:string
property_value: IAO:0000118 "human organizational role" xsd:string

[Term]
id: OMRSE:00000087
name: employer role
def: "a role in human social processes that is realized when the bearer provides a wage or salary in exchange for some labour or services as specified by some declaration" []
is_a: OMRSE:00000024 ! role in human social processes
relationship: BFO:0000054 OMRSE:00000146 ! realized in employment process

[Term]
id: OMRSE:00000088
name: age measurement datum
is_a: IAO:0000416 ! time measurement datum

[Term]
id: OMRSE:00000089
name: contract
def: "A document that records a legally binding agreement between two or more parties." []
is_a: IAO:0000310 ! document
property_value: IAO:0000116 "A contract is a document that is the specified output of a legally binding document act and records a legally binding agreement between two or more parties." xsd:string

[Term]
id: OMRSE:00000090
name: indemnity contract
def: "A contract by which one party secures the other against pecuniary loss by payment of a sum of money if a specified event occurs." []
property_value: IAO:0000117 "Amanda Hicks" xsd:string

[Term]
id: OMRSE:00000091
name: insurance policy
def: "An indemnity contract that distributes risk among a group of people" []
is_a: OMRSE:00000090 ! indemnity contract
property_value: IAO:0000117 "Amanda Hicks" xsd:string

[Term]
id: OMRSE:00000092
name: insured party role
def: "A role that inheres in an organism that is able to receive benefits from an insurance policy. The role, if realized, is realized by receiving benefits that are covered by the insurance policy." []
is_a: OMRSE:00000024 ! role in human social processes
property_value: IAO:0000117 "Amanda Hicks" xsd:string

[Term]
id: OMRSE:00000093
name: insurance company
def: "An organization that secures a group of people against pecuniary loss by payment of a sum of money if a a specified event occurs." []
is_a: OBI:0000245 ! organization
property_value: IAO:0000117 "Amanda Hicks" xsd:string

[Term]
id: OMRSE:00000094
name: policy holder role
def: "An insured party role that inheres in a person who participates in the creation of the insurance contract and is eligible to receive benefits as specified by the insurance contract." []
property_value: IAO:0000117 "Amanda Hicks" xsd:string

[Term]
id: OMRSE:00000095
name: payer role
is_a: OMRSE:00000024 ! role in human social processes

[Term]
id: OMRSE:00000096
name: party to an insurance policy
is_a: OMRSE:00000004 ! party to a legal agreement

[Term]
id: OMRSE:00000097
name: enrollment start date
is_a: BFO:0000038 ! one-dimensional temporal region

[Term]
id: OMRSE:00000098
name: obsolete racial identity datum
def: "A racial identity is an information content entity that is the output of some racial identitification process and is intended to be a truthful statement about the genetic or cultural race of a person.  Unlike data items they are not necessilary contributed or acquired by a reliable method." []
is_a: OMRSE:00000132 ! obsolete identity datum
is_obsolete: true
replaced_by: racial identity information content entity

[Term]
id: OMRSE:00000099
name: racial identification process

[Term]
id: OMRSE:00000100
name: obsolete ethnic identity datum
def: "An ethnic identity datum is an information content entity that is the output of some ethnic identitification process and is intended to be a truthful statement about the cultural or national heritage of a person.  Unlike data items they are not necessilary contributed or acquired by a reliable method." []
is_a: OMRSE:00000132 ! obsolete identity datum
property_value: IAO:0000117 "Amanda Hicks" xsd:string
is_obsolete: true
replaced_by: ethnic identity information content entity

[Term]
id: OMRSE:00000101
name: ethnic identification process

[Term]
id: OMRSE:00000102
name: health care facility
is_a: OMRSE:00000062 ! facility
property_value: IAO:0000117 "A facility bearing the function to provide healthcare and that is administered by a health care organization for the purpose of providing health care to a patient or patient population." xsd:string
property_value: IAO:0000117 "William Hogan" xsd:string

[Term]
id: OMRSE:00000103
name: US Census unemployed role
def: "A human social role that inheres in a human who is legally eligible to work, is conferred by the U.S. Census Bureau, and is realized by the bearer not working and either making active efforts to find employment in the four weeks prior to the reference week or waiting to be recalled from temporary layoff." []
is_a: OMRSE:00000001 ! human social role
property_value: IAO:0000117 "Amanda Hicks" xsd:string

[Term]
id: OMRSE:00000104
name: hospice facility
def: "A health care facility that bears a function to provide healthcare to the sick or terminally ill" []
is_a: OMRSE:00000102 ! health care facility
relationship: BFO:0000067 OMRSE:00000152 ! contains process skilled nursing encounter
relationship: RO:0000053 OMRSE:00000117 ! bearer of hospice function
property_value: IAO:0000117 "Amanda Hicks" xsd:string
property_value: IAO:0000117 "Emma Norris" xsd:string
property_value: IAO:0000117 "William Hogan" xsd:string
property_value: IAO:0000119 "Human Behaviour Change Project" xsd:string

[Term]
id: OMRSE:00000105
name: skilled nursing facility
is_a: OMRSE:00000150 ! community living health care facility
relationship: BFO:0000067 OMRSE:00000152 ! contains process skilled nursing encounter
relationship: RO:0000053 OMRSE:00000123 ! bearer of skilled nursing function
property_value: IAO:0000117 "Amanda Hicks" xsd:string

[Term]
id: OMRSE:00000106
name: rehabilitation facility
def: "A facility to assist in physical or addiction recovery" []
is_a: OMRSE:00000150 ! community living health care facility
relationship: BFO:0000067 OMRSE:00000152 ! contains process skilled nursing encounter
relationship: RO:0000053 OMRSE:00000122 ! bearer of rehabilitation function
property_value: IAO:0000117 "Amanda Hicks" xsd:string
property_value: IAO:0000117 "Emma Norris" xsd:string
property_value: IAO:0000117 "William Hogan" xsd:string
property_value: IAO:0000119 "Human Behaviour Change Project" xsd:string

[Term]
id: OMRSE:00000107
name: nursing home facility
def: "A facility that is run by a nursing home organization and is the bearer of a nursing home function." []
is_a: OMRSE:00000150 ! community living health care facility
relationship: BFO:0000067 OMRSE:00000152 ! contains process skilled nursing encounter
relationship: RO:0000053 OMRSE:00000125 ! bearer of nursing home function
property_value: IAO:0000117 "Amanda Hicks" xsd:string

[Term]
id: OMRSE:00000108
name: residential health care facility
def: "A community living health care facility that provides health care services in a home-like setting" []
is_a: OMRSE:00000150 ! community living health care facility
relationship: RO:0000053 OMRSE:00000124 ! bearer of residential function
property_value: IAO:0000117 "Amanda Hicks" xsd:string
property_value: IAO:0000117 "William Hogan" xsd:string

[Term]
id: OMRSE:00000109
name: overnight dialysis facility
is_a: OMRSE:00000102 ! health care facility
relationship: BFO:0000067 OBI:0600052 ! contains process dialysis
relationship: BFO:0000067 OMRSE:00000152 ! contains process skilled nursing encounter
relationship: RO:0000053 OMRSE:00000121 ! bearer of overnight dialysis function
property_value: IAO:0000117 "Amanda Hicks" xsd:string

[Term]
id: OMRSE:00000110
name: outpatient clinic facility
def: "A health care facility that bears a function to provide low intensity healthcare services to patients on a short-term basis, with patients leaving on the same date as arriving (i.e., without them staying overnight)" []
comment: Broadened from treatment to healthcare services generally.  "Low intensity" is not defined at the moment, but is needed to differentiate from same-day surgery centers or observation stays in hospitals that last <24 hours.  The idea is that few invasive procedures are performed, and the ones that are invasive are not typically much worse than a blood draw.  Maybe bone marrow biopsy is as aggressive as it gets.  I wonder if hematologists do that on an outpatient basis.
is_a: OMRSE:00000102 ! health care facility
relationship: RO:0000053 OMRSE:00000120 ! bearer of outpatient clinic function
property_value: IAO:0000117 "Amanda Hicks" xsd:string
property_value: IAO:0000117 "Emma Norris" xsd:string
property_value: IAO:0000117 "William Hogan" xsd:string
property_value: IAO:0000119 "Human Behaviour Change Project" xsd:string

[Term]
id: OMRSE:00000111
name: physician office facility
is_a: OMRSE:00000102 ! health care facility
relationship: RO:0000053 OMRSE:00000119 ! bearer of physician office function
property_value: IAO:0000117 "Amanda Hicks" xsd:string

[Term]
id: OMRSE:00000112
name: ambulatory surgery facility
is_a: OMRSE:00000102 ! health care facility
relationship: BFO:0000067 OAE:0000067 ! contains process surgery
relationship: RO:0000053 OMRSE:00000116 ! bearer of ambulatory surgery function
property_value: IAO:0000117 "Amanda Hicks" xsd:string

[Term]
id: OMRSE:00000113
name: urgent care facility
is_a: OMRSE:00000102 ! health care facility
relationship: RO:0000053 OMRSE:00000115 ! bearer of urgent care function
property_value: IAO:0000117 "Amanda Hicks" xsd:string

[Term]
id: OMRSE:00000114
name: emergency department facility
def: "A health care facility that bears a function to provide emergency healthcare services and the acute care of patients who present without prior appointment, having arrived either by their own means or by ambulance" []
is_a: OMRSE:00000102 ! health care facility
relationship: BFO:0000067 OMRSE:00000160 ! contains process acute care encounter
relationship: RO:0000053 OMRSE:00000118 ! bearer of emergency department function
property_value: IAO:0000117 "Amanda Hicks" xsd:string
property_value: IAO:0000117 "Emma Norris" xsd:string
property_value: IAO:0000117 "William Hogan" xsd:string
property_value: IAO:0000119 "Adapted from Human Behaviour Change Project" xsd:string

[Term]
id: OMRSE:00000115
name: urgent care function
is_a: BFO:0000034 ! function

[Term]
id: OMRSE:00000116
name: ambulatory surgery function
is_a: BFO:0000034 ! function
relationship: BFO:0000054 OAE:0000067 ! realized in surgery
property_value: IAO:0000117 "Amanda Hicks" xsd:string

[Term]
id: OMRSE:00000117
name: hospice function
is_a: OMRSE:00000169 ! palliative function

[Term]
id: OMRSE:00000118
name: emergency department function
is_a: BFO:0000034 ! function

[Term]
id: OMRSE:00000119
name: physician office function
is_a: BFO:0000034 ! function

[Term]
id: OMRSE:00000120
name: outpatient clinic function
is_a: BFO:0000034 ! function

[Term]
id: OMRSE:00000121
name: overnight dialysis function
is_a: BFO:0000034 ! function
relationship: BFO:0000054 OBI:0600052 ! realized in dialysis

[Term]
id: OMRSE:00000122
name: rehabilitation function
is_a: BFO:0000034 ! function

[Term]
id: OMRSE:00000123
name: skilled nursing function
is_a: BFO:0000034 ! function

[Term]
id: OMRSE:00000124
name: residential function
is_a: BFO:0000034 ! function

[Term]
id: OMRSE:00000125
name: nursing home function
is_a: BFO:0000034 ! function

[Term]
id: OMRSE:00000126
name: patient discharge
def: "A deontic document act that concludes an inpatient encounter." []
is_a: IAO:0021001 ! obsolete_deontic document act
relationship: RO:0002229 OGMS:0000100 ! ends inpatient encounter
property_value: IAO:0000117 "Amanda Hicks" xsd:string
property_value: IAO:0000118 "discharge process" xsd:string

[Term]
id: OMRSE:00000127
name: obsolete hispanic or latino identity datum
def: "An OMB ethnic identity datum that indicates the person identified is of Cuban, Mexican, Puerto Rican, South or Central American, or other Spanish culture or origin regardless of race." []
is_a: OMRSE:00000083 ! obsolete OMB ethnic identity datum
property_value: IAO:0000117 "Amanda Hicks" xsd:string
is_obsolete: true
replaced_by: OMB Hispanic or Latino identity information content entity

[Term]
id: OMRSE:00000128
name: obsolete not hispanic or latino identity datum
def: "An OMB ethnic identity datum that indicates the person identified is not of Cuban, Mexican, Puerto Rican, South or Central American, or other Spanish culture or origin regardless of race." []
is_a: OMRSE:00000083 ! obsolete OMB ethnic identity datum
property_value: IAO:0000117 "Amanda Hicks" xsd:string
is_obsolete: true
replaced_by: OMB not Hispanic or Latino identity information content entity

[Term]
id: OMRSE:00000129
name: US physician assistant role
def: "A human health care provider role that inheres in a human being that is created by state licensing and that is realized by taking patient histories, performing physical exams, diagnosing illnesses, developing treatment plans, ordering lab tests, prescribing medications, counselling and educating patients, suturing wounds, and assisting in surgery under the supervision of a physician or a surgeon." []
is_a: OMRSE:00000012 ! health care provider role
is_a: OMRSE:00000050 ! Homo sapiens role

[Term]
id: OMRSE:00000130
name: anesthesiologist role
def: "A physician role that inheres a human being and, if it is realized, is realized either by administering medication for the temporary general or local suppression of sensory or motor nerve function during some health care encounter or by making decisions independently of a supervising physician regarding the adminstration of such medication." []
is_a: OMRSE:00000013 ! physician role

[Term]
id: OMRSE:00000131
name: OMB racial identification process
is_a: OMRSE:00000099 ! racial identification process
relationship: OBI:0000299 OMRSE:00000185 ! has_specified_output obsolete OMB racial identity datum

[Term]
id: OMRSE:00000132
name: obsolete identity datum
def: "An identity datum is an information content entity that is the output of some identitification process and is intended to be a truthful statement about a person's social identity.  Unlike data items they are not necessilary contributed or acquired by a reliable method." []
is_a: OMRSE:00000179 ! answer to identity question
relationship: BFO:0000050 IAO:0020022 ! part of documented identity
relationship: IAO:0000136 NCBITaxon:9606 ! is about Homo sapiens
property_value: http://purl.org/dc/elements/1.1/creator "Amanda Hicks" xsd:string
is_obsolete: true
replaced_by: social identity information content entity

[Term]
id: OMRSE:00000133
name: obsolete gender identity datum
def: "A gender identity is an information content entity that is the output of some gender identitification process and is intended to be a truthful statement about a person's subjective sense of their gender.  Unlike data items they are not necessilary contributed or acquired by a reliable method." []
is_a: OMRSE:00000132 ! obsolete identity datum
property_value: http://purl.org/dc/elements/1.1/creator "Amanda Hicks" xsd:string
is_obsolete: true
replaced_by: gender identity information content entity

[Term]
id: OMRSE:00000134
name: identification process
is_a: IAO:0021003 ! social act
property_value: http://purl.org/dc/elements/1.1/creator "Amanda Hicks" xsd:string

[Term]
id: OMRSE:00000135
name: gender identification process

[Term]
id: OMRSE:00000138
name: obsolete female gender identity datum
def: "a gender identity datum resulting from a gender identification process in which ‘female’ is selected based on the participant's subjective sense of gender" []
is_a: OMRSE:00000133 ! obsolete gender identity datum
property_value: IAO:0000117 "Amanda Hicks" xsd:string
is_obsolete: true
replaced_by: female gender identity information content entity

[Term]
id: OMRSE:00000139
name: surgeon role
is_a: OMRSE:00000013 ! physician role
relationship: BFO:0000054 OAE:0000067 ! realized in surgery

[Term]
id: OMRSE:00000140
name: neurosurgeon role
def: "A surgeon role realized by its bearer using performing neurosurgery." []
is_a: OMRSE:00000139 ! surgeon role

[Term]
id: OMRSE:00000141
name: obsolete male gender identity datum
def: "a gender identity datum resulting from a gender identification process in which ‘male’ is selected based on the participant's subjective sense of gender" []
is_a: OMRSE:00000133 ! obsolete gender identity datum
property_value: IAO:0000117 "Amanda Hicks" xsd:string
property_value: IAO:0000119 "" xsd:string
is_obsolete: true
replaced_by: male gender identity information content entity

[Term]
id: OMRSE:00000142
name: human traveling information
def: "An information content entity that is about human travel." []
is_a: IAO:0000030 ! information content entity
intersection_of: IAO:0000030 ! information content entity
intersection_of: IAO:0000136 APOLLO_SV:00000532 ! is about human travel
relationship: IAO:0000136 APOLLO_SV:00000532 ! is about human travel
property_value: http://purl.org/dc/elements/1.1/contributor "Jie Zheng" xsd:string
property_value: http://purl.org/dc/elements/1.1/creator "Amanda Hicks" xsd:string
property_value: IAO:0000119 https://github.com/ufbmi/OMRSE/issues/79 xsd:anyURI

[Term]
id: OMRSE:00000143
name: household identifier
is_a: IAO:0000028 ! symbol
intersection_of: IAO:0000028 ! symbol
intersection_of: IAO:0000219 OMRSE:00000076 ! denotes household
relationship: IAO:0000219 OMRSE:00000076 ! denotes household
property_value: http://purl.org/dc/elements/1.1/contributor "A symbol that denotes a specific household" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Jie Zheng" xsd:string
property_value: http://purl.org/dc/elements/1.1/creator "Amanda Hicks" xsd:string

[Term]
id: OMRSE:00000144
name: family identifier
def: "A symbol that denotes a family." []
is_a: IAO:0000028 ! symbol
intersection_of: IAO:0000028 ! symbol
intersection_of: IAO:0000219 PCO:0000020 ! denotes family
relationship: IAO:0000219 PCO:0000020 ! denotes family
property_value: http://purl.org/dc/elements/1.1/contributor "Jie Zheng" xsd:string
property_value: http://purl.org/dc/elements/1.1/creator "Amanda Hicks" xsd:string

[Term]
id: OMRSE:00000145
name: obsolete self-identity data item
def: "an identity datum that has been asserted by the person whom it is about" []
is_a: OMRSE:00000132 ! obsolete identity datum
property_value: IAO:0000117 "Amanda Hicks" xsd:string
is_obsolete: true

[Term]
id: OMRSE:00000146
name: employment process
def: "A planned process in which the bearer of an employer role provides wages or salary to the bearer of an employee roll in fullfillment of the arrangements specified in some declaration" []
is_a: OBI:0000011 ! planned process
relationship: BFO:0000055 OMRSE:00000077 ! realizes job role
relationship: BFO:0000055 OMRSE:00000087 ! realizes employer role

[Term]
id: OMRSE:00000147
name: pediatric surgeon role
def: "A surgeon role borne by a human being and that, if realized, is realized by its bearer using operative manual and instrumental techniques on preadult patients to investigate and/or treat a pathological condition such as disease or injury, to help improve bodily function or appearance or to repair unwanted ruptured areas." []
is_a: OMRSE:00000139 ! surgeon role
property_value: IAO:0000117 "Amanda Hicks" xsd:string

[Term]
id: OMRSE:00000148
name: adult foster home facility
def: "a facility that is run by an adult foster home organization and is the bearer of an adult foster home organization" []
is_a: OMRSE:00000150 ! community living health care facility
relationship: RO:0000053 OMRSE:00000149 ! bearer of adult foster home function
property_value: IAO:0000117 "Amanda Hicks" xsd:string

[Term]
id: OMRSE:00000149
name: adult foster home function
is_a: BFO:0000034 ! function

[Term]
id: OMRSE:00000150
name: community living health care facility
def: "a health care facility that also bears a residence function and thus one in which the patients are also residents of the facility" []
is_a: OMRSE:00000102 ! health care facility
relationship: BFO:0000067 OMRSE:00000154 ! contains process assistance with activities of daily living care encounter
relationship: BFO:0000067 OMRSE:00000155 ! contains process assistance with instrumental activities of daily living encounter
relationship: RO:0000053 OMRSE:00000075 ! bearer of residence function

[Term]
id: OMRSE:00000151
name: registered nurse role
is_a: OMRSE:00000014 ! nurse role

[Term]
id: OMRSE:00000152
name: skilled nursing encounter
is_a: OGMS:0000097 ! health care encounter
relationship: BFO:0000055 OMRSE:00000151 ! realizes registered nurse role

[Term]
id: OMRSE:00000153
name: assistive care encounter
def: "They include assistance with activities of daily living, assistance with instrumental activities of daily living, medication assistance, and health support\n\nhttp://ahca.myflorida.com/Medicaid/acs/index.shtml" []
is_a: OBI:0000011 ! planned process
property_value: IAO:0000117 "Amanda Hicks" xsd:string

[Term]
id: OMRSE:00000154
name: assistance with activities of daily living care encounter
is_a: OMRSE:00000153 ! assistive care encounter

[Term]
id: OMRSE:00000155
name: assistance with instrumental activities of daily living encounter
is_a: OMRSE:00000153 ! assistive care encounter

[Term]
id: OMRSE:00000156
name: medication assistance care encounter
is_a: OMRSE:00000153 ! assistive care encounter

[Term]
id: OMRSE:00000157
name: assisted living facility
def: "A facility that is run by an assisted living facility organization and is the bearer of an assisted living facility function." []
is_a: OMRSE:00000150 ! community living health care facility

[Term]
id: OMRSE:00000158
name: assisted living function
is_a: BFO:0000034 ! function

[Term]
id: OMRSE:00000159
name: post-acute health care encounter
def: "temporally located after some acute care encounter\nSomehow involves skilled nursing encounters" []
is_a: OGMS:0000097 ! health care encounter
disjoint_from: OMRSE:00000160 ! acute care encounter
relationship: BFO:0000066 OMRSE:00000150 ! occurs in community living health care facility

[Term]
id: OMRSE:00000160
name: acute care encounter
is_a: OGMS:0000097 ! health care encounter

[Term]
id: OMRSE:00000161
name: leaving a health care facility after receiving care
is_a: BFO:0000015 ! process

[Term]
id: OMRSE:00000162
name: obsolete medical advice
is_a: IAO:0021003 ! social act
is_obsolete: true

[Term]
id: OMRSE:00000163
name: response to a question asking process
comment: Note that not all responses to a question asking process are answers. For example, a refusal to answer is not an answer. A refusal to answer is also not a specified output of the question asking process since it does not acheive the objective of asking the question, which is to get an answer.
is_a: IAO:0000030 ! information content entity
relationship: RO:0000056 OMRSE:00000168 ! participates in questions asking process

[Term]
id: OMRSE:00000164
name: home health care organization
is_a: OBI:0000245 ! organization
relationship: RO:0000053 BFO:0000034 ! bearer of function

[Term]
id: OMRSE:00000165
name: home health care function
is_a: OMRSE:00000172 ! health care function
relationship: BFO:0000054 OMRSE:00000154 ! realized in assistance with activities of daily living care encounter
relationship: BFO:0000054 OMRSE:00000155 ! realized in assistance with instrumental activities of daily living encounter
relationship: BFO:0000054 OMRSE:00000166 ! realized in home health care encounter

[Term]
id: OMRSE:00000166
name: home health care encounter
is_a: OGMS:0000097 ! health care encounter
relationship: BFO:0000066 OMRSE:00000074 ! occurs in housing unit

[Term]
id: OMRSE:00000168
name: questions asking process
is_a: BFO:0000003 ! occurrent
is_a: ObsoleteClass ! Obsolete Class
relationship: RO:0000057 NCBITaxon:9606 ! has_participant Homo sapiens
relationship: RO:0000057 OMRSE:00000173 ! has_participant material information bearer of question text plus answer set
is_obsolete: true
replaced_by: http://purl.obolibrary.org/obo/OMRSE_00000198

[Term]
id: OMRSE:00000169
name: palliative function
is_a: OMRSE:00000172 ! health care function
relationship: BFO:0000054 OMRSE:00000154 ! realized in assistance with activities of daily living care encounter
relationship: BFO:0000054 OMRSE:00000155 ! realized in assistance with instrumental activities of daily living encounter
relationship: BFO:0000054 OMRSE:00000170 ! realized in palliative care encounter

[Term]
id: OMRSE:00000170
name: palliative care encounter
is_a: OGMS:0000097 ! health care encounter

[Term]
id: OMRSE:00000171
name: hospice organization
is_a: OBI:0000245 ! organization
relationship: RO:0000053 OMRSE:00000117 ! bearer of hospice function

[Term]
id: OMRSE:00000172
name: health care function
is_a: BFO:0000034 ! function
intersection_of: BFO:0000034 ! function
intersection_of: BFO:0000054 OGMS:0000097 ! realized in health care encounter
relationship: BFO:0000054 OGMS:0000097 ! realized in health care encounter

[Term]
id: OMRSE:00000173
name: material information bearer of question text plus answer set
is_a: BFO:0000040 ! material entity
is_obsolete: true

[Term]
id: OMRSE:00000174
name: refusal to answer datum
is_a: OMRSE:00000163 ! response to a question asking process

[Term]
id: OMRSE:00000175
name: response to an identity question asking process
is_a: OMRSE:00000163 ! response to a question asking process

[Term]
id: OMRSE:00000176
name: identity question asking process
is_a: OMRSE:00000168 ! questions asking process
is_obsolete: true

[Term]
id: OMRSE:00000177
name: ethnic identity question asking process
is_a: OMRSE:00000176 ! identity question asking process
is_obsolete: true
replaced_by: http://purl.obolibrary.org/obo/OMRSE_00000199

[Term]
id: OMRSE:00000178
name: race identity question asking process
is_a: OMRSE:00000176 ! identity question asking process
is_obsolete: true
replaced_by: http://purl.obolibrary.org/obo/OMRSE_00000200

[Term]
id: OMRSE:00000179
name: answer to identity question
is_a: OMRSE:00000175 ! response to an identity question asking process

[Term]
id: OMRSE:00000180
name: obsolete American Indian or Alaska Native identity datum
def: "A racial identity that is the output of a racial identification process that uses OMB terminology for race or terminology that is mapped the OMB race terms and that indicates that the subject of the identity has origins in any of the original peoples of North and South America (including Central America), and maintains tribal affiliation or community attachment." []
is_a: OMRSE:00000185 ! obsolete OMB racial identity datum
property_value: IAO:0000117 "Amanda Hicks" xsd:string
is_obsolete: true
replaced_by: OMB American Indian or Alaska Native identity information content entity

[Term]
id: OMRSE:00000181
name: obsolete Asian identity datum
def: "A racial identity that is the output of a racial identification process that uses OMB terminology for race or terminology that is mapped the OMB race terms and that indicates that the subject of the identity has origins in any of the original peoples of the Far East, Southeast Asia, or the Indian subcontinent." []
is_a: OMRSE:00000185 ! obsolete OMB racial identity datum
property_value: IAO:0000117 "Amanda Hicks" xsd:string
is_obsolete: true
replaced_by: OMB Asian identity information content entity

[Term]
id: OMRSE:00000182
name: obsolete black or African American identity datum
def: "A racial identity that is the output of a racial identification process that uses OMB terminology for race or terminology that is mapped the OMB race terms and that indicates that the subject of the identity has origins in any of the black racial groups of Africa." []
is_a: OMRSE:00000185 ! obsolete OMB racial identity datum
property_value: IAO:0000117 "Amanda Hicks" xsd:string
is_obsolete: true
replaced_by: OMB black or African American identity information content entity

[Term]
id: OMRSE:00000183
name: obsolete Native Hawaiian or other Pacific Islander identity datum
def: "A racial identity that is the output of a racial identification process that uses OMB terminology for race or terminology that is mapped the OMB race terms and that indicates that the subject of the identity has origins in any of the original peoples of Hawaii, Guam, Samoa, or other Pacific Islands." []
is_a: OMRSE:00000185 ! obsolete OMB racial identity datum
property_value: IAO:0000117 "Amanda Hicks" xsd:string
is_obsolete: true
replaced_by: OMB Native Hawaiian or other Pacific Islander identity information content entity

[Term]
id: OMRSE:00000184
name: obsolete white identity datum
def: "A racial identity that is the output of a racial identification process that uses OMB terminology for race or terminology that is mapped the OMB race terms and that indicates that the subject of the identity has origins in any of the original peoples of Europe, the Middle East, or North Africa." []
is_a: OMRSE:00000185 ! obsolete OMB racial identity datum
property_value: IAO:0000117 "Amanda Hicks" xsd:string
is_obsolete: true
replaced_by: OMB white identity information content entity

[Term]
id: OMRSE:00000185
name: obsolete OMB racial identity datum
def: "A racial identity that is the output of a racial identification process that uses OMB terminology for race or terminology that is mapped the OMB race terms." []
is_a: OMRSE:00000098 ! obsolete racial identity datum
property_value: IAO:0000117 "Amanda Hicks" xsd:string
is_obsolete: true
replaced_by: OMB racial identity information content entity

[Term]
id: OMRSE:00000186
name: heavy smoker role
def: "A role that inheres in an organism and is realized by habitually smoking 10 or more tobacco cigerettes a day or the equivalent in other tobacco products." []
is_a: OMRSE:00000039 ! smoker role

[Term]
id: OMRSE:00000187
name: light smoker role
def: "A role that inheres in an organism and is realized by habitually smoking 1>10 tobacco cigerettes a day or the equivalent in other tobacco products." []
is_a: OMRSE:00000039 ! smoker role

[Term]
id: OMRSE:00000188
name: answer set
is_a: IAO:0000030 ! information content entity

[Term]
id: OMRSE:00000189
name: question text
is_a: IAO:0000030 ! information content entity

[Term]
id: OMRSE:00000190
name: option as member of some answer set
is_a: IAO:0000030 ! information content entity
relationship: RO:0002350 OMRSE:00000188 ! member of answer set

[Term]
id: OMRSE:00000191
name: residential facility
def: "A facility that has at least one housing unit as part in which a person or persons live" []
is_a: OMRSE:00000062 ! facility
property_value: IAO:0000111 "residential facility" xsd:string
property_value: IAO:0000117 "Emma Norris" xsd:string
property_value: IAO:0000117 "William Hogan" xsd:string
property_value: IAO:0000119 "Modified version of definition provided by Human Behaviour Change Project" xsd:string

[Term]
id: OMRSE:00000192
name: communication
def: "A process in which some participant shares some information content entity about some state of that participant with some other participant." []
comment: The term 'participant' in the definition need not refer to a human agent.
is_a: BFO:0000015 ! process
relationship: RO:0000057 BFO:0000040 ! has_participant material entity
relationship: RO:0000057 IAO:0000030 ! has_participant information content entity
property_value: http://purl.org/dc/elements/1.1/contributor "Mathias Brochhausen" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Matthew Diller" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string
property_value: IAO:0000117 "S. Clint Dowland" xsd:string

[Term]
id: OMRSE:00000193
name: linguistic competence
def: "A disposition inhering in a material entity that, if realized, is realized by that material entity’s communicating via some linguistic concretization." []
is_a: BFO:0000016 ! disposition
relationship: BFO:0000054 OMRSE:00000192 ! realized in communication
relationship: RO:0000052 BFO:0000040 ! inheres in material entity
property_value: http://purl.org/dc/elements/1.1/contributor "Mathias Brochhausen" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Matthew Diller" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string
property_value: IAO:0000117 "S. Clint Dowland" xsd:string

[Term]
id: OMRSE:00000194
name: language
def: "A disposition inhering in a linguistic community that (i) is a maximal aggregate of communicatively compatible linguistic competences, and (ii) if realized, is realized by any and all realizations of those linguistic competences." []
is_a: BFO:0000016 ! disposition
relationship: BFO:0000054 OMRSE:00000192 ! realized in communication
relationship: RO:0002351 OMRSE:00000193 ! has member linguistic competence
property_value: http://purl.org/dc/elements/1.1/contributor "Mathias Brochhausen" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Matthew Diller" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "S. Clint Dowland" xsd:string
property_value: IAO:0000117 "William R. Hogan" xsd:string

[Term]
id: OMRSE:00000195
name: linguistic community
def: "A maximal aggregate of material entities such that each member bears a linguistic competence for the same language." []
is_a: BFO:0000040 ! material entity
relationship: RO:0000053 OMRSE:00000194 ! bearer of language
property_value: http://purl.org/dc/elements/1.1/contributor "Mathias Brochhausen" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "S. Clint Dowland" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string
property_value: IAO:0000117 "Matthew Diller" xsd:string

[Term]
id: OMRSE:00000196
name: expression of preferred language
def: "A communication in which some participant states a preference for some communicative process to be in a certain language, and that has a concretization of a preferred language information content entity as its specified output." []
is_a: OBI:0000011 ! planned process
is_a: OMRSE:00000192 ! communication
property_value: http://purl.org/dc/elements/1.1/contributor "Mathias Brochhausen" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Matthew Diller" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string
property_value: IAO:0000117 "S. Clint Dowland" xsd:string

[Term]
id: OMRSE:00000197
name: preferred language information content entity
def: "An information content entity that (i) is about some person, some language, and some linguistic competence; and (ii) conveys the language with which that person prefers to communicate within some given context." []
is_a: IAO:0000030 ! information content entity
relationship: IAO:0000136 OMRSE:00000193 ! is about linguistic competence
relationship: IAO:0000136 OMRSE:00000194 ! is about language
property_value: http://purl.org/dc/elements/1.1/contributor "Matthew Diller" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "S. Clint Dowland" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string

[Term]
id: OMRSE:00000198
name: information content entity-request process
def: "a communication in which some participant requests of some other participant an information content entity about some portion of reality" []
comment: As with the parent class, 'participant' in the definition need not refer to a human agent.
comment: The medium and grammatical form are irrelevant. For example, the request may be written or spoken, and while it may be in the form of a question, it need not be.
is_a: OMRSE:00000192 ! communication
property_value: IAO:0000117 "S. Clint Dowland" xsd:string

[Term]
id: OMRSE:00000199
name: information content entity request about ethnic identity
def: "an information content entity-request process in which some participant requests of some other participant an information content entity that indicates the ethnic identity of that other participant" []
is_a: OMRSE:00000198 ! information content entity-request process
property_value: IAO:0000117 "S. Clint Dowland" xsd:string

[Term]
id: OMRSE:00000200
name: information content entity request about racial identity
def: "an information content entity-request process in which some participant requests of some other participant an information content entity that indicates the racial identity of that other participant" []
is_a: OMRSE:00000198 ! information content entity-request process
property_value: IAO:0000117 "S. Clint Dowland" xsd:string

[Term]
id: OMRSE:00000201
name: admission process
def: "A deontic document act in which a patient is registered with a health care provider for the purpose of receiving care in an inpatient encounter." []
is_a: IAO:0021001 ! obsolete_deontic document act
relationship: RO:0002083 OMRSE:00000126 ! before patient discharge
relationship: RO:0002223 OGMS:0000100 ! starts inpatient encounter
property_value: IAO:0000117 "Amanda Hicks" xsd:string

[Term]
id: OMRSE:00000202
name: cancer summary staging
def: "A planned process of determining the extent to which a cancer disease has developed by growing and spreading throughout an organism." []
is_a: OBI:0000011 ! planned process
property_value: IAO:0000111 "cancer summary staging" xsd:string
property_value: IAO:0000112 "The cancer summary staging performed on patient John Doe's clinical picture." xsd:string
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
property_value: IAO:0000118 "tumor summary staging" xsd:string

[Term]
id: OMRSE:00000203
name: cancer summary staging code
def: "An information content entity that is the specified output of cancer summary staging." []
property_value: IAO:0000111 "cancer summary staging code" xsd:string
property_value: IAO:0000112 "The cancer summary staging code that is the outcome of the cancer summary staging performed on patient John Doe's clinical picture." xsd:string
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
property_value: IAO:0000118 "tumor summary staging code" xsd:string

[Term]
id: OMRSE:00000204
name: social identity information content entity
def: "An information content entity that is intended to be a truthful statement about some person and whether that person identifies as some particular aspect of social identity—such as a gender, an ethnicity, a race, or a sexual orientation—where the sense of identifying may correspond to either (i) an aspect of one’s cognitive representation of oneself, (ii) how one prefers to be regarded by others within some social context, or (iii) how one chooses to present oneself to others within some social context." []
comment: We include (i)-(iii) to acknowledge that there are different senses of "identify" that are relevant here, and that we may not always be sure which sense the person concretizing the social identity information content entity intended. While (i) concerns how one thinks of oneself, (ii) and (iii) are more focused on one's interactions with others. Importantly, some choose not to share with others how they identify in the sense of (i). For example, one can consider oneself to be some certain gender without either wanting others to know or choosing to present oneself in a corresponding way. We distinguish (ii) and (iii) because one can prefer to be regarded some certain way without attempting to present oneself in any corresponding way.
is_a: IAO:0000030 ! information content entity
property_value: http://purl.org/dc/elements/1.1/contributor "Amanda Hicks" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Mathias Brochhausen" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Matthew Diller" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Sarah Bost" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string
property_value: IAO:0000117 "S. Clint Dowland" xsd:string

[Term]
id: OMRSE:00000205
name: ethnic identity information content entity
def: "A social identity information content entity that is about whether some person identifies as some ethnicity." []
comment: Ethnicity is separate from but related to racial identity. It refers more to identifying with a particular culture than with individuals similar in physical appearance. It includes things like Hispanic ethnicity (which spans many nations) and national cultural identities like Irish and ethnic groups within nations such as Catalan and Armenian.
is_a: OMRSE:00000204 ! social identity information content entity
property_value: http://purl.org/dc/elements/1.1/contributor "Amanda Hicks" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Mathias Brochhausen" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Matthew Diller" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Sarah Bost" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string
property_value: IAO:0000117 "S. Clint Dowland" xsd:string

[Term]
id: OMRSE:00000206
name: OMB ethnic identity information content entity
def: "An ethnic identity information content entity that uses OMB terminology for ethnicity or terminology that is strictly mapped onto the OMB ethnicity terms." []
comment: OMB dichotomizes ethnicity into Hispanic or Latino and Not Hispanic or Latino, and ignores all other forms of ethnicity.
is_a: OMRSE:00000205 ! ethnic identity information content entity
property_value: http://purl.org/dc/elements/1.1/contributor "Amanda Hicks" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Mathias Brochhausen" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Matthew Diller" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Sarah Bost" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string
property_value: IAO:0000117 "S. Clint Dowland" xsd:string

[Term]
id: OMRSE:00000207
name: OMB Hispanic or Latino identity information content entity
def: "An OMB ethnic identity information content entity that is about some person's identifying as Hispanic or Latino, which are intended to mean being of Cuban, Mexican, Puerto Rican, South or Central American, or other Spanish culture or origin, regardless of race." []
comment: It comprehends people of Portuguese culture or origin in Brazil.
is_a: OMRSE:00000206 ! OMB ethnic identity information content entity
property_value: http://purl.org/dc/elements/1.1/contributor "Amanda Hicks" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Mathias Brochhausen" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Matthew Diller" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Sarah Bost" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string
property_value: IAO:0000117 "S. Clint Dowland" xsd:string

[Term]
id: OMRSE:00000208
name: OMB not Hispanic or Latino identity information content entity
def: "An OMB ethnic identity information content entity that is about some person's identifying as neither Hispanic nor Latino, which are intended to mean being of Cuban, Mexican, Puerto Rican, South or Central American, or other Spanish culture or origin, regardless of race." []
is_a: OMRSE:00000206 ! OMB ethnic identity information content entity
property_value: http://purl.org/dc/elements/1.1/contributor "Amanda Hicks" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Mathias Brochhausen" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Matthew Diller" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Sarah Bost" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string
property_value: IAO:0000117 "S. Clint Dowland" xsd:string

[Term]
id: OMRSE:00000209
name: gender identity information content entity
def: "A social identity information content entity that is about whether some person identifies as some gender." []
is_a: OMRSE:00000204 ! social identity information content entity
property_value: http://purl.org/dc/elements/1.1/contributor "Amanda Hicks" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Mathias Brochhausen" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Matthew Diller" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Sarah Bost" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string
property_value: IAO:0000117 "S. Clint Dowland" xsd:string

[Term]
id: OMRSE:00000210
name: female gender identity information content entity
def: "A gender identity information content entity that is about some person's identifying as female in gender." []
is_a: OMRSE:00000209 ! gender identity information content entity
property_value: http://purl.org/dc/elements/1.1/contributor "Amanda Hicks" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Mathias Brochhausen" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Matthew Diller" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Sarah Bost" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string
property_value: IAO:0000117 "S. Clint Dowland" xsd:string

[Term]
id: OMRSE:00000211
name: male gender identity information content entity
def: "A gender identity information content entity that is about some person's identifying as male in gender." []
is_a: OMRSE:00000209 ! gender identity information content entity
property_value: http://purl.org/dc/elements/1.1/contributor "Amanda Hicks" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Mathias Brochhausen" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Matthew Diller" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Sarah Bost" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string
property_value: IAO:0000117 "S. Clint Dowland" xsd:string

[Term]
id: OMRSE:00000212
name: non-binary identity information content entity
def: "A gender identity information content entity that is about some person's identifying as non-binary in gender." []
is_a: OMRSE:00000209 ! gender identity information content entity
property_value: http://purl.org/dc/elements/1.1/contributor "Amanda Hicks" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Mathias Brochhausen" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Matthew Diller" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Sarah Bost" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string
property_value: IAO:0000117 "S. Clint Dowland" xsd:string

[Term]
id: OMRSE:00000213
name: racial identity information content entity
def: "A social identity information content entity that is about whether some person identifies as some race." []
is_a: OMRSE:00000204 ! social identity information content entity
property_value: http://purl.org/dc/elements/1.1/contributor "Amanda Hicks" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Mathias Brochhausen" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Matthew Diller" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Sarah Bost" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string
property_value: IAO:0000117 "S. Clint Dowland" xsd:string

[Term]
id: OMRSE:00000214
name: OMB racial identity information content entity
def: "A racial identity information content entity that uses OMB terminology and definitions for race or terminology that is strictly mapped onto the OMB race terms." []
is_a: OMRSE:00000213 ! racial identity information content entity
property_value: http://purl.org/dc/elements/1.1/contributor "Amanda Hicks" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Mathias Brochhausen" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Matthew Diller" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Sarah Bost" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string
property_value: IAO:0000117 "S. Clint Dowland" xsd:string

[Term]
id: OMRSE:00000215
name: OMB American Indian or Alaska Native identity information content entity
def: "An OMB racial identity information content entity that is about some person's identifying as American Indian or Alaska Native, which is intended to mean having origins in any of the original peoples of North and South America (including Central America), and maintains tribal affiliation or community attachment." []
comment: This definition corresponds to that used by OMB. It is worth noting that the OMB definition from which this one is derived is problematic, in that it implies that one's race cannot be Native American or Alaskan Native unless one maintains tribal affiliations or community attachment.
is_a: OMRSE:00000214 ! OMB racial identity information content entity
property_value: http://purl.org/dc/elements/1.1/contributor "Amanda Hicks" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Mathias Brochhausen" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Matthew Diller" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Sarah Bost" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string
property_value: IAO:0000117 "S. Clint Dowland" xsd:string

[Term]
id: OMRSE:00000216
name: OMB Asian identity information content entity
def: "An OMB racial identity information content entity that is about some person's identifying as Asian, which is intended to mean having origins in any of the original peoples of the Far East, Southeast Asia, or the Indian subcontinent." []
is_a: OMRSE:00000214 ! OMB racial identity information content entity
property_value: http://purl.org/dc/elements/1.1/contributor "Amanda Hicks" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Mathias Brochhausen" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Matthew Diller" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Sarah Bost" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string
property_value: IAO:0000117 "S. Clint Dowland" xsd:string

[Term]
id: OMRSE:00000217
name: OMB black or African American identity information content entity
def: "An OMB racial identity information content entity that is about some person's identifying as black or African American which is intended to mean having origins in any of the black racial groups of Africa." []
is_a: OMRSE:00000214 ! OMB racial identity information content entity
property_value: http://purl.org/dc/elements/1.1/contributor "Amanda Hicks" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Mathias Brochhausen" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Matthew Diller" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Sarah Bost" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string
property_value: IAO:0000117 "S. Clint Dowland" xsd:string

[Term]
id: OMRSE:00000218
name: OMB Native Hawaiian or other Pacific Islander identity information content entity
def: "An OMB racial identity information content entity that is about some person's identifying as Native Hawaiian or other Pacific Islander, which is intended to mean having origins in any of the original peoples of Hawaii, Guam, Samoa, or other Pacific Islands." []
is_a: OMRSE:00000214 ! OMB racial identity information content entity
property_value: http://purl.org/dc/elements/1.1/contributor "Amanda Hicks" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Mathias Brochhausen" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Matthew Diller" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Sarah Bost" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string
property_value: IAO:0000117 "S. Clint Dowland" xsd:string

[Term]
id: OMRSE:00000219
name: OMB white identity information content entity
def: "An OMB racial identity information content entity that is about some person's identifying as white which is intended to mean having origins in any of the original peoples of Europe, the Middle East, or North Africa." []
is_a: OMRSE:00000214 ! OMB racial identity information content entity
property_value: http://purl.org/dc/elements/1.1/contributor "Amanda Hicks" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Mathias Brochhausen" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Matthew Diller" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Sarah Bost" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string
property_value: IAO:0000117 "S. Clint Dowland" xsd:string

[Term]
id: OMRSE:00000220
name: sexual orientation identity information content entity
def: "A social identity information content entity that is about whether some person identifies as having some sexual orientation." []
is_a: OMRSE:00000204 ! social identity information content entity
property_value: http://purl.org/dc/elements/1.1/contributor "Amanda Hicks" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Mathias Brochhausen" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Matthew Diller" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Sarah Bost" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string

[Term]
id: OMRSE:00000221
name: residence ZIP code information content entity
def: "An information content entity that is about some geographical region, in which a postal delivery route denoted by a particular ZIP code is realized, and that is the specified output of a disclosure of residence." []
is_a: IAO:0000030 ! information content entity
property_value: http://purl.org/dc/elements/1.1/contributor "Hansi Zhang" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Mathias Brochhausen" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "S. Clint Dowland" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Sarah Bost" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string
property_value: IAO:0000117 "Matthew Diller" xsd:string

[Term]
id: OMRSE:00000223
name: disclosure of residence
def: "A social act that creates an information content entity that is about some geographical region in which a human being dwells." []
is_a: IAO:0021003 ! social act
property_value: http://purl.org/dc/elements/1.1/contributor "Hansi Zhang" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Mathias Brochhausen" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "S. Clint Dowland" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Sarah Bost" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string
property_value: IAO:0000117 "Matthew Diller" xsd:string

[Term]
id: OMRSE:00000224
name: electronic health record data set
def: "A data set whose members are obtained from one or more electronic health records." []
is_a: IAO:0000100 ! data set
property_value: http://purl.org/dc/elements/1.1/contributor "Alan Ruttenberg" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Mathias Brocchausen" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "S. Clint Dowland" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Sarah Bost" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string
property_value: IAO:0000117 "Matthew Diller" xsd:string
property_value: IAO:0000118 "EHR data set" xsd:string

[Term]
id: OMRSE:00000225
name: health care claim data set
def: "A data set whose members are the specified output of some process of adjudicating health care insurance claims (and whose inputs are at least partly some members of a health care billing data set)." []
comment: It covers prescription claims because pharmacies bill insurance companies for patients’ prescriptions via submitting insurance claims.
comment: The insurance claim is submitted to the insurance company by either the patient or the provider. It is not necessarily always the provider, although in the United States, it typically is.
comment: The outcome of the adjudication of a claim in the claims dataset could be favorable or unfavorable for the healthcare provider, the patient, or both. The idea is just that they’ve been adjudicated, one way or the other (or anything in between if that’s a possibility).
comment: The reason we say billing data are only part of the input is because we are not conflating the insurance claim with the bill. It is our understanding that the provider’s bill of services is either part of the claim or “attached” to it in some manner, but doesn’t constitute the entire claim itself.
comment: The sources of these data are held by insurers or other health plan providers.
is_a: IAO:0000100 ! data set
property_value: http://purl.org/dc/elements/1.1/contributor "Alan Ruttenberg" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Mathias Brocchausen" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Matthew Diller" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "S. Clint Dowland" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Sarah Bost" xsd:string
property_value: IAO:0000117 "William R. Hogan" xsd:string

[Term]
id: OMRSE:00000226
name: health care billing data set
def: "A data set whose members are obtained from billing-related data sources that (i) are generated by a health care organization as a result of internal administrative processes, and (ii) are about services rendered or materials used during some health care encounter." []
is_a: IAO:0000100 ! data set
property_value: http://purl.org/dc/elements/1.1/contributor "Alan Ruttenberg" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Mathias Brochhausen" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Matthew Diller" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Sarah Bost" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string
property_value: IAO:0000117 "S. Clint Dowland" xsd:string

[Term]
id: OMRSE:00000227
name: health care administrative process
def: "A planned process (i) that is neither a health care process nor an ancillary health care process, and (ii) in which some employee of a health care organization manages, or helps to manage, the performance of tasks that realize the functions of that organization." []
is_a: OBI:0000011 ! planned process
property_value: http://purl.org/dc/elements/1.1/contributor "S. Clint Dowland" xsd:string
property_value: IAO:0000112 "Recording data in an EHR. Financial tasks for a healthcare organization. Scheduling shifts for health care workers." xsd:string
property_value: IAO:0000117 "Matthew Diller" xsd:string

[Term]
id: OMRSE:00000228
name: principal diagnosis-assignment process
def: "A health care administrative process that has as input a diagnosis, and has as output a value indicating that diagnosis is about the condition that prompts the admission process that starts the encounter during which the diagnostic process that outputs that diagnosis begins." []
is_a: OMRSE:00000227 ! health care administrative process
property_value: http://purl.org/dc/elements/1.1/contributor "Matthew Diller" xsd:string
property_value: IAO:0000117 "S. Clint Dowland" xsd:string

[Term]
id: OMRSE:00000229
name: secondary diagnosis-assignment process
def: "A health care administrative process that has as input a diagnosis, and has as output a value indicating that diagnosis is about an underlying condition that is distinct from the condition that prompts the admission process that starts the encounter during which the diagnostic process that outputs that diagnosis begins." []
is_a: OMRSE:00000227 ! health care administrative process
property_value: http://purl.org/dc/elements/1.1/contributor "Matthew Diller" xsd:string
property_value: IAO:0000117 "S. Clint Dowland" xsd:string

[Term]
id: OMRSE:00000230
name: county smoking survey plan specification
def: "A survey plan specification that aims to collect information about the smoking behavior or lack thereof of a population on a county level. Concretization of a smoking survey plan that is stratified by county." []
is_a: OMIABIS:0001025 ! survey plan specification
property_value: http://purl.org/dc/elements/1.1/contributor "Hansi Zhang" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Jiang Bian" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Matthew Diller" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "S. Clint Dowland" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Sarah Bost" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string
property_value: IAO:0000112 "The Alachua county smoking survey plan specification." xsd:string
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string

[Term]
id: OMRSE:00000231
name: county smoking survey execution
def: "A survey execution that realizes the concretization of a smoking survey plan specification that is stratified by county." []
is_a: OMIABIS:0001035 ! survey execution
property_value: http://purl.org/dc/elements/1.1/contributor "Hansi Zhang" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Jiang Bian" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Matthew Diller" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "S. Clint Dowland" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Sarah Bost" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string
property_value: IAO:0000112 "The Alachua county smoking survey execution." xsd:string
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string

[Term]
id: OMRSE:00000232
name: county smoking survey data
def: "Survey data that is the specified output of a county smoking survey execution." []
is_a: OMIABIS:0000060 ! survey data
relationship: OBI:0000312 OMRSE:00000231 ! is_specified_output_of county smoking survey execution
property_value: http://purl.org/dc/elements/1.1/contributor "Hansi Zhang" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Jiang Bian" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Matthew Diller" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "S. Clint Dowland" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Sarah Bost" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string
property_value: IAO:0000112 "The Alachua county smoking survey data." xsd:string
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string

[Term]
id: OMRSE:00000233
name: smoking rate calculation
def: "A data transformation that has data about the smoking status of a population as its specified input and a percentage or ratio of smokers in that population as a specified output." []
is_a: OBI:0200000 ! data transformation
property_value: IAO:0000112 "Calculating the Alachua County smoking rate from Alachua County smoking data." xsd:string
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string

[Term]
id: OMRSE:00000234
name: county smoking rate data
def: "A data item that is the specified output of a smoking rate calculation that has data about smoking behavior or lack there of on a county level." []
is_a: IAO:0000027 ! data item
property_value: IAO:0000112 "The Alachua County smoking rate." xsd:string
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string

[Term]
id: OMRSE:00000500
name: job role data item
def: "A data item that is about a person's job role and/or its realization." []
is_a: IAO:0000027 ! data item
property_value: http://purl.org/dc/elements/1.1/contributor "Chris Stoeckert" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "S. Clint. Dowland" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string
property_value: IAO:0000112 "Can be about any aspect of employment, such as salary, work location, or employer." xsd:string
property_value: IAO:0000117 "Matthew Diller" xsd:string
property_value: IAO:0000118 "employment data item" xsd:string

[Term]
id: OMRSE:00000501
name: income data item
is_a: OMRSE:00000506 ! socio-economic data item

[Term]
id: OMRSE:00000502
name: government assistance health care plan data item
is_a: OMRSE:00000506 ! socio-economic data item

[Term]
id: OMRSE:00000503
name: health care plan data item
is_a: OMRSE:00000506 ! socio-economic data item

[Term]
id: OMRSE:00000504
name: government assistance income data item
is_a: OMRSE:00000506 ! socio-economic data item

[Term]
id: OMRSE:00000505
name: WIC data item
is_a: OMRSE:00000506 ! socio-economic data item

[Term]
id: OMRSE:00000506
name: socio-economic data item
is_a: IAO:0000027 ! data item

[Term]
id: OMRSE:00000507
name: obsolete non-binary gender identity datum
def: "A gender identity datum resulting from a gender identification process in which ‘non binary’ is selected based on the participant's subjective sense of gender." []
comment: Alternatively: A gender identity datum stating that a person's subjective sense of gender is non-binary.)\n\nExamples of usage: ‘Non-binary’, ‘Trigender’, ‘Agender’, ‘Genderfluid’, ‘2’ (intended to refer to a non-binary gender role)
is_a: OMRSE:00000133 ! obsolete gender identity datum
property_value: IAO:0000111 "non-binary gender identity datum" xsd:string
property_value: IAO:0000117 "Paul Fabry" xsd:string
property_value: IAO:0000117 "William Hogan" xsd:string
is_obsolete: true
replaced_by: non-binary gender identity information content entity

[Term]
id: OMRSE:00002029
name: education process
def: "A planned process with an active participant who acquires mental representations of information content entities (ICEs), which had no previous mental representation in the cognitive system, and through repeated use or application of these ICEs becomes the bearer of a new instance of some type of capability, and the participant was not previously the bearer of that instance of that type of capability." []
comment: An interesting question is whether there must be another participant who is the "educator".  Some might object that many people are "self taught".  A real case of being self taught is the first person who learned to play a stringed instrument, or to spin a ball on the top of a finger.  There was no previous information about that.  The ICEs acquired are via one's sensory systems (vision, proprioception, auditory, etc.).\n\nOn the other hand, in the case of those who are self-taught by reading books or watching videos, or acquiring some other form of ICEs concretized outside their brain, one argument might be that the author of those ICEs somehow "plays a role" in the education, although they cannot participate in the education process itself (If I read Aristotle, and through repeated application of the information I acquire through doing so, develop the ability to write better ontology definitions, surely Aristotle did not actively participate in my particular education process, although he did influence it in a very real way).
is_a: OBI:0000011 ! planned process
property_value: IAO:0000111 "educating" xsd:string
property_value: IAO:0000117 "William R. Hogan" xsd:string
property_value: IAO:0000600 "An act of acquiring new information and repeatedly applying that information to develop a new skill." xsd:string

[Term]
id: OMRSE:00002030
name: educational objective
def: "An objective specification that describes the type of capability or capabilities to be imparted by its realization, which is an educating (education process)." []
is_a: IAO:0000005 ! objective specification
property_value: IAO:0000111 "educational objective specification" xsd:string
property_value: IAO:0000117 "William R. Hogan" xsd:string
property_value: IAO:0000600 "An objective specification that describes the new knowledge & skill(s) to be obtained via an education process." xsd:string

[Term]
id: OMRSE:00002031
name: educational program
def: "A plan specification with an educational objective specification as part." []
comment: Very broad.  Covers everything from grade school to high school to college to graduate education, a MOOC, an individual course, a tutorial at a conference, a continuing education course or program, an informed consent video, etc, etc.
is_a: IAO:0000104 ! plan specification
intersection_of: IAO:0000104 ! plan specification
intersection_of: BFO:0000051 OMRSE:00002030 ! has part educational objective
relationship: BFO:0000051 OMRSE:00002030 ! has part educational objective
property_value: IAO:0000111 "educational plan specification" xsd:string
property_value: IAO:0000117 "William R. Hogan" xsd:string
property_value: IAO:0000600 "A plan specification with one or more educational objectives." xsd:string

[Term]
id: OMRSE:00002032
name: completing a program of education
def: "An educating that realizes a concretization of some program of education." []
comment: Note that parent class 'educating' and referenced class 'program of education' are defined elsewhere in this education module of OMRSE.
comment: This class refers extremely broadly to the successful realization of any program of education: a single course, first grade, MD, PhD, high school, the ninth grade, getting a black belt in karate, getting a master mechanic certification, a bachelor's degree, a masters degree, a graduate certificate, early childhood education program, and even getting a certificate at the end of some week-long workshop, summer camp, a certifcate from a cooking class, an actuarial certification.
is_a: OMRSE:00002029 ! education process
property_value: IAO:0000111 "completing a program of eduction" xsd:string
property_value: IAO:0000117 "William R. Hogan" xsd:string

[Term]
id: OMRSE:00002033
name: early childhood education plan specification
def: "An educational program whose intended active participant, when a concretization of it is realized, is a human child of age birth to 8 years or a human fetus prior to birth." []
is_a: OMRSE:00002031 ! educational program
property_value: IAO:0000111 "early childhood education program" xsd:string
property_value: IAO:0000117 "William R. Hogan" xsd:string
property_value: IAO:0000118 "pre-K education program" xsd:string
property_value: IAO:0000118 "prekindergarten education program" xsd:string
property_value: IAO:0000118 "preschool education program" xsd:string
property_value: IAO:0000119 https://apps.who.int/iris/bitstream/handle/10665/69729/a91213.pdf?sequence xsd:string

[Term]
id: OMRSE:00002034
name: primary education program
def: "An education plan specification with one or more primary education objective specifications as parts, and these are the only objective specifications it has as parts." []
comment: In the united states, also called "elementary education"
comment: It can still have action specifications as parts, and possibly other ICEs as parts.  That's why we cannot say it has only primary education objectives as parts, and we have to introduce the double negative in the class axiom.
comment: Primary education provides learning and educational activities typically designed to provide students with fundamental skills in reading, writing and mathematics (i.e. literacy and numeracy), and to establish a sound foundation for learning and solid understanding of core areas of knowledge and personal development, preparing for lower secondary education. It aims at learning at a basic level of complexity with little if any specialisation.
is_a: OMRSE:00002031 ! educational program
relationship: BFO:0000051 OMRSE:00002035 ! has part primary education objective
property_value: IAO:0000111 "primary education plan specification" xsd:string
property_value: IAO:0000117 "William R. Hogan" xsd:string
property_value: IAO:0000118 "elementary education" xsd:string

[Term]
id: OMRSE:00002035
name: primary education objective
def: "An education objective specification that has a concretization that, when realized, results in the active participant's acquisition and development of fundamental skills in reading, writing and mathematics (i.e. literacy and numeracy)." []
comment: By the end of primary education, the student has established a sound foundation for learning and solid understanding of core areas of knowledge and personal development, preparing for lower secondary education. It aims at learning at a basic level of complexity with little if any specialisation.
is_a: OMRSE:00002030 ! educational objective
property_value: IAO:0000111 "primary education objective specification" xsd:string
property_value: IAO:0000117 "William R. Hogan" xsd:string
property_value: IAO:0000119 http://uis.unesco.org/en/glossary-term/primary-education-isced-1 xsd:string

[Term]
id: OMRSE:00002036
name: lower secondary education objective
def: "An education objective specification that has a concretization that, when realized, confers to the active participant skills and knowledge in subject areas more specialized than basic reading, writing, and mathematics, with the overall goal of laying the foundation for lifelong learning and human development on which education systems may systematically expand further educational opportunities." []
comment: Examples of specific subjects could--but are not necessarily required to--include biology, history, science, literature, music, art.  Programs at this level are usually organized around a more subject-oriented curriculum, introducing theoretical concepts across a broad range of subjects.
comment: Programmes at ISCED level 2, or ‘lower secondary’ education, are typically designed to build upon the fundamental teaching and learning processes which begin at ISCED level 1. Usually, the educational aim is to lay the foundation for lifelong learning and human development on which education systems may systematically expand further educational opportunities. Programmes at this level are usually organized around a more subject-oriented curriculum, introducing theoretical concepts across a broad range of subjects.
is_a: OMRSE:00002030 ! educational objective
property_value: IAO:0000111 "lower secondary education objective specification" xsd:string
property_value: IAO:0000117 "William R. Hogan" xsd:string
property_value: IAO:0000119 http://uis.unesco.org/en/glossary-term/lower-secondary-education-isced-2 xsd:string

[Term]
id: OMRSE:00002037
name: awarding an academic degree
def: "A deontic document act that has as specified output an academic degree and that confers on recipient of the academic degree the recognition and the claims and obligations that accompany the degree." []
comment: Different degrees have different claims and obligations associated with them.  For example, having a medical degree (either M.D. or D.O.) entitles a person to sit for stage 3 of the US Medical Licensing Exam (otherwise one may not take the exam).
is_a: IAO:0021001 ! obsolete_deontic document act
intersection_of: IAO:0021001 ! obsolete_deontic document act
intersection_of: OBI:0000299 OOSTT:00000074 ! has_specified_output academic degree
relationship: OBI:0000299 OOSTT:00000074 ! has_specified_output academic degree
property_value: IAO:0000111 "awarding of an academic degree" xsd:string
property_value: IAO:0000117 "William R. Hogan" xsd:string

[Term]
id: OMRSE:00002038
name: basic education program
def: "An education plan specification that has as part both a primary educational objective specification and a lower secondary educational objective specification." []
comment: Most nations in the world mandate that children complete at least a basic education program.  Some nations go further and include upper secondary education after basic education.
comment: Whole range of educational activities, taking place in various settings, that aim to meet basic learning needs as defined in the World Declaration on Education for All (Jomtien, Thailand, 1990). According to ISCED standard, basic education comprises primary education (first stage of basic education) and lower secondary education (second stage). It also covers a wide variety of non-formal and informal public and private activities intended to meet the basic learning needs of people of all ages.
is_a: OMRSE:00002031 ! educational program
intersection_of: OMRSE:00002031 ! educational program
intersection_of: BFO:0000051 OMRSE:00002035 ! has part primary education objective
intersection_of: BFO:0000051 OMRSE:00002036 ! has part lower secondary education objective
relationship: BFO:0000051 OMRSE:00002035 ! has part primary education objective
relationship: BFO:0000051 OMRSE:00002036 ! has part lower secondary education objective
property_value: IAO:0000111 "basic education plan specification" xsd:string
property_value: IAO:0000117 "William R. Hogan" xsd:string
property_value: IAO:0000119 http://uis.unesco.org/en/glossary-term/basic-education xsd:string

[Term]
id: OMRSE:00002039
name: lower secondary education program
def: "An education plan specification with one or more lower secondary education objective specifications as parts, and these are the only objective specifications it has as parts." []
comment: It can still have action specifications as parts, and possibly other ICEs as parts.  That's why we cannot say it has only lower secondary education objectives as parts, and we have to introduce the double negative in the class axiom.
comment: Programmes at ISCED level 2, or ‘lower secondary’ education, are typically designed to build upon the fundamental teaching and learning processes which begin at ISCED level 1. Usually, the educational aim is to lay the foundation for lifelong learning and human development on which education systems may systematically expand further educational opportunities. Programmes at this level are usually organized around a more subject-oriented curriculum, introducing theoretical concepts across a broad range of subjects.
comment: Requires successful completion of a primary education program as a pre-requisite.
is_a: OMRSE:00002031 ! educational program
relationship: BFO:0000051 OMRSE:00002036 ! has part lower secondary education objective
property_value: IAO:0000111 "lower secondary education plan specification" xsd:string
property_value: IAO:0000117 "William R. Hogan" xsd:string

[Term]
id: OMRSE:00002040
name: upper secondary education objective
def: "An educational objective specification that has a concretization that, when realized, confers on the active participant skills and knowledge that prepare them for tertiary education, or employment, or both." []
comment: Programmes at ISCED level 3, or ‘upper secondary’ education, are typically designed to complete secondary education in preparation for tertiary education, or to provide skills relevant to employment, or both. Programmes at this level offer students more varied, specialised and in-depth instruction than programmes at lower secondary education (ISCED level 2). They are more differentiated, with an increased range of options and streams available.
is_a: OMRSE:00002030 ! educational objective
property_value: IAO:0000111 "upper secondary education objective specification" xsd:string
property_value: IAO:0000117 "William R. Hogan" xsd:string
property_value: IAO:0000119 http://uis.unesco.org/en/glossary-term/upper-secondary-education-isced-3 xsd:string

[Term]
id: OMRSE:00002041
name: upper secondary education program
def: "An education plan specification with one or more upper secondary education objective specifications as parts, and these are the only objective specifications it has as parts." []
comment: It can still have action specifications as parts, and possibly other ICEs as parts.  That's why we cannot say it has only lower secondary education objectives as parts, and we have to introduce the double negative in the class axiom.
comment: Programmes at ISCED level 3, or ‘upper secondary’ education, are typically designed to complete secondary education in preparation for tertiary education, or to provide skills relevant to employment, or both. Programmes at this level offer students more varied, specialised and in-depth instruction than programmes at lower secondary education (ISCED level 2). They are more differentiated, with an increased range of options and streams available.
comment: Requires successful completion of a lower secondary education program as a pre-requisite.
is_a: OMRSE:00002031 ! educational program
relationship: BFO:0000051 OMRSE:00002040 ! has part upper secondary education objective
property_value: IAO:0000111 "upper secondary education plan specification" xsd:string
property_value: IAO:0000117 "William R. Hogan" xsd:string

[Term]
id: OMRSE:00002042
name: higher education program
comment: Includes college, university, community college, professional schools (MD, RN, PharmD, PT, OT, DDS, dental hygienist, etc.), and so on.
comment: Refers to all higher education beyond secondary education, and thus encompasses ISCED levels 5 and above, which will eventually be subclasses of this one.
comment: Requires successful completion of a secondary education program as a pre-requisite.
is_a: OMRSE:00002031 ! educational program
relationship: BFO:0000051 OMRSE:00002043 ! has part higher education objective
property_value: IAO:0000111 "higher education plan specification" xsd:string
property_value: IAO:0000117 "William R. Hogan" xsd:string
property_value: IAO:0000118 "post-secondary education plan specification" xsd:string
property_value: IAO:0000118 "post-secondary education program" xsd:string

[Term]
id: OMRSE:00002043
name: higher education objective
def: "An educational objective specification that has a concretization that, when realized, confers on the active participant skills and knowledge in a specialized discipline, and culminates in the awarding of an academic degree." []
comment: Refers to all education beyond secondary education that leads to the awarding of an academic degree.
is_a: OMRSE:00002030 ! educational objective
property_value: IAO:0000111 "higher education objective specification" xsd:string
property_value: IAO:0000117 "William R. Hogan" xsd:string
property_value: IAO:0000118 "post-secondary education objective" xsd:string

[Term]
id: OMRSE:00002044
name: vocational education objective
def: "An educational objective specification that has a concretization that, when realized, is realized by a process that confers on the active participant knowledge and skills required to realize a particular type of employee role for a given occupation or trade." []
comment: Usually the skills are a major focus moreso than in other types of education.  For example, auto mechanics, plumbers, and electricians.
is_a: OMRSE:00002030 ! educational objective
property_value: IAO:0000111 "vocational education objective specification" xsd:string
property_value: IAO:0000117 "William R. Hogan" xsd:string
property_value: IAO:0000119 http://uis.unesco.org/sites/default/files/documents/international-standard-classification-of-education-isced-2011-en.pdf xsd:string

[Term]
id: OMRSE:00002045
name: highest level of education data item
def: "A socio-economic data item that is about a person and their completion of an education program (and its type), where that education progam is the last one in a sequence (of education programs) that the person has completed, where each education program completed except the last one is a pre-requisite to the education program completed after it." []
comment: This data item in a typical attribute-value system such as table, XML, JSON takes values like "secondary education", "Associate Degree", "Bachelor Degree", "High School", and so on.
is_a: OMRSE:00000506 ! socio-economic data item
property_value: IAO:0000111 "highest level of education socio-economic data item" xsd:string
property_value: IAO:0000117 "William R. Hogan" xsd:string

[Term]
id: OMRSE:00002046
def: "An educational plan specification that has a vocational objective specification as part." []
comment: vocational education program
comment: Vocational education programs are designed for learners to acquire the knowledge, skills and competencies specific to a particular occupation, trade, or class of occupations or trades. Such programs may have work-based components (e.g. apprenticeships, dual-system education programmes). Successful completion of such programs leads to labor market-relevant, vocational qualifications acknowledged as occupationally-oriented by the relevant national authorities and/or the labor market.
is_a: OMRSE:00002031 ! educational program
intersection_of: OMRSE:00002031 ! educational program
intersection_of: BFO:0000051 OMRSE:00002044 ! has part vocational education objective
relationship: BFO:0000051 OMRSE:00002044 ! has part vocational education objective
property_value: IAO:0000111 "vocational education plan specification" xsd:string
property_value: IAO:0000117 "William R. Hogan" xsd:string
property_value: IAO:0000119 http://uis.unesco.org/sites/default/files/documents/international-standard-classification-of-education-isced-2011-en.pdf xsd:string

[Term]
id: OMRSE:00002047
def: "A primary education plan specification that specifies the competencies and information content entities that should be acquired by students in the first year of primary education in the United States." []
is_a: OMRSE:00002034 ! primary education program
property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0002-9881-1017
property_value: http://purl.org/dc/elements/1.1/date 2020-09-02T12:38:43Z xsd:dateTime
property_value: IAO:0000111 "kindergarten education plan specification" xsd:string
property_value: IAO:0000117 "kindergarten education program" xsd:string
property_value: IAO:0000117 "William R. Hogan" xsd:string

[Term]
id: OMRSE:00002048
name: undergraduate higher education program
def: "A higher education plan specification that specifies the awarding of an associates or bachelors degree in the United States or equivalent degrees in other nations, and specifies as a pre-requisite the completion of some secondary education program." []
is_a: OMRSE:00002042 ! higher education program
property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0002-9881-1017
property_value: http://purl.org/dc/elements/1.1/date 2020-09-02T12:52:46Z xsd:dateTime
property_value: IAO:0000111 "undergraduate higher education plan specification" xsd:string
property_value: IAO:0000117 "William R. Hogan" xsd:string
property_value: IAO:0000118 "undergraduate education program" xsd:string

[Term]
id: OMRSE:00002049
name: graduate higher education program
def: "A higher education plan specification that specifies the awarding of a graduate certificate or degree, and specifies as a pre-requisite the awarding of an undergraduate degree." []
comment: Graduate degrees include masters, PhD, MD, PharmD, and other post-graduate professional degrees.  To distinguish MS/PhD from the professional ones, subclass this class.
comment: The prerequisite degree is at the bachelors level or equivalent.  An associates degree is almost never sufficient for entry into graduate education programs.
is_a: OMRSE:00002042 ! higher education program
property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0002-9881-1017
property_value: http://purl.org/dc/elements/1.1/date 2020-09-02T13:01:34Z xsd:dateTime
property_value: IAO:0000111 "graduate higher education plan specification" xsd:string
property_value: IAO:0000118 "graduate education program" xsd:string

[Term]
id: OMRSE:00002050
name: highest level of education is grades 1 through 6 data item
def: "A highest level of education socio-economic data item that represents the fact that the highest level of education achieved by an individual in the United States is in the range of first through sixth grade." []
comment: Note: this broad, very loose level of grouping emerged as an early requirement from the SODA project, funded by a PCORI Methods Grant, at the University of Florida with Dr. Yonghui Wu as PI.\n\nIt indicates completion of some to all of primary education in the United States.
is_a: OMRSE:00002045 ! highest level of education data item
property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0002-9881-1017
property_value: http://purl.org/dc/elements/1.1/date 2020-09-02T13:23:46Z xsd:dateTime
property_value: IAO:0000111 "highest level of education is completion of grades one through six socio-economic data item" xsd:string
property_value: IAO:0000117 "William R. Hogan" xsd:string

[Term]
id: OMRSE:00002051
name: highest level of education is grades 7 through 9 data item
def: "A highest level of education socio-economic data item that represents the fact that the highest level of education achieved by an individual in the United States is in the range of seventh (7th) through ninth (9th) grade." []
comment: Note: this broad, very loose level of grouping emerged as an early requirement from the SODA project, funded by a PCORI Methods Grant, at the University of Florida with Dr. Yonghui Wu as PI.\n\nIt indicates completion of some to all of lower secondary education in the United States.
is_a: OMRSE:00002045 ! highest level of education data item
property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0002-9881-1017
property_value: http://purl.org/dc/elements/1.1/date 2020-09-02T13:27:15Z xsd:dateTime
property_value: IAO:0000111 "highest level of education is completion of grades seven through nine socio-economic data item" xsd:string
property_value: IAO:0000117 "William R. Hogan" xsd:string

[Term]
id: OMRSE:00002052
name: highest level of education is grades 10 through 12 data item
def: "A highest level of education socio-economic data item that represents the fact that the highest level of education achieved by an individual in the United States is in the range of tenth (10th) through twelfth (12th) grade." []
comment: Note: this broad, very loose level of grouping emerged as an early requirement from the SODA project, funded by a PCORI Methods Grant, at the University of Florida with Dr. Yonghui Wu as PI.\n\nIt indicates completion of some to all of upper secondary education in the United States.
is_a: OMRSE:00002045 ! highest level of education data item
property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0002-9881-1017
property_value: http://purl.org/dc/elements/1.1/date 2020-09-02T13:27:50Z xsd:dateTime
property_value: IAO:0000111 "highest level of education is completion of grades ten through twelve socio-economic data item" xsd:string
property_value: IAO:0000117 "William R. Hogan" xsd:string

[Term]
id: OMRSE:00002053
name: highest level of education is completion of undergraduate degree data item
def: "A highest level of education socio-economic data item that represents the fact that the highest level of education achieved by an individual in the United States is completion of some undergraduate degree." []
comment: Note: The requirement for this class emerged as an early requirement from the SODA project, funded by a PCORI Methods Grant, at the University of Florida with Dr. Yonghui Wu as PI.
is_a: OMRSE:00002045 ! highest level of education data item
property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0002-9881-1017
property_value: http://purl.org/dc/elements/1.1/date 2020-09-02T13:28:27Z xsd:dateTime
property_value: IAO:0000111 "highest level of education is completion of some undergraduate degree socio-economic data item" xsd:string
property_value: IAO:0000117 "William R. Hogan" xsd:string

[Term]
id: OMRSE:00002054
name: highest level of education is completion of graduate certificate or degree data item
def: "A highest level of education socio-economic data item that represents the fact that the highest level of education achieved by an individual in the United States is completion of some graduate certificate or degree." []
comment: Note: The requirement for this class emerged as an early requirement from the SODA project, funded by a PCORI Methods Grant, at the University of Florida with Dr. Yonghui Wu as PI.
is_a: OMRSE:00002045 ! highest level of education data item
property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0002-9881-1017
property_value: http://purl.org/dc/elements/1.1/date 2020-09-02T13:28:49Z xsd:dateTime
property_value: IAO:0000111 "highest level of education is completion of some graduate degree socio-economic data item" xsd:string
property_value: IAO:0000117 "William R. Hogan" xsd:string

[Term]
id: OMRSE:00002055
name: highest level of education is completion of vocaational education program data item
def: "A highest level of education socio-economic data item that represents the fact that the highest level of education achieved by an individual in the United States is completion of some vocational education program." []
comment: Note: The requirement for this class emerged as an early requirement from the SODA project, funded by a PCORI Methods Grant, at the University of Florida with Dr. Yonghui Wu as PI.
is_a: OMRSE:00002045 ! highest level of education data item
property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0002-9881-1017
property_value: http://purl.org/dc/elements/1.1/date 2020-09-02T13:29:28Z xsd:dateTime
property_value: IAO:0000111 "highest level of education is completion of some vocational education program socio-economic data item" xsd:string
property_value: IAO:0000117 "William R. Hogan" xsd:string

[Term]
id: OMRSE:00002056
name: highest level of education is completion of kindergarten data item
def: "A highest level of education socio-economic data item that represents the fact that the highest level of education achieved by an individual in the United States is pre-kindergarten." []
comment: Note: The requirement for this class emerged as an early requirement from the SODA project, funded by a PCORI Methods Grant, at the University of Florida with Dr. Yonghui Wu as PI.\n\nIt indicates that a person has completed only early childhood education and nothing more.
is_a: OMRSE:00002045 ! highest level of education data item
property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0002-9881-1017
property_value: http://purl.org/dc/elements/1.1/date 2020-09-02T13:47:38Z xsd:dateTime
property_value: IAO:0000111 "highest level of education is completion of kindergarten socio-economic data item" xsd:string
property_value: IAO:0000117 "William R. Hogan" xsd:string

[Term]
id: OMRSE:00002057
name: highest level of education is completion of pre-kindergarten data item
def: "A highest level of education socio-economic data item that represents the fact that the highest level of education achieved by an individual in the United States is kindergarten." []
comment: Note: The requirement for this class emerged as an early requirement from the SODA project, funded by a PCORI Methods Grant, at the University of Florida with Dr. Yonghui Wu as PI.
is_a: OMRSE:00002045 ! highest level of education data item
property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0002-9881-1017
property_value: http://purl.org/dc/elements/1.1/date 2020-09-02T13:48:10Z xsd:dateTime
property_value: IAO:0000111 "highest level of education is completion of pre-kindergarten socio-economic data item" xsd:string
property_value: IAO:0000117 "William R. Hogan" xsd:string

[Term]
id: OMRSE:00002058
name: linguistic literacy competence
def: "A disposition borne by a human being that (1) has a linguistic competence as a dispositional part and (2) if realized, is realized by the bearer's achievement of some personal goal." []
comment: Other dispositions that it can and likely does have as dispositional parts include cultural competencies, interpersonal competencies, competencies for navigating a society's systems of laws, claims, obligations, deontic declarations, and norms of financial and other economic exchange.
comment: The realization of this disposition by definition realizes the bearer's linguistic competence that is a dispositional part of this disposition.  The realization of the linguistic competence would be an occurrent part of the realization of this disposition (and not a temporal part).
comment: Whereas linguistic competence may be afforded to non-human agents, literacy is nearly always considered in the context of human beings.
is_a: BFO:0000016 ! disposition
property_value: http://purl.org/dc/elements/1.1/contributor "Jiang Bian" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Xi Yang" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Yonghui Wu" xsd:string
property_value: IAO:0000111 "language literacy competence" xsd:string
property_value: IAO:0000117 "William R. Hogan" xsd:string
property_value: IAO:0000118 "human literacy" xsd:string
property_value: IAO:0000118 "linguistic literacy" xsd:string

[Term]
id: OMRSE:00002059
name: caregiver role
def: "A human social role that, if realized, is realized in providing assistance in the activities of daily living of another human being who possesses reduced capability to complete some of these activities alone." []
is_a: OMRSE:00000001 ! human social role
property_value: http://purl.org/dc/elements/1.1/contributor "John Judkins" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "S. Clint Dowland" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string
property_value: IAO:0000117 "Matthew Diller" xsd:string

[Term]
id: OMRSE:00002060
name: family relationship
def: "A relational quality that inheres within two or more persons related as members of a domestic group, or a number of domestic groups linked through descent from a common ancestor, marriage, or adoption." []
comment: We are also intending on including other family arrangements. This is something we are working on.
is_a: BFO:0000145 ! relational quality
property_value: http://purl.org/dc/elements/1.1/contributor "John Judkins" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "S. Clint Dowland" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ERO_0002033 xsd:string

[Term]
id: OOSTT:00000074
name: academic degree
def: "An information content entity that is the specified outcome of and documents the sucessful completion of a tertiary education program." []
is_a: IAO:0000030 ! information content entity
property_value: IAO:0000117 "John Judkins" xsd:string
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
property_value: OOSTT:00000030 "Recognized degree awarded after successful completion of a college or post-graduate porgram." xsd:string

[Term]
id: OOSTT:00000081
name: associate degree
def: "An academic degree awarded by colleges and universities upon completion of a program of study lasting two years." []
is_a: OOSTT:00000074 ! academic degree
property_value: IAO:0000117 "John Judkins" xsd:string
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
property_value: IAO:0000119 https://en.wikipedia.org/w/index.php?title=Associate_degree&oldid=723897149 xsd:string
property_value: OOSTT:00000030 "Recognition awarded after completion of a specific curriculum from an accredited tertiary education provider that falls between high school and bachelor's degree program." xsd:string

[Term]
id: OOSTT:00000082
name: master's degree
def: "An academic degree awarded by universities upon completion of a course of study demonstrating a mastery or high-order overview of a specific field of study or area of professional practice.[1] Within the area studied, graduates are posited to possess advanced knowledge of a specialized body of theoretical and applied topics; high order skills in analysis, critical evaluation, or professional application; and the ability to solve complex problems and think rigorously and independently." []
is_a: OOSTT:00000074 ! academic degree
property_value: IAO:0000117 "John Judkins" xsd:string
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
property_value: IAO:0000119 https://en.wikipedia.org/w/index.php?title=Master%27s_degree&oldid=726036185 xsd:string

[Term]
id: OOSTT:00000083
name: bachelor's degree
def: "An academic degree awarded by colleges and universities upon completion of a course of study lasting three to seven years." []
is_a: OOSTT:00000074 ! academic degree
property_value: IAO:0000117 "John Judkins" xsd:string
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
property_value: IAO:0000119 https://en.wikipedia.org/w/index.php?title=Bachelor%27s_degree&oldid=725713923 xsd:string

[Term]
id: OOSTT:00000084
name: bachelor's of nursing degree
def: "An academic degree in the science and principles of nursing, granted by an accredited tertiary education provider after the successful completion of a bachelor's of nursing program." []
is_a: OOSTT:00000083 ! bachelor's degree
property_value: IAO:0000117 "John Judkins" xsd:string
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
property_value: IAO:0000119 https://en.wikipedia.org/w/index.php?title=Bachelor_of_Science_in_Nursing&oldid=725962822 xsd:string

[Term]
id: OOSTT:00000086
name: master's in the science of nursing degree
def: "An academic degree in the science and principles of nursing, granted by an accredited tertiary education provider after the successful completion of a master's of nursing program." []
is_a: OOSTT:00000082 ! master's degree
property_value: IAO:0000117 "John Judkins" xsd:string
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
property_value: OOSTT:00000030 "An advanced academic degree in the principles and practices of nursing, with a focus on administration, education, or advanced nursing practice, granted by an accredited college or university after the successful completion of a master's of nursing program." xsd:string

[Term]
id: ORCS:00000027
name: admitting diagnosis
def: "a diagnosis that is about some patient and that is the specified output of a diagnostic process that occurs before or during the admission of that patient" []
is_a: OGMS:0000073 ! diagnosis
disjoint_from: ORCS:00000045 ! interim diagnosis
relationship: IAO:0000219 OGMS:0000073 ! denotes diagnosis
property_value: IAO:0000117 "Amanda Hicks" xsd:string
property_value: IAO:0000117 "S. Clint Dowland" xsd:string
property_value: IAO:0000119 "PCORnet CDM 4.1" xsd:string

[Term]
id: ORCS:00000028
name: obsolete PCORnet racial identity datum
comment: A racial identity that is the output of a racial identification process that uses the PCORnet CDM race or terminology. PCORnet CDM claims to use the OMB racial classification, but the crucial difference is that PCORnet CDM requires persons to identify with only one category whereas the OMB allows for multiple racial identities as outputs of an identification process.
is_a: OMRSE:00000098 ! obsolete racial identity datum
property_value: IAO:0000117 "Amanda Hicks" xsd:string
is_obsolete: true
replaced_by: 'PCORnet racial identity information content entity'

[Term]
id: ORCS:00000030
name: obsolete PCORnet American Indian or Alaska Native identity datum
is_a: ORCS:00000028 ! obsolete PCORnet racial identity datum
property_value: IAO:0000117 "Amanda Hicks" xsd:string
is_obsolete: true
replaced_by: 'PCORnet American Indian or Alaska Native identity information content entity'

[Term]
id: ORCS:00000031
name: obsolete PCORnet Asian identity datum
is_a: ORCS:00000028 ! obsolete PCORnet racial identity datum
property_value: IAO:0000117 "Amanda Hicks" xsd:string
is_obsolete: true
replaced_by: 'PCORnet Asian identity information content entity'

[Term]
id: ORCS:00000032
name: obsolete PCORnet black or African American identity datum
name: obsolete PCORnet item
is_a: ORCS:00000028 ! obsolete PCORnet racial identity datum
property_value: IAO:0000117 "Amanda Hicks" xsd:string
is_obsolete: true
replaced_by: 'PCORnet black or African American identity information content entity'

[Term]
id: ORCS:00000033
name: obsolete PCORnet CDM item identifier
is_a: IAO:0000030 ! information content entity
is_obsolete: true

[Term]
id: ORCS:00000034
name: obsolete PCORnet item
is_a: IAO:0000030 ! information content entity
is_obsolete: true

[Term]
id: ORCS:00000035
name: obsolete PCORnet Native Hawaiian or other Pacific Islander identity datum
is_a: ORCS:00000028 ! obsolete PCORnet racial identity datum
property_value: IAO:0000117 "Amanda Hicks" xsd:string
is_obsolete: true
replaced_by: 'PCORnet Native Hawaiian or other Pacific Islander identity information content entity'

[Term]
id: ORCS:00000036
name: obsolete PCORnet white identity datum
is_a: ORCS:00000028 ! obsolete PCORnet racial identity datum
property_value: IAO:0000117 "Amanda Hicks" xsd:string
is_obsolete: true
replaced_by: 'PCORnet white identity information content entity'

[Term]
id: ORCS:00000037
name: obsolete PCORnet multiple race identity datum
is_a: ORCS:00000028 ! obsolete PCORnet racial identity datum
property_value: IAO:0000117 "Amanda Hicks" xsd:string
is_obsolete: true
replaced_by: 'PCORnet multiple race identity information content entity'

[Term]
id: ORCS:00000038
name: obsolete PCORnet Hispanic identity datum
comment: From PCORnet CDM "A person of Cuban, Mexican, Puerto Rican, South or Central American, or other Spanish culture or origin, regardless of race."
is_a: OMRSE:00000127 ! obsolete hispanic or latino identity datum
property_value: IAO:0000117 "Amanda Hicks" xsd:string
is_obsolete: true
replaced_by: 'PCORnet Hispanic identity information content entity'

[Term]
id: ORCS:00000039
name: obsolete PCORnet not Hispanic identity datum
is_a: OMRSE:00000128 ! obsolete not hispanic or latino identity datum
property_value: IAO:0000117 "Amanda Hicks" xsd:string
is_obsolete: true
replaced_by: 'PCORnet non-Hispanic identity information content entity'

[Term]
id: ORCS:00000040
name: obsolete PCORnet ethnic identity datum
is_a: OMRSE:00000100 ! obsolete ethnic identity datum
property_value: IAO:0000117 "Amanda Hicks" xsd:string
is_obsolete: true
replaced_by: 'PCORnet ethnic identity information content entity'

[Term]
id: ORCS:00000041
name: PCORnet patient identifier
def: "A centrally registered identifier that denotes a person in a PCORnet data mart and is used to link across tables. This identifier is not necessarily unique within PCORnet." []
is_a: IAO:0020000 ! identifier
property_value: IAO:0000117 "Amanda Hicks" xsd:string

[Term]
id: ORCS:00000042
name: obsolete admission process
def: "a social act in which a patient is registered with a health care provider for the purposes of recieving care in an inpatient encounter" []
is_a: IAO:0021002 ! obsolete_document act
property_value: IAO:0000117 "Amanda Hicks" xsd:string
is_obsolete: true
replaced_by: 'admission process'\nhttp://purl.obolibrary.org/obo/OMRSE_00000201

[Term]
id: ORCS:00000043
name: discharge diagnosis
def: "a diagnosis that is about some patient and that is the specified output of a diagnostic process that occurs before or simultaneously with the discharge of that patient" []
is_a: OGMS:0000073 ! diagnosis
disjoint_from: ORCS:00000045 ! interim diagnosis
property_value: IAO:0000117 "Amanda Hicks" xsd:string
property_value: IAO:0000117 "S. Clint Dowland" xsd:string
property_value: IAO:0000119 "PCORnet CDM 4.1" xsd:string

[Term]
id: ORCS:00000044
name: final diagnosis
def: "a diagnosis that is about some patient and that is the specified output of a diagnostic process that occurs during an outpatient encounter" []
is_a: OGMS:0000073 ! diagnosis
property_value: IAO:0000117 "Amanda Hicks" xsd:string
property_value: IAO:0000117 "S. Clint Dowland" xsd:string
property_value: IAO:0000119 "PCORnet CDM 4.1" xsd:string

[Term]
id: ORCS:00000045
name: interim diagnosis
def: "a diagnosis that is about some patient and that is the specified output of a diagnostic process that occurs during an inpatient encounter, after admission, and before discharge of that patient" []
is_a: OGMS:0000073 ! diagnosis
property_value: IAO:0000117 "Amanda Hicks" xsd:string
property_value: IAO:0000117 "S. Clint Dowland" xsd:string
property_value: IAO:0000119 "PCORnet CDM 4.1" xsd:string

[Term]
id: ORCS:00000046
name: PCORnet racial identification process
is_a: OMRSE:00000099 ! racial identification process

[Term]
id: ORCS:00000047
name: obsolete PCORnet sexual orientation identity datum
is_a: ORCS:00000050 ! obsolete sexual orientation identity datum
is_obsolete: true
replaced_by: 'PCORnet sexual orientation identity information content entity'

[Term]
id: ORCS:00000048
name: ambulatory visit
def: "An outpatient encounter that occurs in an outpatient clinic, physician\noffice, ambulatory surgery facility, urgent care\nfacilitu, or a hospital encounters and\nthat does not occur in an emergency department facillity." []
is_a: OGMS:0000099 ! outpatient encounter
disjoint_from: ORCS:00000049 ! deprecated emergency department encounter
property_value: IAO:0000117 "Amanda Hicks" xsd:string
property_value: IAO:0000119 "PCORnet CDM 4.1" xsd:string
property_value: ORCS:00000090 "Includes visits at outpatient clinics, physician\noffices, same day/ambulatory surgery centers, urgent care\nfacilities, and other same-day ambulatory hospital encounters, but\nexcludes emergency department encounters" xsd:string

[Term]
id: ORCS:00000049
name: deprecated emergency department encounter
def: "A health care encounter that occurs in an emergency department facillity and realizes the health care provider role of an organization and the emergency department function of the facility." []
is_a: OGMS:0000097 ! health care encounter
property_value: IAO:0000117 "Amanda Hicks" xsd:string
property_value: IAO:0000119 "PCORnet CDM 4.1" xsd:string
property_value: ORCS:00000090 "Includes ED encounters that become inpatient stays (in which case inpatient stays would be a separate encounter). Excludes urgent care facility visits. ED claims should be pulled before hospitalization claims to ensure that ED with subsequent admission won't be rolled up in the hospital event. Does not include observation stays, where known." xsd:string
is_obsolete: true

[Term]
id: ORCS:00000050
name: obsolete sexual orientation identity datum
comment: A sexual orientation identity datum sis an information content entity that is the output of some sexual orientation identitification process and is intended to be a truthful statement about the subjective feelings of sexual attration, emotional attraction, and romantic attatchments of the person.  Unlike data items they are not necessilary contributed or acquired by a reliable method.
is_a: OMRSE:00000132 ! obsolete identity datum
property_value: IAO:0000117 "Amanda Hicks" xsd:string
is_obsolete: true
replaced_by: 'sexual orientation identity information content entity'

[Term]
id: ORCS:00000051
name: obsolete inpatient hospital encounter
name: obsolete PCORnet asexual identity datum
is_a: ORCS:00000047 ! obsolete PCORnet sexual orientation identity datum
is_obsolete: true
replaced_by: 'PCORnet asexual identity information content entity'

[Term]
id: ORCS:00000052
name: obsolete PCORnet gay identity datum
is_a: ORCS:00000047 ! obsolete PCORnet sexual orientation identity datum
is_obsolete: true
replaced_by: 'PCORnet gay identity information content entity'

[Term]
id: ORCS:00000053
name: obsolete PCORnet lesbian identity datum
is_a: ORCS:00000047 ! obsolete PCORnet sexual orientation identity datum
is_obsolete: true
replaced_by: 'PCORnet lesbian identity information content entity'

[Term]
id: ORCS:00000054
name: obsolete PCORnet multiple sexual orientations identity datum
is_a: ORCS:00000047 ! obsolete PCORnet sexual orientation identity datum
is_obsolete: true
replaced_by: 'PCORnet multiple sexual orientations identity information content entity'

[Term]
id: ORCS:00000055
name: obsolete PCORnet queer identity datum
is_a: ORCS:00000047 ! obsolete PCORnet sexual orientation identity datum
is_obsolete: true
replaced_by: 'PCORnet queer identity information content entity'

[Term]
id: ORCS:00000056
name: obsolete PCORnet questioning identity datum
is_a: ORCS:00000047 ! obsolete PCORnet sexual orientation identity datum
is_obsolete: true
replaced_by: 'PCORnet questioning sexual orientation identity information content entity'

[Term]
id: ORCS:00000057
name: obsolete PCORnet something else identity datum
is_a: ORCS:00000047 ! obsolete PCORnet sexual orientation identity datum
is_obsolete: true
replaced_by: 'PCORnet something else sexual orientation identity information content entity'

[Term]
id: ORCS:00000058
name: obsolete PCORnet straight identity datum
is_a: ORCS:00000047 ! obsolete PCORnet sexual orientation identity datum
is_obsolete: true
replaced_by: 'PCORnet straight identity information content entity'

[Term]
id: ORCS:00000059
name: obsolete PCORnet gender identity datum
comment: A gender identity that is the output of a racial identification process that uses the PCORnet CDM race or terminology. PCORnet CDM claims to use the 2015 Edition Health Information Technology (Health IT) Certification Criteria, 2015 Edition Base Electronic Health Record (EHR) Definition, but the crucial difference is that PCORnet CDM requires persons to identify with only one category whereas the other does not have a multiple gender option, which changes the meaning of the values in the value set.
is_a: OMRSE:00000133 ! obsolete gender identity datum
is_obsolete: true
replaced_by: 'PCORnet gender identity information content entity'

[Term]
id: ORCS:00000060
name: obsolete PCORnet genderqueer identity datum
is_a: ORCS:00000059 ! obsolete PCORnet gender identity datum
is_obsolete: true
replaced_by: 'PCORnet genderqueer/non-binary identity information content entity'

[Term]
id: ORCS:00000061
name: obsolete PCORnet man identity datum
is_a: ORCS:00000059 ! obsolete PCORnet gender identity datum
is_obsolete: true
replaced_by: 'PCORnet man identity information content entity'

[Term]
id: ORCS:00000062
name: obsolete PCORnet multiple genders datum
is_a: ORCS:00000059 ! obsolete PCORnet gender identity datum
is_obsolete: true
replaced_by: 'PCORnet multiple gender categories identity information content entity'

[Term]
id: ORCS:00000063
name: obsolete PCORnet something else identity datum
is_a: ORCS:00000059 ! obsolete PCORnet gender identity datum
is_obsolete: true
replaced_by: 'PCORnet something else gender identity information content entity'

[Term]
id: ORCS:00000064
name: obsolete PCORnet transgenderfemale/transwoman/male-to-female identity datum
is_a: ORCS:00000059 ! obsolete PCORnet gender identity datum
is_obsolete: true
replaced_by: 'PCORnet transgender female/trans woman/male-to-female identity information content entity'

[Term]
id: ORCS:00000065
name: obsolete PCORnet transgendermale/transman/female-to-male identity datum
is_a: ORCS:00000059 ! obsolete PCORnet gender identity datum
is_obsolete: true
replaced_by: 'PCORnet transgender male/trans man/female-to-male identity information content entity'

[Term]
id: ORCS:00000066
name: obsolete PCORnet woman identity datum
is_a: ORCS:00000059 ! obsolete PCORnet gender identity datum
is_obsolete: true
replaced_by: 'PCORnet woman identity information content entity'

[Term]
id: ORCS:00000067
name: PCORnet diagnosis identifier
def: "An identifier that denotes a diagnosis." []
is_a: IAO:0020000 ! identifier

[Term]
id: ORCS:00000068
name: DEPRECATED obsolete code set
comment: This class is superfluous, given the addition of PNO: code set.
property_value: seeAlso IAO:0020020
is_obsolete: true

[Term]
id: ORCS:00000069
name: PCORnet discharge status data item
def: "A data item that is about a documentation activity that records either (i) that some healthcare encounter ends with a patient discharge; (ii) that some healthcare encounter is terminated by a patient without any patient discharge; or (iii) that some healthcare encounter continues while the patient remains in the same hospital and while the hospital is billing a healthcare payor for services after a specified period." []
is_a: IAO:0000027 ! data item
property_value: IAO:0000116 "If the healthcare encounter ends with a patient discharge, then the status might also indicate the type of facility or organization, if any, to which the patient is discharged." xsd:string
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
property_value: IAO:0000117 "Matthew Diller" xsd:string
property_value: IAO:0000117 "S. Clint Dowland" xsd:string
property_value: IAO:0000117 "William R. Hogan" xsd:string

[Term]
id: ORCS:00000070
name: PCORnet skilled nursing facility discharge status data item
def: "A PCORnet discharge status data item that is about a discharge process in which a patient is discharged to a skilled nursing facility." []
is_a: ORCS:00000069 ! PCORnet discharge status data item
property_value: IAO:0000117 "Matthew Diller" xsd:string
property_value: IAO:0000117 "S. Clint Dowland" xsd:string

[Term]
id: ORCS:00000071
name: PCORnet adult foster home facility discharge status data item
def: "A PCORnet discharge status data item that is about a discharge process in which a patient is discharged to an adult foster home facility." []
is_a: ORCS:00000069 ! PCORnet discharge status data item
property_value: IAO:0000117 "Matthew Diller" xsd:string
property_value: IAO:0000117 "S. Clint Dowland" xsd:string

[Term]
id: ORCS:00000072
name: PCORnet assisted living facility discharge status data item
def: "A PCORnet discharge status data item that is about a discharge process in which a patient is discharged to an assisted living facility." []
is_a: ORCS:00000069 ! PCORnet discharge status data item
property_value: IAO:0000117 "Matthew Diller" xsd:string
property_value: IAO:0000117 "S. Clint Dowland" xsd:string

[Term]
id: ORCS:00000073
name: PCORnet other acute inpatient hospital discharge status data item
def: "A PCORnet discharge status data item that is about a discharge process in which a patient is discharged to another hospital." []
is_a: ORCS:00000069 ! PCORnet discharge status data item
property_value: IAO:0000117 "Amanda Hicks" xsd:string
property_value: IAO:0000117 "Matthew Diller" xsd:string
property_value: IAO:0000117 "S. Clint Dowland" xsd:string

[Term]
id: ORCS:00000074
name: PCORnet nursing home facility discharge status data item
def: "A PCORnet discharge status data item that is about a discharge process in which a patient is discharged to a nursing home facility." []
is_a: ORCS:00000069 ! PCORnet discharge status data item
property_value: IAO:0000117 "Matthew Diller" xsd:string
property_value: IAO:0000117 "S. Clint Dowland" xsd:string

[Term]
id: ORCS:00000075
name: PCORnet rehabilitation facility discharge status data item
def: "A PCORnet discharge status data item that is about a discharge process in which a patient is discharged to a rehabilitation facility." []
is_a: ORCS:00000069 ! PCORnet discharge status data item
property_value: IAO:0000117 "Matthew Diller" xsd:string
property_value: IAO:0000117 "S. Clint Dowland" xsd:string

[Term]
id: ORCS:00000076
name: PCORnet residential facility discharge status data item
def: "A PCORnet discharge status data item that is about a discharge process in which a patient is discharged to a residential facility." []
is_a: ORCS:00000069 ! PCORnet discharge status data item
property_value: IAO:0000117 "Matthew Diller" xsd:string
property_value: IAO:0000117 "S. Clint Dowland" xsd:string

[Term]
id: ORCS:00000077
name: PCORnet hospice discharge status data item
def: "A PCORnet discharge status data item that is about a discharge process in which a patient is discharged under the care of a hospice organization." []
is_a: ORCS:00000069 ! PCORnet discharge status data item
property_value: IAO:0000117 "Matthew Diller" xsd:string
property_value: IAO:0000117 "S. Clint Dowland" xsd:string

[Term]
id: ORCS:00000078
name: PCORnet against medical advice discharge status data item
def: "A PCORnet discharge status data item that is about a discharge process in which a patient is discharged upon deciding to end the encounter against the advice of a healthcare provider." []
is_a: ORCS:00000069 ! PCORnet discharge status data item
property_value: IAO:0000117 "Matthew Diller" xsd:string
property_value: IAO:0000117 "S. Clint Dowland" xsd:string

[Term]
id: ORCS:00000079
name: PCORnet still in hospital discharge status data item
def: "A PCORnet discharge status data item that is about a healthcare encounter that continues while the patient remains in the same hospital, and while the hospital is billing a healthcare payor for services after a specified period (typically 90 days)." []
is_a: ORCS:00000069 ! PCORnet discharge status data item
property_value: IAO:0000117 "Matthew Diller" xsd:string
property_value: IAO:0000117 "S. Clint Dowland" xsd:string
property_value: IAO:0000117 "William R. Hogan" xsd:string

[Term]
id: ORCS:00000080
name: PCORnet home health discharge status data item
def: "A PCORnet discharge status data item that is about a discharge process in which a patient is discharged (i) to a housing unit, and (ii) under the care of a home healthcare organization." []
is_a: ORCS:00000069 ! PCORnet discharge status data item
property_value: IAO:0000117 "Matthew Diller" xsd:string
property_value: IAO:0000117 "S. Clint Dowland" xsd:string
property_value: IAO:0000117 "William R. Hogan" xsd:string

[Term]
id: ORCS:00000081
name: PCORnet admitting source data item
def: "A data item that is about a patient admission and the type of facility from which a patient was discharged prior to admission." []
is_a: IAO:0000027 ! data item
property_value: IAO:0000117 "Matthew Diller" xsd:string
property_value: IAO:0000117 "S. Clint Dowland" xsd:string

[Term]
id: ORCS:00000082
name: PCORnet home health admitting source data item
def: "A PCORnet data item that is about a home healthcare organization and the household from which a patient was discharged prior to admission." []
is_a: ORCS:00000081 ! PCORnet admitting source data item
property_value: IAO:0000117 "Matthew Diller" xsd:string
property_value: IAO:0000117 "S. Clint Dowland" xsd:string

[Term]
id: ORCS:00000083
name: PCORnet skilled nursing facility admitting source data item
def: "A PCORnet data item that is about a skilled nursing facility from which a patient was discharged prior to admission." []
is_a: ORCS:00000081 ! PCORnet admitting source data item
property_value: IAO:0000117 "Matthew Diller" xsd:string
property_value: IAO:0000117 "S. Clint Dowland" xsd:string

[Term]
id: ORCS:00000091
name: PCORnet ethnic identity information content entity
def: "An ethnic identity information content entity that uses PCORnet CDM terminology for ethnicity, where this terminology corresponds to values for the \"Hispanic\" field of the Demographic Table." []
is_a: OMRSE:00000205 ! ethnic identity information content entity
property_value: http://purl.org/dc/elements/1.1/contributor "Mathias Brochhausen" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Matthew Diller" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Sarah Bost" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string
property_value: IAO:0000117 "S. Clint Dowland" xsd:string

[Term]
id: ORCS:00000092
name: PCORnet Hispanic identity information content entity
def: "A PCORnet ethnic identity information content entity that is about some person's identifying as Hispanic, which is intended to mean being of Cuban, Mexican, Puerto Rican, South or Central American, or other Spanish culture or origin, regardless of race." []
is_a: ORCS:00000091 ! PCORnet ethnic identity information content entity
property_value: http://purl.org/dc/elements/1.1/contributor "Amanda Hicks" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Mathias Brochhausen" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Matthew Diller" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Sarah Bost" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string
property_value: IAO:0000117 "S. Clint Dowland" xsd:string

[Term]
id: ORCS:00000093
name: PCORnet non-Hispanic identity information content entity
def: "A PCORnet ethnic identity information content entity that is about some person's identifying as not Hispanic, where \"Hispanic\" is intended to mean being of Cuban, Mexican, Puerto Rican, South or Central American, or other Spanish culture or origin, regardless of race." []
is_a: ORCS:00000091 ! PCORnet ethnic identity information content entity
property_value: http://purl.org/dc/elements/1.1/contributor "Mathias Brochhausen" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Matthew Diller" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Sarah Bost" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string
property_value: IAO:0000117 "S. Clint Dowland" xsd:string

[Term]
id: ORCS:00000094
name: PCORnet gender identity information content entity
def: "A gender identity information content entity that uses the PCORnet CDM terminology for gender, where this terminology corresponds to values for the \"gender identity\" field of the Demographic Table." []
comment: The PCORnet CDM cites the "2015 Edition Health Information Technology (Health IT) Certification Criteria, 2015 Edition Base Electronic Health Record (EHR) Definition, and ONC Health IT Certification Program Modifications" of the US Department of Health and Human Services as the source for its terminology, but the two differ in that the PCORnet CDM allows one to select only one value for gender and includes 'multiple gender' as an option, while the other lacks a 'multiple gender' option and allows multiple options to be selected. For that source used by PCORnet, see here: https://www.federalregister.gov/documents/2015/10/16/2015-25597/2015-edition-health-information-technology-health-it-certification-criteria-2015-edition-base
is_a: OMRSE:00000209 ! gender identity information content entity
property_value: http://purl.org/dc/elements/1.1/contributor "Amanda Hicks" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Mathias Brochhausen" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Matthew Diller" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Sarah Bost" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string
property_value: IAO:0000117 "S. Clint Dowland" xsd:string

[Term]
id: ORCS:00000095
name: PCORnet genderqueer/non-binary identity information content entity
def: "A PCORnet gender identity information content entity that is about some person's identifying as neither exclusively male nor exclusively female in gender." []
is_a: ORCS:00000094 ! PCORnet gender identity information content entity
property_value: http://purl.org/dc/elements/1.1/contributor "Mathias Brochhausen" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Matthew Diller" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Sarah Bost" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string
property_value: IAO:0000117 "S. Clint Dowland" xsd:string

[Term]
id: ORCS:00000096
name: PCORnet man identity information content entity
def: "A PCORnet gender identity information content entity that is about some person's identifying as a man." []
is_a: ORCS:00000094 ! PCORnet gender identity information content entity
property_value: http://purl.org/dc/elements/1.1/contributor "Mathias Brochhausen" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Matthew Diller" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Sarah Bost" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string
property_value: IAO:0000117 "S. Clint Dowland" xsd:string

[Term]
id: ORCS:00000097
name: PCORnet multiple gender categories identity information content entity
def: "A PCORnet gender identity information content entity that is about some person's identifying as more than one gender." []
is_a: ORCS:00000094 ! PCORnet gender identity information content entity
property_value: http://purl.org/dc/elements/1.1/contributor "Mathias Brochhausen" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Matthew Diller" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Sarah Bost" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string
property_value: IAO:0000117 "S. Clint Dowland" xsd:string

[Term]
id: ORCS:00000098
name: PCORnet something else gender identity information content entity
def: "A PCORnet gender identity information content entity that is about some person's identifying as some gender that is not referred to or described by the other value options for the \"gender identity\" field of the PCORnet Demographic Table." []
is_a: ORCS:00000094 ! PCORnet gender identity information content entity
property_value: http://purl.org/dc/elements/1.1/contributor "Mathias Brochhausen" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Matthew Diller" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Sarah Bost" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string
property_value: IAO:0000117 "S. Clint Dowland" xsd:string

[Term]
id: ORCS:00000099
name: PCORnet transgender female/trans woman/male-to-female identity information content entity
def: "A PCORnet gender identity information content entity that is about some person's identifying as transgender female, a trans woman, or male-to-female." []
is_a: ORCS:00000094 ! PCORnet gender identity information content entity
property_value: http://purl.org/dc/elements/1.1/contributor "Mathias Brochhausen" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Matthew Diller" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Sarah Bost" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string
property_value: IAO:0000117 "S. Clint Dowland" xsd:string

[Term]
id: ORCS:00000100
name: PCORnet transgender male/trans man/female-to-male identity information content entity
def: "A PCORnet gender identity information content entity that is about some person's identifying as transgender male, a trans man, or female-to-male." []
is_a: ORCS:00000094 ! PCORnet gender identity information content entity
property_value: http://purl.org/dc/elements/1.1/contributor "Sarah Bost" xsd:string
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
property_value: IAO:0000117 "Matthew Diller" xsd:string
property_value: IAO:0000117 "S. Clint Dowland" xsd:string
property_value: IAO:0000117 "William R. Hogan" xsd:string

[Term]
id: ORCS:00000123
name: PCORnet woman identity information content entity
def: "A PCORnet gender identity information content entity that is about some person's identifying as a woman." []
is_a: ORCS:00000094 ! PCORnet gender identity information content entity
property_value: http://purl.org/dc/elements/1.1/contributor "Mathias Brochhausen" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Matthew Diller" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Sarah Bost" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string
property_value: IAO:0000117 "S. Clint Dowland" xsd:string

[Term]
id: ORCS:00000124
name: PCORnet racial identity information content entity
def: "A racial identity information content entity that uses the PCORnet CDM terminology for race, where this terminology corresponds to the values for the \"race\" field of the Demographic Table." []
comment: The PCORnet CDM's values for the race field are based on the OMB racial classification, but differ in that the PCORnet CDM allows one to select only one value for race and includes "multiple race" as an option, while OMB lacks a 'multiple race' option and allows multiple options to be selected.
is_a: OMRSE:00000213 ! racial identity information content entity
property_value: http://purl.org/dc/elements/1.1/contributor "Amanda Hicks" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Mathias Brochhausen" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Matthew Diller" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Sarah Bost" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string
property_value: IAO:0000117 "S. Clint Dowland" xsd:string

[Term]
id: ORCS:00000125
name: PCORnet American Indian or Alaska Native identity information content entity
def: "A PCORnet racial identity information content entity that is about some person's identifying as American Indian or Alaska Native, which is intended to mean having origins in any of the original peoples of North and South America (including Central America), and maintains tribal affiliation or community attachment." []
comment: This definition corresponds to that used by OMB, which is PCORnet's source for the terminology used for the value options of the 'race' field. It is worth noting that the OMB definition from which this one is derived is problematic, in that it implies that one's race cannot be Native American or Alaskan Native unless one maintains tribal affiliations or community attachment.
is_a: ORCS:00000124 ! PCORnet racial identity information content entity
property_value: http://purl.org/dc/elements/1.1/contributor "Mathias Brochhausen" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Matthew Diller" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Sarah Bost" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string
property_value: IAO:0000117 "S. Clint Dowland" xsd:string

[Term]
id: ORCS:00000126
name: PCORnet Asian identity information content entity
def: "A PCORnet racial identity information content entity that is about some person's identifying as Asian, which is intended to mean having origins in any of the original peoples of the Far East, Southeast Asia, or the Indian subcontinent." []
is_a: ORCS:00000124 ! PCORnet racial identity information content entity
property_value: http://purl.org/dc/elements/1.1/contributor "Mathias Brochhausen" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Matthew Diller" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Sarah Bost" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string
property_value: IAO:0000117 "S. Clint Dowland" xsd:string

[Term]
id: ORCS:00000127
name: PCORnet black or African American identity information content entity
def: "A PCORnet racial identity information content entity that is about some person's identifying as black or African American, which is intended to mean having origins in any of the black racial groups of Africa." []
is_a: ORCS:00000124 ! PCORnet racial identity information content entity
property_value: http://purl.org/dc/elements/1.1/contributor "Mathias Brochhausen" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Matthew Diller" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Sarah Bost" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string
property_value: IAO:0000117 "S. Clint Dowland" xsd:string

[Term]
id: ORCS:00000128
name: PCORnet multiple race identity information content entity
def: "A PCORnet racial identity information content entity that is about some person's identifying as more than one race." []
is_a: ORCS:00000124 ! PCORnet racial identity information content entity
property_value: http://purl.org/dc/elements/1.1/contributor "Mathias Brochhausen" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Matthew Diller" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Sarah Bost" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string
property_value: IAO:0000117 "S. Clint Dowland" xsd:string

[Term]
id: ORCS:00000129
name: PCORnet Native Hawaiian or other Pacific Islander identity information content entity
def: "A PCORnet racial identity information content entity that is about some person's identifying as Native Hawaiian or other Pacific Islander, which is intended to mean having origins in any of the original peoples of Hawaii, Guam, Samoa, or other Pacific Islands." []
is_a: ORCS:00000124 ! PCORnet racial identity information content entity
property_value: http://purl.org/dc/elements/1.1/contributor "Mathias Brochhausen" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Matthew Diller" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Sarah Bost" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string
property_value: IAO:0000117 "S. Clint Dowland" xsd:string

[Term]
id: ORCS:00000130
name: PCORnet white identity information content entity
def: "A PCORnet racial identity information content entity that is about some person's identifying as white which is intended to mean having origins in any of the original peoples of Europe, the Middle East, or North Africa." []
is_a: ORCS:00000124 ! PCORnet racial identity information content entity
property_value: http://purl.org/dc/elements/1.1/contributor "Mathias Brochhausen" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Matthew Diller" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Sarah Bost" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string
property_value: IAO:0000117 "S. Clint Dowland" xsd:string

[Term]
id: ORCS:00000131
name: PCORnet sexual orientation identity information content entity
def: "A sexual orientation identity information content entity that uses the PCORnet terminology for sexual orientation, where this terminology corresponds to the permitted values for the \"sexual orientation\" field of the Demographic Table." []
comment: The labels and definitions used for the subclasses of 'PCORnet sexual orientation identity information content entity' are based on the terminology used for the value set options for the PCORnet Common Data Model's 'sexual orientation' field, which is a modifed version of the terms for, and categories of, sexual orientation that are found in the "2015 Edition Health Information Technology (Health IT) Certification Criteria, 2015 Edition Base Electronic Health Record (EHR) Definition, and ONC Health IT Certification Program Modifications" of the US Department of Health and Human Services (https://www.federalregister.gov/documents/2015/10/16/2015-25597/2015-edition-health-information-technology-health-it-certification-criteria-2015-edition-base). Neither the PCORnet CDM nor the other source provide definitions of their terms for sexual orientations. Our definitions for the corresponding classes thus point to the terms, rather than explain what they mean, as it is unclear how PCORnet intends them to be understood. Furthermore, these terms may be understood differently by different patients who select them as self-descriptions, as some may understand them to be defined in terms of phenotypic sex, others in terms of gender, and others in terms of some combination of the two.
is_a: OMRSE:00000220 ! sexual orientation identity information content entity
property_value: http://purl.org/dc/elements/1.1/contributor "Mathias Brochhausen" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Matthew Diller" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Sarah Bost" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string
property_value: IAO:0000117 "S. Clint Dowland" xsd:string

[Term]
id: ORCS:00000132
name: PCORnet asexual identity information content entity
def: "A PCORnet sexual orientation identity information content entity that is about some person's identifying as having a sexual orientation referred to by the PCORnet CDM with the term \"asexual.\"" []
comment: The labels and definitions used for the subclasses of 'PCORnet sexual orientation identity information content entity' are based on the terminology used for the value set options for the PCORnet Common Data Model's 'sexual orientation' field, which is a modifed version of the terms for, and categories of, sexual orientation that are found in the "2015 Edition Health Information Technology (Health IT) Certification Criteria, 2015 Edition Base Electronic Health Record (EHR) Definition, and ONC Health IT Certification Program Modifications" of the US Department of Health and Human Services (https://www.federalregister.gov/documents/2015/10/16/2015-25597/2015-edition-health-information-technology-health-it-certification-criteria-2015-edition-base). Neither the PCORnet CDM nor the other source provide definitions of their terms for sexual orientations. Our definitions for the corresponding classes thus point to the terms, rather than explain what they mean, as it is unclear how PCORnet intends them to be understood. Furthermore, these terms may be understood differently by different patients who select them as self-descriptions, as some may understand them to be defined in terms of phenotypic sex, others in terms of gender, and others in terms of some combination of the two.
is_a: ORCS:00000131 ! PCORnet sexual orientation identity information content entity
property_value: http://purl.org/dc/elements/1.1/contributor "Mathias Brochhausen" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Matthew Diller" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Sarah Bost" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string
property_value: IAO:0000117 "S. Clint Dowland" xsd:string

[Term]
id: ORCS:00000133
name: PCORnet bisexual identity information content entity
def: "A PCORnet sexual orientation identity information content entity that is about some person's identifying as having a sexual orientation referred to by the PCORnet CDM with the term \"bisexual.\"" []
comment: The labels and definitions used for the subclasses of 'PCORnet sexual orientation identity information content entity' are based on the terminology used for the value set options for the PCORnet Common Data Model's 'sexual orientation' field, which is a modifed version of the terms for, and categories of, sexual orientation that are found in the "2015 Edition Health Information Technology (Health IT) Certification Criteria, 2015 Edition Base Electronic Health Record (EHR) Definition, and ONC Health IT Certification Program Modifications" of the US Department of Health and Human Services (https://www.federalregister.gov/documents/2015/10/16/2015-25597/2015-edition-health-information-technology-health-it-certification-criteria-2015-edition-base). Neither the PCORnet CDM nor the other source provide definitions of their terms for sexual orientations. Our definitions for the corresponding classes thus point to the terms, rather than explain what they mean, as it is unclear how PCORnet intends them to be understood. Furthermore, these terms may be understood differently by different patients who select them as self-descriptions, as some may understand them to be defined in terms of phenotypic sex, others in terms of gender, and others in terms of some combination of the two.
is_a: ORCS:00000131 ! PCORnet sexual orientation identity information content entity
property_value: http://purl.org/dc/elements/1.1/contributor "Mathias Brochhausen" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Matthew Diller" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Sarah Bost" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string
property_value: IAO:0000117 "S. Clint Dowland" xsd:string

[Term]
id: ORCS:00000134
name: PCORnet gay identity information content entity
def: "A PCORnet sexual orientation identity information content entity that is about some person's identifying as having a sexual orientation referred to by the PCORnet CDM with the term \"gay.\"" []
comment: The labels and definitions used for the subclasses of 'PCORnet sexual orientation identity information content entity' are based on the terminology used for the value set options for the PCORnet Common Data Model's 'sexual orientation' field, which is a modifed version of the terms for, and categories of, sexual orientation that are found in the "2015 Edition Health Information Technology (Health IT) Certification Criteria, 2015 Edition Base Electronic Health Record (EHR) Definition, and ONC Health IT Certification Program Modifications" of the US Department of Health and Human Services (https://www.federalregister.gov/documents/2015/10/16/2015-25597/2015-edition-health-information-technology-health-it-certification-criteria-2015-edition-base). Neither the PCORnet CDM nor the other source provide definitions of their terms for sexual orientations. Our definitions for the corresponding classes thus point to the terms, rather than explain what they mean, as it is unclear how PCORnet intends them to be understood. Furthermore, these terms may be understood differently by different patients who select them as self-descriptions, as some may understand them to be defined in terms of phenotypic sex, others in terms of gender, and others in terms of some combination of the two.
is_a: ORCS:00000131 ! PCORnet sexual orientation identity information content entity
property_value: http://purl.org/dc/elements/1.1/contributor "Mathias Brochhausen" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Matthew Diller" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Sarah Bost" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string
property_value: IAO:0000117 "S. Clint Dowland" xsd:string

[Term]
id: ORCS:00000135
name: PCORnet lesbian identity information content entity
def: "A PCORnet sexual orientation identity information content entity that is about some person's identifying as having a sexual orientation referred to by the PCORnet CDM with the term \"lesbian.\"" []
comment: The labels and definitions used for the subclasses of 'PCORnet sexual orientation identity information content entity' are based on the terminology used for the value set options for the PCORnet Common Data Model's 'sexual orientation' field, which is a modifed version of the terms for, and categories of, sexual orientation that are found in the "2015 Edition Health Information Technology (Health IT) Certification Criteria, 2015 Edition Base Electronic Health Record (EHR) Definition, and ONC Health IT Certification Program Modifications" of the US Department of Health and Human Services (https://www.federalregister.gov/documents/2015/10/16/2015-25597/2015-edition-health-information-technology-health-it-certification-criteria-2015-edition-base). Neither the PCORnet CDM nor the other source provide definitions of their terms for sexual orientations. Our definitions for the corresponding classes thus point to the terms, rather than explain what they mean, as it is unclear how PCORnet intends them to be understood. Furthermore, these terms may be understood differently by different patients who select them as self-descriptions, as some may understand them to be defined in terms of phenotypic sex, others in terms of gender, and others in terms of some combination of the two.
is_a: ORCS:00000131 ! PCORnet sexual orientation identity information content entity
property_value: http://purl.org/dc/elements/1.1/contributor "Mathias Brochhausen" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Matthew Diller" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Sarah Bost" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string
property_value: IAO:0000117 "S. Clint Dowland" xsd:string

[Term]
id: ORCS:00000136
name: Internationalized Resource Identifier
def: "An identifier that is the specified output of a planned process that realizes the Internet standard RFC 3987 which is available from http://www.ietf.org/rfc/rfc3987.txt." []
comment: RFC 3987 has the title "Internationalized Resource Identifiers (IRIs)".  It was published in 2005.
is_a: IAO:0020000 ! identifier
property_value: IAO:0000111 "Internationalized Resource Identifier" xsd:string
property_value: IAO:0000118 "IRI" xsd:string

[Term]
id: ORCS:00000137
name: PCORnet emergency department admitting source data item
def: "A PCORnet data item that is about an emergency department from which a patient was discharged prior to admission." []
is_a: ORCS:00000081 ! PCORnet admitting source data item
property_value: IAO:0000117 "Matthew Diller" xsd:string
property_value: IAO:0000117 "S. Clint Dowland" xsd:string

[Term]
id: ORCS:00000138
name: PCORnet intra-hospital admitting source data item
def: "A PCORnet data item that is about another department in the same hospital from which a patient was discharged prior to admission." []
is_a: ORCS:00000081 ! PCORnet admitting source data item
property_value: IAO:0000117 "Matthew Diller" xsd:string
property_value: IAO:0000117 "S. Clint Dowland" xsd:string

[Term]
id: ORCS:00000139
name: PCORnet ambulatory visit admitting source data item
def: "A PCORnet data item that is about a patient admission that is causally upstream of an outpatient encounter." []
is_a: ORCS:00000081 ! PCORnet admitting source data item
property_value: IAO:0000117 "Matthew Diller" xsd:string
property_value: IAO:0000117 "S. Clint Dowland" xsd:string

[Term]
id: ORCS:00000140
name: PCORnet health care encounter identifier
def: "An identifier that denotes a health care encounter and has part some symbol." []
is_a: IAO:0020000 ! identifier
property_value: IAO:0000117 "Matthew Diller" xsd:string
property_value: IAO:0000117 "S. Clint Dowland" xsd:string

[Term]
id: ORCS:00000141
name: PCORnet facility identifier
def: "An identifier that denotes a health care facility and has part some symbol." []
is_a: IAO:0020000 ! identifier
property_value: IAO:0000117 "Matthew Diller" xsd:string
property_value: IAO:0000117 "S. Clint Dowland" xsd:string

[Term]
id: ORCS:00000142
name: institutional professional consult
def: "A health care encounter that realizes some health care provider role that inheres in some Homo sapiens." []
is_a: OGMS:0000097 ! health care encounter
property_value: IAO:0000117 "Matthew Diller" xsd:string
property_value: IAO:0000117 "S. Clint Dowland" xsd:string

[Term]
id: ORCS:00000143
name: non-acute institutional stay
def: "A health care encounter that occurs in some hospice facility, skilled nursing facility, rehabilitation facility, nursing home facility, residential home facility, overnight non-hospital dialysis facility, adult foster home facility, or assisted living facility." []
is_a: OGMS:0000097 ! health care encounter
property_value: IAO:0000117 "Matthew Diller" xsd:string
property_value: IAO:0000117 "S. Clint Dowland" xsd:string

[Term]
id: ORCS:00000144
name: PCORnet absent without leave discharge status data item
def: "A PCORnet discharge status data item that is about a termination of an inpatient encounter, initiated by the patient, that lacks a discharge process as a proper part." []
is_a: ORCS:00000069 ! PCORnet discharge status data item
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
property_value: IAO:0000117 "Matthew Diller" xsd:string
property_value: IAO:0000117 "S. Clint Dowland" xsd:string
property_value: IAO:0000117 "William R. Hogan" xsd:string

[Term]
id: ORCS:00000145
name: observation stay
def: "A health care encounter that occurs in some hospital facility or emergency department and that realizes some healthcare provider role that inheres in some organization." []
is_a: OGMS:0000097 ! health care encounter
property_value: IAO:0000117 "Matthew Diller" xsd:string

[Term]
id: ORCS:00000146
name: PCORnet provider identifier
def: "An identifier that denotes a human being who is a bearer of a person healthcare provider role." []
is_a: IAO:0020000 ! identifier
property_value: IAO:0000117 "Matthew Diller" xsd:string
property_value: IAO:0000117 "S. Clint Dowland" xsd:string

[Term]
id: ORCS:00000147
name: PCORnet multiple sexual orientations identity information content entity
def: "A PCORnet sexual orientation identity information content entity that is about some person's identifying as having multiple sexual orientations." []
comment: The labels and definitions used for the subclasses of 'PCORnet sexual orientation identity information content entity' are based on the terminology used for the value set options for the PCORnet Common Data Model's 'sexual orientation' field, which is a modifed version of the terms for, and categories of, sexual orientation that are found in the "2015 Edition Health Information Technology (Health IT) Certification Criteria, 2015 Edition Base Electronic Health Record (EHR) Definition, and ONC Health IT Certification Program Modifications" of the US Department of Health and Human Services (https://www.federalregister.gov/documents/2015/10/16/2015-25597/2015-edition-health-information-technology-health-it-certification-criteria-2015-edition-base). Neither the PCORnet CDM nor the other source provide definitions of their terms for sexual orientations. Our definitions for the corresponding classes thus point to the terms, rather than explain what they mean, as it is unclear how PCORnet intends them to be understood. Furthermore, these terms may be understood differently by different patients who select them as self-descriptions, as some may understand them to be defined in terms of phenotypic sex, others in terms of gender, and others in terms of some combination of the two.
is_a: ORCS:00000131 ! PCORnet sexual orientation identity information content entity
property_value: http://purl.org/dc/elements/1.1/contributor "Mathias Brochhausen" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Matthew Diller" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Sarah Bost" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string
property_value: IAO:0000117 "S. Clint Dowland" xsd:string

[Term]
id: ORCS:00000148
name: PCORnet queer identity information content entity
def: "A PCORnet sexual orientation identity information content entity that is about some person's identifying as having a sexual orientation referred to by the PCORnet CDM with the term \"queer.\"" []
comment: The labels and definitions used for the subclasses of 'PCORnet sexual orientation identity information content entity' are based on the terminology used for the value set options for the PCORnet Common Data Model's 'sexual orientation' field, which is a modifed version of the terms for, and categories of, sexual orientation that are found in the "2015 Edition Health Information Technology (Health IT) Certification Criteria, 2015 Edition Base Electronic Health Record (EHR) Definition, and ONC Health IT Certification Program Modifications" of the US Department of Health and Human Services (https://www.federalregister.gov/documents/2015/10/16/2015-25597/2015-edition-health-information-technology-health-it-certification-criteria-2015-edition-base). Neither the PCORnet CDM nor the other source provide definitions of their terms for sexual orientations. Our definitions for the corresponding classes thus point to the terms, rather than explain what they mean, as it is unclear how PCORnet intends them to be understood. Furthermore, these terms may be understood differently by different patients who select them as self-descriptions, as some may understand them to be defined in terms of phenotypic sex, others in terms of gender, and others in terms of some combination of the two.
is_a: ORCS:00000131 ! PCORnet sexual orientation identity information content entity
property_value: http://purl.org/dc/elements/1.1/contributor "Mathias Brochhausen" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Matthew Diller" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Sarah Bost" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string
property_value: IAO:0000117 "S. Clint Dowland" xsd:string

[Term]
id: ORCS:00000149
name: PCORnet questioning sexual orientation identity information content entity
def: "A PCORnet sexual orientation identity information content entity that is about some person's identifying as having a sexual orientation referred to by the PCORnet CDM with the term \"queer.\"" []
comment: The labels and definitions used for the subclasses of 'PCORnet sexual orientation identity information content entity' are based on the terminology used for the value set options for the PCORnet Common Data Model's 'sexual orientation' field, which is a modifed version of the terms for, and categories of, sexual orientation that are found in the "2015 Edition Health Information Technology (Health IT) Certification Criteria, 2015 Edition Base Electronic Health Record (EHR) Definition, and ONC Health IT Certification Program Modifications" of the US Department of Health and Human Services (https://www.federalregister.gov/documents/2015/10/16/2015-25597/2015-edition-health-information-technology-health-it-certification-criteria-2015-edition-base). Neither the PCORnet CDM nor the other source provide definitions of their terms for sexual orientations. Our definitions for the corresponding classes thus point to the terms, rather than explain what they mean, as it is unclear how PCORnet intends them to be understood. Furthermore, these terms may be understood differently by different patients who select them as self-descriptions, as some may understand them to be defined in terms of phenotypic sex, others in terms of gender, and others in terms of some combination of the two.
comment: While this is not about one's identifying as having or not having some sexual orientation, we regard it as a 'sexual orientation identity information content entity,' which is defined as being about "whether one identifies as having some sexual orientation." For example, if one is uncertain whether one is bisexual or heterosexual, one might be in a state of questioning one's sexuality, and an information content entity about that would seem to qualify as being about whether one identifies as having some sexual orientations. Indeed, there would be two sexual orientations in that example, and the information content entity could be both about whether one identifies as bisexual and about whether one identifies as heterosexual.
is_a: ORCS:00000131 ! PCORnet sexual orientation identity information content entity
property_value: http://purl.org/dc/elements/1.1/contributor "Mathias Brochhausen" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Matthew Diller" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Sarah Bost" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string
property_value: IAO:0000117 "S. Clint Dowland" xsd:string

[Term]
id: ORCS:00000150
name: PCORnet something else sexual orientation identity information content entity
def: "A PCORnet sexual orientation identity information content entity that is about some person's identifying as some sexual orientation that is not represented by the other value set options for the \"sexual orientation\" field of the PCORnet Demographic Table." []
comment: The labels and definitions used for the subclasses of 'PCORnet sexual orientation identity information content entity' are based on the terminology used for the value set options for the PCORnet Common Data Model's 'sexual orientation' field, which is a modifed version of the terms for, and categories of, sexual orientation that are found in the "2015 Edition Health Information Technology (Health IT) Certification Criteria, 2015 Edition Base Electronic Health Record (EHR) Definition, and ONC Health IT Certification Program Modifications" of the US Department of Health and Human Services (https://www.federalregister.gov/documents/2015/10/16/2015-25597/2015-edition-health-information-technology-health-it-certification-criteria-2015-edition-base). Neither the PCORnet CDM nor the other source provide definitions of their terms for sexual orientations. Our definitions for the corresponding classes thus point to the terms, rather than explain what they mean, as it is unclear how PCORnet intends them to be understood. Furthermore, these terms may be understood differently by different patients who select them as self-descriptions, as some may understand them to be defined in terms of phenotypic sex, others in terms of gender, and others in terms of some combination of the two.
is_a: ORCS:00000131 ! PCORnet sexual orientation identity information content entity
property_value: http://purl.org/dc/elements/1.1/contributor "Mathias Brochhausen" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Matthew Diller" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Sarah Bost" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string
property_value: IAO:0000117 "S. Clint Dowland" xsd:string

[Term]
id: ORCS:00000151
name: PCORnet straight identity information content entity
def: "A PCORnet sexual orientation identity information content entity that is about some person's identifying as having a sexual orientation referred to by the PCORnet CDM with the term \"straight.\"" []
comment: The labels and definitions used for the subclasses of 'PCORnet sexual orientation identity information content entity' are based on the terminology used for the value set options for the PCORnet Common Data Model's 'sexual orientation' field, which is a modifed version of the terms for, and categories of, sexual orientation that are found in the "2015 Edition Health Information Technology (Health IT) Certification Criteria, 2015 Edition Base Electronic Health Record (EHR) Definition, and ONC Health IT Certification Program Modifications" of the US Department of Health and Human Services (https://www.federalregister.gov/documents/2015/10/16/2015-25597/2015-edition-health-information-technology-health-it-certification-criteria-2015-edition-base). Neither the PCORnet CDM nor the other source provide definitions of their terms for sexual orientations. Our definitions for the corresponding classes thus point to the terms, rather than explain what they mean, as it is unclear how PCORnet intends them to be understood. Furthermore, these terms may be understood differently by different patients who select them as self-descriptions, as some may understand them to be defined in terms of phenotypic sex, others in terms of gender, and others in terms of some combination of the two.
is_a: ORCS:00000131 ! PCORnet sexual orientation identity information content entity
property_value: http://purl.org/dc/elements/1.1/contributor "Mathias Brochhausen" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Matthew Diller" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Sarah Bost" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string
property_value: IAO:0000117 "S. Clint Dowland" xsd:string

[Term]
id: ORCS:00000152
name: patient PCORnet specimen source value name
def: "A PCORnet specimen source value name that is about a patient." []
comment: The LOINC codes that this value name applies to are 59768-2 (Procedure indications [Interpretation] Narrative), 32624-9 (Race), 56850-1 (Interpretation and review of laboratory results), and 56794-1 (Internal identifier).
comment: This value name is not about an actual specimen.
is_a: ORCS:00000156 ! PCORnet specimen source value name
property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string
property_value: IAO:0000117 "Matthew Diller" xsd:string

[Term]
id: ORCS:00000153
name: provider PCORnet specimen source value name
def: "A PCORnet specimen source value name that is about some identifier that denotes a physician." []
comment: The PROVIDER value name might denote something other than a physician identifier, like a telephone number, depending on the data source. We limit it to being about an identifier that denotes a physician because this is what our data sources apply the value name to.
comment: This value name is not about an actual specimen.
is_a: ORCS:00000156 ! PCORnet specimen source value name
property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string
property_value: IAO:0000117 "Matthew Diller" xsd:string

[Term]
id: ORCS:00000154
name: emergency department admit to inpatient hospital stay
def: "A health care encounter that first occurs as an emergency department visit and then becomes an inpatient hospital stay" []
is_a: OGMS:0000097 ! health care encounter
property_value: IAO:0000117 "Amanda Hicks" xsd:string
property_value: IAO:0000119 "PCORnet CDM 4.1" xsd:string
property_value: ORCS:00000090 "Permissible substitution for preferred state of separate ED and IP records. Only for use with data sources where the individual records for ED and IP cannot be distinguished." xsd:string

[Term]
id: ORCS:00000155
name: PCORnet medical procedure
def: "A planned process that realizes a patient role." []
is_a: OBI:0000011 ! planned process
relationship: BFO:0000055 OMRSE:00000011 ! realizes patient role
property_value: http://purl.org/dc/elements/1.1/contributor "Matthew Diller" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "S. Clint Dowland" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Sarah Bost" xsd:string
property_value: IAO:0000117 "William R. Hogan" xsd:string

[Term]
id: ORCS:00000156
name: PCORnet specimen source value name
def: "An identifier that denotes a LOINC information content entity that itself is about some material entity that is the bearer of a specimen role." []
comment: The use of 'value name' in the label is a product of PCORnet calling these identifiers "value names."
is_a: IAO:0020000 ! identifier
property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string
property_value: IAO:0000117 "Matthew Diller" xsd:string
property_value: IAO:0000119 "PCORnet Common Data Model Specification v5.1" xsd:string

[Term]
id: ORCS:00000157
name: serum, plasma, or urine PCORnet specimen source value name
def: "A PCORnet specimen source value name that is about some blood serum, blood plasma, or urine samples." []
comment: The use of 'value name' in the label is a product of PCORnet calling these identifiers "value names."
comment: This class, while not ideal in that it doesn’t refer to an actual universal, is a consequence of LOINC system identifiers that consist of disjunctions (e.g., ‘Serum or plasma’).
is_a: ORCS:00000156 ! PCORnet specimen source value name
property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string
property_value: IAO:0000117 "Matthew Diller" xsd:string

[Term]
id: ORCS:00000158
name: serum or plasma PCORnet specimen source value name
def: "A PCORnet specimen source value name that is about some blood serum or blood plasma samples." []
comment: The use of 'value name' in the label is a product of PCORnet calling these identifiers "value names."
comment: This class, while not ideal in that it doesn’t refer to an actual universal, is a consequence of LOINC system identifiers that consist of disjunctions (e.g., ‘Serum or plasma’).
is_a: ORCS:00000156 ! PCORnet specimen source value name
property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string
property_value: IAO:0000117 "Matthew Diller" xsd:string

[Term]
id: ORCS:00000159
name: serum, plasma, or blood PCORnet specimen source value name
def: "A PCORnet specimen source value name that is about some blood serum, blood plasma, or whole blood samples." []
comment: The use of 'value name' in the label is a product of PCORnet calling these identifiers "value names."
comment: This class, while not ideal in that it doesn’t refer to an actual universal, is a consequence of LOINC system identifiers that consist of disjunctions (e.g., ‘Serum or plasma’).
is_a: ORCS:00000156 ! PCORnet specimen source value name
property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string
property_value: IAO:0000117 "Matthew Diller" xsd:string

[Term]
id: ORCS:00000160
name: blood or tissue PCORnet specimen source value name
def: "A PCORnet specimen source value name that is about some blood plasma or tissue samples." []
comment: The use of 'value name' in the label is a product of PCORnet calling these identifiers "value names."
comment: This class, while not ideal in that it doesn’t refer to an actual universal, is a consequence of LOINC system identifiers that consist of disjunctions (e.g., ‘Serum or plasma’).
is_a: ORCS:00000156 ! PCORnet specimen source value name
property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string
property_value: IAO:0000117 "Matthew Diller" xsd:string

[Term]
id: ORCS:00000161
name: blood plasma PCORnet specimen source value name
def: "A PCORnet specimen source value name that is about some specimen of blood plasma." []
comment: The use of 'value name' in the label is a product of PCORnet calling these identifiers "value names."
is_a: ORCS:00000156 ! PCORnet specimen source value name
property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string
property_value: IAO:0000117 "Matthew Diller" xsd:string

[Term]
id: ORCS:00000162
name: cerebrospinal fluid PCORnet specimen source value name
def: "A PCORnet specimen source value name that is about some specimen of cerebrospinal fluid." []
comment: The use of 'value name' in the label is a product of PCORnet calling these identifiers "value names."
is_a: ORCS:00000156 ! PCORnet specimen source value name
property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string
property_value: IAO:0000117 "Matthew Diller" xsd:string

[Term]
id: ORCS:00000163
name: vagina PCORnet specimen source value name
def: "A PCORnet specimen source value name that is about some vaginal specimen." []
comment: The use of 'value name' in the label is a product of PCORnet calling these identifiers "value names."
is_a: ORCS:00000156 ! PCORnet specimen source value name
property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string
property_value: IAO:0000117 "Matthew Diller" xsd:string

[Term]
id: ORCS:00000164
name: cervix PCORnet specimen source value name
def: "A PCORnet specimen source value name that is about some cervical specimen." []
comment: The use of 'value name' in the label is a product of PCORnet calling these identifiers "value names."
is_a: ORCS:00000156 ! PCORnet specimen source value name
property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string
property_value: IAO:0000117 "Matthew Diller" xsd:string

[Term]
id: ORCS:00000165
name: pericardial fluid PCORnet specimen source value name
def: "A PCORnet specimen source value name that is about some specimen of pericardial fluid." []
comment: The use of 'value name' in the label is a product of PCORnet calling these identifiers "value names."
is_a: ORCS:00000156 ! PCORnet specimen source value name
property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string
property_value: IAO:0000117 "Matthew Diller" xsd:string

[Term]
id: ObsoleteClass
name: Obsolete Class

[Term]
id: PATO:0000047
name: biological sex
namespace: quality
def: "An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved." []
subset: attribute_slim
is_a: PATO:0001995 ! organismal quality
property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl xsd:string

[Term]
id: PATO:0000051
name: morphology
def: "A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure." []
is_a: PATO:0001241 ! physical object quality
property_value: IAO:0000111 "morphology" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl

[Term]
id: PATO:0000122
name: length
def: "A 1-D extent quality which is equal to the distance between two points." []
is_a: PATO:0000051 ! morphology
property_value: IAO:0000111 "length" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl

[Term]
id: PATO:0000125
name: mass
def: "A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter." []
is_a: PATO:0001018 ! physical quality
property_value: IAO:0000111 "mass" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl

[Term]
id: PATO:0000169
name: viability
namespace: quality
def: "An organismal quality inhering in a bearer or a population by virtue of the bearer's disposition to survive and develop normally or the number of surviving individuals in a given population." []
subset: attribute_slim
subset: disposition_slim
is_a: PATO:0001995 ! organismal quality
property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl xsd:string

[Term]
id: PATO:0000383
name: female
namespace: quality
def: "A biological sex quality inhering in an individual or a population that only produces gametes that can be fertilised by male gametes." []
subset: mpath_slim
subset: value_slim
is_a: PATO:0001894 ! phenotypic sex
property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl xsd:string

[Term]
id: PATO:0000384
name: male
namespace: quality
def: "A biological sex quality inhering in an individual or a population whose sex organs contain only male gametes." []
subset: mpath_slim
subset: value_slim
is_a: PATO:0001894 ! phenotypic sex
property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl xsd:string

[Term]
id: PATO:0001018
name: physical quality
def: "A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities." []
is_a: PATO:0001241 ! physical object quality
property_value: IAO:0000111 "physical quality" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl

[Term]
id: PATO:0001241
name: physical object quality
def: "A quality which inheres in a continuant." []
is_a: BFO:0000019 ! quality
property_value: IAO:0000111 "physical object quality" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl

[Term]
id: PATO:0001421
name: alive
namespace: quality
def: "A viability quality inhering in a bearer by virtue of the bearer's condition before death." []
subset: value_slim
is_a: PATO:0000169 ! viability
property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl xsd:string

[Term]
id: PATO:0001422
name: dead
namespace: quality
def: "A viability quality inhering in a bearer by virtue of the cessation of the bearer's life." []
subset: value_slim
is_a: PATO:0000169 ! viability
property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl xsd:string

[Term]
id: PATO:0001894
name: phenotypic sex
namespace: quality
subset: attribute_slim
is_a: PATO:0000047 ! biological sex
property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl xsd:string

[Term]
id: PATO:0001995
name: organismal quality
namespace: quality
def: "A quality that inheres in an entire organism or part of an organism." []
is_a: BFO:0000019 ! quality
property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl xsd:string

[Term]
id: PATO_0001025
name: pressure
namespace: quality
subset: attribute_slim
is_a: BFO:0000019 ! quality

[Term]
id: PCO:0000020
name: family
def: "A domestic group, or a number of domestic groups linked through descent (demonstrated or stipulated) from a common ancestor, marriage, or adoption." []
comment: Family membership through marriage or adoption apply primarily to human families. In most species, family membership is defined by common anscestry.
is_a: OMRSE:00000022 ! aggregate of objectual organisms
property_value: IAO:0000114 IAO:0000123
property_value: IAO:0000116 "Needs axioms for family relationships." xsd:string
property_value: IAO:0000119 http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25173 xsd:string

[Term]
id: RO:0002577
name: system
def: "A material entity consisting of multiple components that are causally integrated." []
is_a: BFO:0000040 ! material entity
property_value: IAO:0000116 "May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://www.jbiomedsem.com/content/4/1/43 xsd:string

[Term]
id: UBERON:0000002
name: uterine cervix
namespace: uberon
def: "Lower, narrow portion of the uterus where it joins with the top end of the vagina." []
subset: efo_slim
subset: pheno_slim
subset: uberon_slim
synonym: "canalis cervicis uteri" EXACT []
synonym: "caudal segment of uterus" EXACT []
synonym: "cervical canal" RELATED []
synonym: "cervical canal of uterus" EXACT []
synonym: "cervix" BROAD []
synonym: "cervix of uterus" RELATED []
synonym: "cervix uteri" EXACT []
synonym: "neck of uterus" EXACT []
synonym: "uterine cervix" EXACT []
xref: BTO:0001421
xref: BTO:0002249
xref: CALOHA:TS-0134
xref: EFO:0000979
xref: EMAPA:29927
xref: EV:0100114
xref: FMA:17740
xref: FMA:TA
xref: GAID:376
xref: galen:CervixUteri
xref: http://en.wikipedia.org/wiki/Cervix
xref: http://linkedlifedata.com/resource/umls/id/C0007874
xref: http://orcid.org/0000-0002-6601-2165
xref: http://www.snomedbrowser.com/Codes/Details/181453009
xref: MA:0000392
xref: MAT:0000292
xref: MESH:D002584
xref: NCIT:C12311
xref: OpenCyc:Mx4rvVipEJwpEbGdrcN5Y29ycA
xref: UMLS:C0007874
xref: VHOG:0001359
is_a: UBERON:0001560 ! neck of organ
property_value: date_retrieved "2012-09-17" xsd:string
property_value: external_class VHOG:0001359 xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2019-11-22/uberon.owl xsd:string
property_value: source "DOI:10.1098/rspb.2004.2848 Lynch VJ, Roth JJ, Takahashi K, Dunn CW, Nonaka DF, Stopper GF, Wagner GP, Adaptive evolution of HoxA-11 and HoxA-13 at the origin of the uterus in mammals. Proceedings of the Royal Society of London, Series B (2004)" xsd:string
property_value: source http://bgee.unil.ch/
property_value: source http://medical-dictionary.thefreedictionary.com/uterine+cervix
property_value: source ncithesaurus:Cervix xsd:string
property_value: UBPROP:0000001 "The narrow caudal end of the uterus that opens into the vagina. [TFD][VHOG]" xsd:string
property_value: UBPROP:0000003 "The evolution of mammals is associated with radical changes in their reproductive biology, particularly the structure and function of the female reproductive organs. These changes include the evolution of the uterus, cervix, vagina, placenta and specialized cell types associated with each of those structures.[well established][VHOG]" xsd:string
property_value: UBPROP:0000007 "cervical" xsd:string
has_synonym_type: LATIN
ontology: VHOG

[Term]
id: UBERON:0000004
name: nose
namespace: uberon
def: "The olfactory organ of vertebrates, consisting of nares, olfactory epithelia and the structures and skeletal framework of the nasal cavity." []
subset: efo_slim
subset: major_organ
subset: pheno_slim
subset: uberon_slim
subset: vertebrate_core
synonym: "nasal sac" EXACT []
synonym: "nasus" RELATED []
synonym: "nose" EXACT []
synonym: "olfactory apparatus" RELATED []
synonym: "peripheral olfactory organ" EXACT []
synonym: "proboscis" RELATED []
xref: BTO:0000840
xref: CALOHA:TS-2037
xref: EHDAA2:0001274
xref: EHDAA:1502
xref: EMAPA:16542
xref: EV:0100037
xref: EV:0100370
xref: FMA:46472
xref: GAID:77
xref: galen:Nose
xref: http://en.wikipedia.org/wiki/Nose
xref: http://linkedlifedata.com/resource/umls/id/C0028429
xref: http://www.snomedbrowser.com/Codes/Details/181195007
xref: MA:0000281
xref: MAT:0000139
xref: MESH:D009666
xref: MIAA:0000139
xref: NCIT:C12756
xref: OpenCyc:Mx4rvViCbJwpEbGdrcN5Y29ycA
xref: TAO:0000047
xref: UBERON:cjm
xref: UMLS:C0028429
xref: ZFA:0000047
is_a: UBERON:0002268 ! olfactory organ
property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/d/d0/Canine-nose.jpg
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string
property_value: source http://en.wikipedia.org/wiki/Nose
property_value: source MP:0002233 xsd:string
property_value: source ncithesaurus:Nose xsd:string
property_value: source ZFA:0000047 xsd:string
property_value: UBPROP:0000001 "a protuberance in vertebrates that houses the nostrils, or nares, which admit and expel air for respiration in conjunction with the mouth. Behind the nose are the olfactory mucosa and the sinuses. Behind the nasal cavity, air next passes through the pharynx, shared with the digestive system, and then into the rest of the respiratory system. In humans, the nose is located centrally on the face; on most other mammals, it is on the upper tip of the snout[WP]. GO: The nose is the specialized structure of the face that serves as the organ of the sense of smell and as part of the respiratory system. Includes the nasi externus (external nose) and cavitas nasi (nasal cavity)[Wikipedia:Nose]." xsd:string
property_value: UBPROP:0000001 "Organ that is the specialized structure of the face that contains olfactory neurons. The peripheral olfactory organ is paired[ZFA:0000047]." xsd:string
property_value: UBPROP:0000001 "the organ that is specialized for smell and is part of the respiratory system" xsd:string
property_value: UBPROP:0000008 "the structure of the nose varies across vertebrates. In tetrapods the nose is part of the respiratory system.[PMID:25312359]" xsd:string
has_synonym_type: HUMAN_PREFERRED
has_synonym_type: LATIN
has_synonym_type: SENSU

[Term]
id: UBERON:0000014
name: zone of skin
namespace: uberon
def: "Any portion of the organ that covers that body and consists of a layer of epidermis and a layer of dermis." []
subset: pheno_slim
synonym: "portion of skin" EXACT []
synonym: "region of skin" EXACT []
synonym: "skin" EXACT []
synonym: "skin region" EXACT []
synonym: "skin zone" EXACT []
xref: EHDAA2:0001844
xref: EHDAA:6530
xref: EMAPA:17525
xref: EV:0100152
xref: FMA:86166
xref: GAID:933
xref: http://en.wikipedia.org/wiki/Skin
xref: http://orcid.org/0000-0002-6601-2165
xref: http://www.snomedbrowser.com/Codes/Details/20795001
xref: MA:0000151
xref: MAT:0000284
xref: MESH:D012867
xref: MIAA:0000284
xref: OpenCyc:Mx4rvVjX3ZwpEbGdrcN5Y29ycA
xref: VHOG:0000860
is_a: UBERON:0034944 ! zone of organ
property_value: date_retrieved "2012-09-17" xsd:string
property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/6/6d/Skin.svg
property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/e/e8/HumanSkinDiagram.jpg
property_value: external_class VHOG:0000860 xsd:string
property_value: IAO:0000232 "Note the distinction between the entire skin of the body, of which there is only 1 in an organism, and zones of skin, of which there can be many. Examples: skin of knee" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string
property_value: source "DOI:10.1111/j.1469-7580.2008.01043.x Vickaryous MK, Sire JY, The integumentary skeleton of tetrapods: origin, evolution, and development. J Anat (2009)" xsd:string
property_value: source http://bgee.unil.ch/
property_value: UBPROP:0000003 "(...) it is well-established that neural crest cells contribute to both the dermal skeleton (craniofacial bone, teeth, and the caudal fin rays of teleosts) and the integument, including craniofacial dermis and all pigment cells outside the retina (...).[well established][VHOG]" xsd:string
property_value: UBPROP:0000012 "we assume that mouse, HOG and GAID all mean zone of skin when they say skin. We also choose skin as an exact synonym, as it is more intuitive" xsd:string
ontology: VHOG

[Term]
id: UBERON:0000020
name: sense organ
namespace: uberon
def: "An organ that is capable of transducing sensory stimulus to the nervous system." []
subset: uberon_slim
synonym: "organ of sense organ system" EXACT []
synonym: "organ of sensory organ system" EXACT []
synonym: "organ of sensory system" EXACT []
synonym: "sense organ system organ" EXACT []
synonym: "sensillum" NARROW []
synonym: "sensor" RELATED []
synonym: "sensory organ" EXACT []
synonym: "sensory organ system organ" EXACT []
synonym: "sensory system organ" EXACT []
synonym: "Sinnesorgan" RELATED []
xref: AEO:0000094
xref: BSA:0000121
xref: BTO:0000202
xref: CALOHA:TS-2043
xref: EHDAA2:0001824
xref: EHDAA:500
xref: EMAPA:35955
xref: FBbt:00005155
xref: GAID:63
xref: HAO:0000930
xref: http://linkedlifedata.com/resource/umls/id/C0935626
xref: http://www.snomedbrowser.com/Codes/Details/244485009
xref: https://github.com/obophenotype/uberon/issues/549
xref: https://orcid.org/0000-0002-6601-2165
xref: MA:0000017
xref: MESH:D012679
xref: NCIT:C33224
xref: OBOL:accepted
xref: OBOL:automatic
xref: UMLS:C0935626
xref: VHOG:0001407
xref: WBbt:0006929
is_a: UBERON:0000062 ! organ
property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray722.png
property_value: http://purl.org/dc/elements/1.1/contributor https://github.com/cmungall
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string
property_value: source ncithesaurus:Organ_of_the_Special_Sense xsd:string

[Term]
id: UBERON:0000021
name: cutaneous appendage
namespace: uberon
def: "Anatomical projection that protrudes from the skin. Examples: hair, nail, feather, claw, hoof, horn, wattle, spur, beak, antler, bristle and some scales." []
subset: uberon_slim
synonym: "epidermal appendage" NARROW []
synonym: "epidermal growth" RELATED []
synonym: "skin appendage" EXACT []
xref: CALOHA:TS-0051
xref: FMA:71012
xref: http://www.snomedbrowser.com/Codes/Details/276160000
xref: https://orcid.org/0000-0002-6601-2165
is_a: UBERON:0013703 ! integumentary projection
property_value: IAO:0000116 "Mammary glands develop by similar mechanisms, and there is an argument for including them here (e.g. http://www.ncbi.nlm.nih.gov/pubmed/20484386), but these structures do not fit the current definition (lactiferous glands are part of the integumentary system in FMA). Note the FMA class is a subdivision of epidermis, which may be too restrictive for our purposes here." xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string

[Term]
id: UBERON:0000022
name: feather
namespace: uberon
def: "one of the epidermal growths that form the distinctive outer covering, or plumage, on birds. Feathers are formed in tiny follicles in the epidermis, or outer skin layer, that produce keratin proteins." []
subset: efo_slim
subset: uberon_slim
xref: BTO:0000447
xref: EFO:0000955
xref: GAID:1214
xref: http://en.wikipedia.org/wiki/Feather
xref: http://www.snomedbrowser.com/Codes/Details/410027006
xref: MAT:0000156
xref: MESH:D005241
xref: OpenCyc:Mx4rvVjW-5wpEbGdrcN5Y29ycA
is_a: UBERON:0000021 ! cutaneous appendage
property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/4/41/Parts_of_feather_modified.jpg
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string
property_value: seeAlso http://xkcd.com/1104/ xsd:anyURI
property_value: UBPROP:0000008 "Among the characteristics that distinguish the extant Aves from other living groups. Feathers have also been noticed in those Theropoda which have been termed feathered dinosaurs. Although feathers cover most parts of the body of birds, they arise only from certain well-defined tracts on the skin. They aid in flight, thermal insulation, waterproofing and coloration that helps in communication and protection" xsd:string
property_value: UBPROP:0000010 "The beta-keratins in feathers, beaks and claws - and the claws, scales and shells of reptiles - are composed of protein strands hydrogen-bonded into beta-pleated sheets, which are then further twisted and crosslinked by disulfide bridges into structures even tougher than the alpha-keratins of mammalian hair, horns and hoof." xsd:string

[Term]
id: UBERON:0000042
name: serous membrane
namespace: uberon
def: "multi-tissue structure that is comprised of a secretory epithelial layer (mesothelium) and a connective tissue layer." []
subset: uberon_slim
subset: vertebrate_core
synonym: "serosa" RELATED []
synonym: "tunica serosa" EXACT []
synonym: "wall of serous sac" EXACT []
xref: FMA:9581
xref: GAID:19
xref: http://linkedlifedata.com/resource/umls/id/C0036760
xref: http://www.snomedbrowser.com/Codes/Details/362878009
xref: https://github.com/obophenotype/uberon/issues/86
xref: MESH:D012704
xref: NCIT:C13169
xref: Serous:membrane
xref: TAO:0005425
xref: UMLS:C0036760
xref: ZFA:0005425
is_a: UBERON:0000481 ! multi-tissue structure
property_value: date_retrieved "2012-08-14" xsd:string
property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/4/4e/Ens.png
property_value: depicted:by http://upload.wikimedia.org/wikipedia/en/thumb/4/4e/Ens.png/200px-Ens.png
property_value: external_class TAO:0005425 xsd:string
property_value: external_ontology "FMA" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor https://github.com/cmungall
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string
property_value: source ncithesaurus:Serosa xsd:string
property_value: source Serous:membrane
property_value: UBPROP:0000001 "A multi-tissue structure that is comprised of a secretory epithelial layer and a connective tissue layer.[TAO]" xsd:string
property_value: UBPROP:0000001 "a smooth membrane consisting of a thin layer of cells which excrete serous fluid. Serous membranes line and enclose several body cavities, known as serous cavities, where they secrete a lubricating fluid which reduces friction from muscle movement. Serosa is not to be confused with adventitia, a connective tissue layer which binds together structures rather than reducing friction between them. Each serous membrane is composed of a secretory epithelial layer and a connective tissue layer underneath. The epithelial layer, known as mesothelium, consists of a single layer of avascular flat nucleated cells (cuboidal epithelium) which produce the lubricating serous fluid. This fluid has a consistency similar to thin mucus. These cells are bound tightly to the underlying connective tissue. The connective tissue layer provides the blood vessels and nerves for the overlying secretory cells, and also serves as the binding layer which allows the whole serous membrane to adhere to organs and other structures.[WP]" xsd:string
property_value: UBPROP:0000012 "in FMA, SM = mesothelium + connective tissue. It excludes the cavity. Serous sac = SM + cavity. Note that the SM is a subtype of wall in FMA." xsd:string
has_synonym_type: LATIN
ontology: TAO

[Term]
id: UBERON:0000057
name: urethra
namespace: uberon
def: "the fibromuscular tubular canal through which urine is discharged from the bladder to the exterior via the external urinary meatus; in males, the urethra is joined by the ejaculatory ducts and serves as a passageway for semen during ejaculation, as well as a canal for urine during voiding; in females, the urethra is shorter and emerges above the vaginal opening" []
subset: efo_slim
subset: major_organ
subset: organ_slim
subset: pheno_slim
subset: uberon_slim
xref: BTO:0001426
xref: CALOHA:TS-1132
xref: EFO:0000931
xref: EMAPA:30901
xref: EV:0100099
xref: FMA:19667
xref: GAID:390
xref: galen:Urethra
xref: http://en.wikipedia.org/wiki/Urethra
xref: http://linkedlifedata.com/resource/umls/id/C0041967
xref: http://www.snomedbrowser.com/Codes/Details/302513006
xref: MA:0000379
xref: MAT:0000121
xref: MESH:D014521
xref: MGI:anna
xref: MIAA:0000121
xref: MP:0000537
xref: NCIT:C12417
xref: OpenCyc:Mx4rvVjkypwpEbGdrcN5Y29ycA
xref: UMLS:C0041967
xref: VHOG:0001264
xref: XAO:0000153
is_a: UBERON:0000062 ! organ
property_value: depicted:by Female:anatomy.png
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string
property_value: source ncithesaurus:Urethra xsd:string
property_value: UBPROP:0000007 "urethral" xsd:string
property_value: UBPROP:0000008 "In human males, the urethra travels through the penis, and carries semen as well as urine. In females, the urethra is shorter and emerges above the vaginal opening." xsd:string

[Term]
id: UBERON:0000061
name: anatomical structure
namespace: uberon
def: "Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome." []
subset: upper_level
synonym: "biological structure" EXACT []
synonym: "connected biological structure" EXACT []
xref: AAO:0010825
xref: AEO:0000003
xref: BILA:0000003
xref: CARO:0000003
xref: EHDAA2:0003003
xref: EMAPA:0
xref: FBbt:00007001
xref: FMA:305751
xref: FMA:67135
xref: GAID:781
xref: HAO:0000003
xref: http://dbpedia.org/ontology/AnatomicalStructure
xref: http://www.snomedbrowser.com/Codes/Details/362889002
xref: MA:0003000
xref: MESH:D000825
xref: TAO:0000037
xref: TGMA:0001823
xref: VHOG:0001759
xref: XAO:0003000
xref: ZFA:0000037
is_a: UBERON:0000465 ! material anatomical entity
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string

[Term]
id: UBERON:0000062
name: organ
namespace: uberon
def: "Anatomical structure that performs a specific function or group of functions [WP]." []
subset: upper_level
synonym: "anatomical unit" RELATED []
synonym: "body organ" RELATED []
synonym: "element" RELATED []
xref: birnlex:4
xref: CARO:0020004
xref: EFO:0000634
xref: EMAPA:35949
xref: ENVO:01000162
xref: FMA:67498
xref: http://linkedlifedata.com/resource/umls/id/C0178784
xref: http://orcid.org/0000-0002-6601-2165
xref: http://www.snomedbrowser.com/Codes/Details/272625005
xref: MA:0003001
xref: NCIT:C13018
xref: OpenCyc:Mx4rv5XMb5wpEbGdrcN5Y29ycA
xref: OpenCyc:Mx4rwP3iWpwpEbGdrcN5Y29ycA
xref: Organ:(anatomy)
xref: UMLS:C0178784
xref: WBbt:0003760
is_a: UBERON:0010000 ! multicellular anatomical structure
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string
property_value: source GO:0048513 xsd:string
property_value: source ncithesaurus:Organ xsd:string
property_value: UBPROP:0000001 "Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions." xsd:string
property_value: UBPROP:0000012 "CARO v1 does not include a generic 'organ' class, only simple and compound organ. CARO v2 may include organ, see https://github.com/obophenotype/caro/issues/4" xsd:string

[Term]
id: UBERON:0000064
name: organ part
namespace: uberon
def: "A multicellular structure that is a part of an organ." []
subset: efo_slim
subset: non_informative
subset: upper_level
synonym: "cardinal organ part" EXACT []
synonym: "regional part of organ" RELATED []
xref: AAO:0011124
xref: birnlex:16
xref: EFO:0000635
xref: FMA:82472
xref: http://orcid.org/0000-0002-6601-2165
xref: http://www.snomedbrowser.com/Codes/Details/113343008
xref: http://www.snomedbrowser.com/Codes/Details/91717005
xref: NIFSTD:birnlex_16
is_a: UBERON:0010000 ! multicellular anatomical structure
property_value: IAO:0000232 "currently defined in a very broad sense, may be replaced by more specific classes in the future" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string

[Term]
id: UBERON:0000071
name: death stage
namespace: uberon
def: "End of the life of an organism." []
synonym: "death" RELATED []
xref: XAO:0000437
xref: XtroDO:0000085
is_a: UBERON:0000105 ! life cycle stage
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl xsd:string
property_value: UBPROP:0000012 "ncit:Death is an outcome" xsd:string

[Term]
id: UBERON:0000079
name: male reproductive system
namespace: uberon
def: "The organs associated with producing offspring in the gender that produces spermatozoa." []
subset: efo_slim
subset: pheno_slim
synonym: "genitalia of male organism" EXACT []
synonym: "male genital organ" RELATED []
synonym: "male genital system" EXACT []
synonym: "male genital tract" RELATED []
synonym: "male genitalia" EXACT []
synonym: "male genitals" EXACT []
synonym: "male organism genitalia" EXACT []
synonym: "male organism reproductive system" EXACT []
synonym: "male reproductive tract" RELATED []
synonym: "reproductive system of male organism" EXACT []
synonym: "systema genitale masculinum" RELATED []
xref: BTO:0000082
xref: CALOHA:TS-1310
xref: EFO:0000970
xref: EHDAA2:0001054
xref: EHDAA:8136
xref: EMAPA:17968
xref: EV:0100101
xref: FBbt:00004927
xref: FMA:45664
xref: GAID:386
xref: HAO:0000505
xref: http://en.wikipedia.org/wiki/Male_reproductive_system_%28human%29
xref: http://linkedlifedata.com/resource/umls/id/C0017422
xref: http://linkedlifedata.com/resource/umls/id/C1963704
xref: http://www.snomedbrowser.com/Codes/Details/361340001
xref: MA:0000396
xref: MESH:D005837
xref: MP:0001145
xref: NCIT:C12722
xref: OBOL:automatic
xref: OpenCyc:Mx4rvViCepwpEbGdrcN5Y29ycA
xref: TGMA:0000634
xref: UMLS:C0017422
xref: UMLS:C1963704
xref: VHOG:0000725
xref: WBbt:0008423
xref: XAO:0000155
is_a: UBERON:0003133 ! reproductive organ
property_value: date_retrieved "2012-09-17" xsd:string
property_value: external_class VHOG:0000725 xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string
property_value: source http://bgee.unil.ch/
property_value: source "ISBN:978-0792383369 Lombardi J, Comparative vertebrate reproduction (1998) p.43" xsd:string
property_value: source ncithesaurus:Male_Genitalia xsd:string
property_value: source ncithesaurus:Male_Reproductive_System xsd:string
property_value: UBPROP:0000003 "By far, sexual reproduction is the more common pattern among living vertebrate forms and its widespread occurrence suggests that it is the plesiomorphic, or primitive, reproductive mode among the vertebrates.[well established][VHOG]" xsd:string
ontology: VHOG

[Term]
id: UBERON:0000104
name: life cycle
namespace: uberon
def: "An entire span of an organism's life, commencing with the zygote stage and ending in the death of the organism." []
subset: upper_level
synonym: "entire life cycle" EXACT []
synonym: "entire lifespan" EXACT []
synonym: "life" EXACT []
synonym: "lifespan" EXACT []
xref: FBdv:00000000
xref: HsapDv:0000001
xref: MmusDv:0000001
xref: ncithesaurus:Life
xref: OGES:000011
is_a: BFO:0000182 ! history
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl xsd:string
property_value: seeAlso https://github.com/obophenotype/uberon/issues/532

[Term]
id: UBERON:0000105
name: life cycle stage
namespace: uberon
def: "A spatiotemporal region encompassing some part of the life cycle of an organism." []
subset: efo_slim
subset: upper_level
synonym: "developmental stage" NARROW []
synonym: "stage" NARROW []
xref: BILS:0000105
xref: EFO:0000399
xref: FBdv:00007012
xref: FMA:24120
xref: HsapDv:0000000
xref: MmusDv:0000000
xref: ncithesaurus:Developmental_Stage
xref: OlatDv:0000010
xref: PdumDv:0000090
xref: WBls:0000002
xref: XAO:1000000
xref: ZFS:0000000
xref: ZFS:0100000
is_a: BFO:0000011 ! spatiotemporal region
property_value: IAO:0000116 "this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl xsd:string
property_value: UBPROP:0000012 "the WBls class 'all stages' belongs here as it is the superclass of other WBls stages" xsd:string
property_value: UBPROP:0000012 "we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage" xsd:string

[Term]
id: UBERON:0000165
name: mouth
namespace: uberon
def: "The proximal portion of the digestive tract, containing the oral cavity and bounded by the oral opening. In vertebrates, this extends to the pharynx and includes gums, lips, tongue and parts of the palate. Typically also includes the teeth, except where these occur elsewhere (e.g. pharyngeal jaws) or protrude from the mouth (tusks)." []
subset: efo_slim
subset: major_organ
subset: pheno_slim
subset: uberon_slim
subset: vertebrate_core
synonym: "adult mouth" NARROW []
synonym: "cavital oralis" RELATED []
synonym: "cavitas oris" RELATED []
synonym: "cavum oris" RELATED []
synonym: "mouth cavity" RELATED []
synonym: "oral region" RELATED []
synonym: "oral vestibule" RELATED []
synonym: "regio oralis" EXACT []
synonym: "rima oris" RELATED []
synonym: "stoma" RELATED []
synonym: "stomatodaeum" RELATED []
synonym: "trophic apparatus" RELATED []
synonym: "vestibule of mouth" RELATED []
synonym: "vestibulum oris" RELATED []
xref: AAO:0010355
xref: BTO:0001090
xref: BTO:0004698
xref: CALOHA:TS-1315
xref: EFO:0000825
xref: EHDAA2:0001326
xref: EHDAA:542
xref: EMAPA:16262
xref: FBbt:00003126
xref: FMA:49184
xref: FMA:TA
xref: GAID:75
xref: galen:Mouth
xref: http://en.wikipedia.org/wiki/Mouth
xref: http://orcid.org/0000-0002-6601-2165
xref: http://purl.obolibrary.org/obo/uberon/images/lamprey_sucker_rosava_3238889218.jpg
xref: http://www.snomedbrowser.com/Codes/Details/21082005
xref: https://github.com/obophenotype/uberon/wiki/The-digestive-tract
xref: MA:0000341
xref: MA:0002474
xref: MAT:0000038
xref: MESH:D009055
xref: MIAA:0000038
xref: OpenCyc:Mx4rvVidh5wpEbGdrcN5Y29ycA
xref: TADS:0000040
xref: TAO:0000547
xref: TAO:0000590
xref: TGMA:0000131
xref: VHOG:0000280
xref: VHOG:0000812
xref: XAO:0003029
xref: ZFA:0000547
xref: ZFA:0000590
is_a: UBERON:0004921 ! subdivision of digestive tract
property_value: date_retrieved "2012-06-20" xsd:string
property_value: date_retrieved "2012-09-17" xsd:string
property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/0/06/Mouth_illustration-Otis_Archives.jpg
property_value: external_class AAO:0010355 xsd:string
property_value: external_class VHOG:0000812 xsd:string
property_value: external_ontology "FMA" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string
property_value: seeAlso https://github.com/obophenotype/uberon/issues/661
property_value: source AAO:BJB xsd:string
property_value: source "DOI:10.1038/nature07309 Hejnol A, Martindale MQ, Acoel development indicates the independent evolution of the bilaterian mouth and anus. Nature (2008)" xsd:string
property_value: source http://bgee.unil.ch/
property_value: UBPROP:0000001 "Cavity in which food is initially ingested and generally contains teeth, tongue and glands.[AAO]" xsd:string
property_value: UBPROP:0000003 "Molecular and developmental cell lineage data suggest that the acoel mouth opening is homologous to the mouth of protostomes and deuterostomes and that the last common ancestor of the Bilateria (the 'urbilaterian') had only this single digestive opening.[well established][VHOG]" xsd:string
property_value: UBPROP:0000007 "oral" xsd:string
property_value: UBPROP:0000011 "some AOs place this as developing from the stomodeum but we weaken this to developmental contribution, as the mouth includes non-ectodermal derivatives" xsd:string
property_value: UBPROP:0000012 "in FMA, the tongue, palate etc are part of the mouth which is itself a subdivision of the face. ZFA includes a separate class 'oral region' which is part of the mouth, but excludes tongue and lips" xsd:string
has_synonym_type: LATIN
ontology: AAO
ontology: VHOG

[Term]
id: UBERON:0000172
name: vomit
namespace: uberon
def: "A bodily fluid consisting of the expulsed contents of the stomach disgorged through the mouth or nose that happens as a result of a vomit reflex." []
synonym: "vomitus" EXACT []
xref: ENVO:00000338
xref: galen:Vomitus
xref: http://en.wikipedia.org/wiki/Vomiting
xref: NCIT:C77666
xref: OpenCyc:Mx4rvViQTJwpEbGdrcN5Y29ycA
xref: UBERON:cjm
is_a: UBERON:0036017 ! regurgitated substance
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string
has_synonym_type: LATIN

[Term]
id: UBERON:0000173
name: amniotic fluid
namespace: uberon
def: "Amniotic fluid is a bodily fluid consisting of watery liquid surrounding and cushioning a growing fetus within the amnion. It allows the fetus to move freely without the walls of the uterus being too tight against its body. Buoyancy is also provided. The composition of the fluid changes over the course of gestation. Initially, amniotic fluid is similar to maternal plasma, mainly water with electrolytes. As the fetus develops, proteins, carbohydrates, lipids, phospholipids originating from the lungs, fetal cells, and urea are deposited in the fluid." []
subset: pheno_slim
synonym: "acqua amnii" RELATED []
synonym: "liquor amnii" RELATED []
xref: BTO:0000068
xref: CALOHA:TS-0034
xref: EMAPA:36771
xref: ENVO:02000021
xref: EV:0100123
xref: FMA:305905
xref: GAID:1155
xref: http://linkedlifedata.com/resource/umls/id/C0002638
xref: MA:0002893
xref: MESH:D000653
xref: MP:MP
xref: NCIT:C13188
xref: UMLS:C0002638
xref: VHOG:0001267
is_a: UBERON:0000463 ! organism substance
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2019-11-22/uberon.owl xsd:string
property_value: source ncithesaurus:Amniotic_Fluid xsd:string
has_synonym_type: LATIN

[Term]
id: UBERON:0000174
name: excreta
namespace: uberon
alt_id: UBERON:0000324
alt_id: UBERON:0007550
def: "A portion of organism substance that is the product of an excretion process that will be eliminated from the body. An excretion process is elimination by an organism of the waste products that arise as a result of metabolic activity" []
synonym: "excreted substance" EXACT []
synonym: "excretion" RELATED []
synonym: "portion of excreted substance" EXACT []
synonym: "waste substance" EXACT []
xref: AEO:0000184
xref: BTO:0000491
xref: EHDAA2_RETIRED:0003184
xref: ENVO:02000022
xref: FMA:9674
xref: galen:Excretion
xref: GO:0007588
xref: http://orcid.org/0000-0002-6601-2165
is_a: UBERON:0000463 ! organism substance
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string

[Term]
id: UBERON:0000177
name: pus
namespace: uberon
def: "Pus is a bodily fluid consisting of a whitish-yellow or yellow substance produced during inflammatory responses of the body that can be found in regions of pyogenic bacterial infections. Pus is produced from the dead and living cells which travel into the intercellular spaces around the affected cells." []
synonym: "purulent exudate" RELATED []
xref: ENVO:02000038
xref: galen:Pus
xref: http://en.wikipedia.org/wiki/Pus
xref: ncithesaurus:Pus
xref: OpenCyc:Mx4rvVjG6ZwpEbGdrcN5Y29ycA
is_a: UBERON:0000463 ! organism substance
property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/9/90/Swollen_eye_with_conjunctivitis.jpg
property_value: external_ontology "NCIT" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string
property_value: UBPROP:0000012 "biospecimen in NCIT" xsd:string

[Term]
id: UBERON:0000178
name: blood
namespace: uberon
def: "A fluid that is composed of blood plasma and erythrocytes." []
subset: efo_slim
subset: pheno_slim
subset: uberon_slim
subset: vertebrate_core
synonym: "portion of blood" EXACT []
synonym: "vertebrate blood" EXACT []
synonym: "whole blood" RELATED []
xref: AAO:0000046
xref: BTO:0000089
xref: CALOHA:TS-0079
xref: EFO:0000296
xref: EHDAA2:0000176
xref: EHDAA:418
xref: EMAPA:16332
xref: ENVO:02000027
xref: EV:0100047
xref: FMA:9670
xref: GAID:965
xref: galen:Blood
xref: http://en.wikipedia.org/wiki/Blood
xref: http://linkedlifedata.com/resource/umls/id/C0005767
xref: http://orcid.org/0000-0002-6601-2165
xref: https://github.com/obophenotype/uberon/issues/9
xref: MA:0000059
xref: MESH:D001769
xref: MIAA:0000315
xref: NCIT:C12434
xref: OpenCyc:Mx4rvVjI8JwpEbGdrcN5Y29ycA
xref: TAO:0000007
xref: UMLS:C0005767
xref: VHOG:0000224
xref: XAO:0000124
xref: ZFA:0000007
is_a: UBERON:0000179 ! haemolymphatic fluid
property_value: date_retrieved "2012-06-20" xsd:string
property_value: date_retrieved "2012-08-14" xsd:string
property_value: date_retrieved "2012-09-17" xsd:string
property_value: external_class AAO:0000046 xsd:string
property_value: external_class TAO:0000007 xsd:string
property_value: external_class VHOG:0000224 xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor https://github.com/cmungall
property_value: http://purl.org/dc/elements/1.1/contributor https://github.com/tmeehan
property_value: IAO:0000232 "This class excludes blood analogues, such as the insect analog of blood. See UBERON:0000179 haemolymphatic fluid." xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string
property_value: source AAO:LAP xsd:string
property_value: source "DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood cells and blood cell development in the animal kingdom. Annual review of cell and developmental biology (2006) " xsd:string
property_value: source http://bgee.unil.ch/
property_value: source ncithesaurus:Blood xsd:string
property_value: source ZFIN:curator xsd:string
property_value: UBPROP:0000001 "A complex mixture of cells suspended in a liquid matrix that delivers nutrients to cells and removes wastes. (Source: BioGlossary, www.Biology-Text.com)[TAO]" xsd:string
property_value: UBPROP:0000001 "Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[AAO]" xsd:string
property_value: UBPROP:0000002 "relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO]" xsd:string
property_value: UBPROP:0000003 "Recent findings strongly suggest that the molecular pathways involved in the development and function of blood cells are highly conserved among vertebrates and various invertebrates phyla. (...) There is now good reason to believe that, in vertebrates and invertebrates alike, blood cell lineages diverge from a common type of progenitor cell, the hemocytoblast.[well established][VHOG]" xsd:string
ontology: AAO
ontology: TAO
ontology: VHOG

[Term]
id: UBERON:0000179
name: haemolymphatic fluid
namespace: uberon
def: "Circulating fluid that is part of the hemolymphoid system. Blood, lymph, interstitial fluid or its analogs." []
synonym: "blood or blood analog" RELATED []
synonym: "circulating fluid" RELATED []
xref: CARO:0000081
xref: http://orcid.org/0000-0002-6601-2165
is_a: UBERON:0006314 ! bodily fluid
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string
created_by: cjm
creation_date: 2009-04-08T04:38:19Z

[Term]
id: UBERON:0000310
name: breast
namespace: uberon
def: "The upper ventral region of the torso of an organism." []
subset: pheno_slim
synonym: "mamma" RELATED []
synonym: "mammary part of chest" EXACT []
synonym: "mammary region" EXACT []
xref: BTO:0000149
xref: CALOHA:TS-2083
xref: EV:0100124
xref: FMA:9601
xref: GAID:33
xref: galen:Breast
xref: http://en.wikipedia.org/wiki/Breast
xref: http://linkedlifedata.com/resource/umls/id/C0006141
xref: http://www.snomedbrowser.com/Codes/Details/181131000
xref: MESH:D001940
xref: NCIT:C12971
xref: OpenCyc:Mx4rvVjV7ZwpEbGdrcN5Y29ycA
xref: UMLS:C0006141
is_a: UBERON:0034929 ! external soft tissue zone
property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/6/6e/Closeup_of_female_breast.jpg
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string
property_value: source ncithesaurus:Breast xsd:string
property_value: source "WP,unvetted" xsd:string
property_value: UBPROP:0000008 "The breasts of a female primate's body contain the mammary glands, which secrete milk used to feed infants. Both men and women develop breasts from the same embryological tissues. However, at puberty female sex hormones, mainly estrogens, promote breast development, which does not happen with men. As a result women's breasts become more prominent than men's." xsd:string
has_synonym_type: LATIN

[Term]
id: UBERON:0000456
name: secretion of exocrine gland
namespace: uberon
alt_id: UBERON:0006540
def: "A portion of organism substance that is produced by exocrine glands." []
synonym: "bodily secretion" EXACT []
synonym: "exocrine gland fluid" RELATED []
synonym: "exocrine gland fluid or secretion" RELATED []
synonym: "exocrine gland fluid/secretion" EXACT []
synonym: "exocrine gland secretion" RELATED []
synonym: "external secretion" RELATED []
synonym: "secreted substance" EXACT []
synonym: "secretion" BROAD []
xref: AEO:0001005
xref: BTO:0002977
xref: BTO:0002979
xref: EMAPA:36535
xref: FMA:9675
xref: galen:Secretion
xref: http://linkedlifedata.com/resource/umls/id/C1516992
xref: http://orcid.org/0000-0002-6601-2165
xref: MA:0002504
xref: MESH:D012634
xref: NCIT:C34062
xref: UMLS:C1516992
is_a: UBERON:0000463 ! organism substance
property_value: external_ontology "BTO" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string
property_value: source ncithesaurus:Exocrine_Gland_Fluid_or_Secretion xsd:string
property_value: UBPROP:0000012 "BTO has two distunct classes, with exocrine glandular secretion a subtype of secretion - however, all examples in BTO directly under secretion appear to be exocrine gland secretions" xsd:string

[Term]
id: UBERON:0000463
name: organism substance
namespace: uberon
def: "Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body." []
subset: pheno_slim
subset: upper_level
synonym: "body fluid or substance" EXACT []
synonym: "body substance" EXACT []
synonym: "organism substance" EXACT []
synonym: "portion of body substance" EXACT []
synonym: "portion of organism substance" EXACT []
xref: AAO:0010839
xref: AEO:0000004
xref: BILA:0000004
xref: CALOHA:TS-2101
xref: CARO:0000004
xref: EHDAA2:0003004
xref: EMAPA:35178
xref: FBbt:00007019
xref: FMA:9669
xref: galen:BodySubstance
xref: HAO:0000004
xref: http://orcid.org/0000-0001-9114-8737
xref: MA:0002450
xref: NCIT:C13236
xref: SPD:0000008
xref: TAO:0001487
xref: TGMA:0001824
xref: VHOG:0001726
xref: XAO:0004001
xref: ZFA:0001487
is_a: UBERON:0000465 ! material anatomical entity
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string

[Term]
id: UBERON:0000465
name: material anatomical entity
namespace: uberon
def: "Anatomical entity that has mass." []
subset: upper_level
xref: AAO:0010264
xref: AEO:0000006
xref: BILA:0000006
xref: CARO:0000006
xref: EHDAA2:0003006
xref: FBbt:00007016
xref: FMA:67165
xref: HAO:0000006
xref: http://orcid.org/0000-0001-9114-8737
xref: TAO:0001836
xref: TGMA:0001826
xref: VHOG:0001721
is_a: UBERON:0001062 ! anatomical entity
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string

[Term]
id: UBERON:0000473
name: testis
namespace: uberon
alt_id: UBERON:0002117
def: "A gonad of a male animal. A gonad produces and releases sperm." []
subset: efo_slim
subset: organ_slim
subset: pheno_slim
subset: uberon_slim
subset: vertebrate_core
synonym: "gonad of male genitalia" EXACT []
synonym: "gonad of male reproductive system" EXACT []
synonym: "male gonad" EXACT []
synonym: "orchis" RELATED []
synonym: "testes" RELATED []
synonym: "testicle" EXACT []
synonym: "testiculus" RELATED []
xref: AAO:0000606
xref: BILA:0000124
xref: BSA:0000085
xref: BTO:0001363
xref: CALOHA:TS-1030
xref: EFO:0000984
xref: EHDAA2:0002007
xref: EHDAA:8146
xref: EMAPA:17972
xref: EV:0100102
xref: FBbt:00004928
xref: FMA:7210
xref: GAID:396
xref: galen:Testis
xref: HAO:0001007
xref: http://en.wikipedia.org/wiki/Testis
xref: http://linkedlifedata.com/resource/umls/id/C0039597
xref: http://orcid.org/0000-0002-6601-2165
xref: http://www.snomedbrowser.com/Codes/Details/181431007
xref: MA:0000411
xref: MAT:0000132
xref: MESH:D013737
xref: MIAA:0000132
xref: NCIT:C12412
xref: OBOL:automatic
xref: OpenCyc:Mx4rvVjM25wpEbGdrcN5Y29ycA
xref: TAO:0000598
xref: UMLS:C0039597
xref: VHOG:0000252
xref: WBbt:0006794
xref: XAO:0000157
xref: ZFA:0000598
is_a: UBERON:0000991 ! gonad
property_value: date_retrieved "2012-08-14" xsd:string
property_value: date_retrieved "2012-09-17" xsd:string
property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/c/c3/Gray1144.png
property_value: external_class TAO:0000598 xsd:string
property_value: external_class VHOG:0000252 xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string
property_value: source "DOI:10.1093/icb/icm052 Extavour CGM, Gray anatomy: phylogenetic patterns of somatic gonad structures and reproductive strategies across the Bilateria. Integrative and Comparative Biology (2007), DOI:10.1146/annurev.cellbio.042308.13350 DeFalco T and Capel B, Gonad morphogenesis in vertebrates: divergent means to a convergent end. Annual review of cell and developmental biology (2009)" xsd:string
property_value: source http://bgee.unil.ch/
property_value: source ISBN-10:0123971756 xsd:string
property_value: source ncithesaurus:Testis xsd:string
property_value: source ZFIN:curator xsd:string
property_value: taxon NCBITaxon:40674 xsd:string
property_value: UBPROP:0000001 "Male reproductive organ.[TAO]" xsd:string
property_value: UBPROP:0000003 "(...) while it is likely that Urbilateria lacked a complex somatic reproductive system, it is at present impossible to speculate on whether or not it possessed a true gonad, let alone any other somatic adaptations for reproduction (reference 1); Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved (reference 2).[uncertain][VHOG]" xsd:string
property_value: UBPROP:0000007 "testicular" xsd:string
property_value: UBPROP:0000008 "The testes are descended in metatherian and eutherian mammals, first transabdominally, then inguinoscrotally" xsd:string
has_synonym_type: LATIN
has_synonym_type: PLURAL
ontology: TAO
ontology: VHOG

[Term]
id: UBERON:0000479
name: tissue
namespace: uberon
def: "Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation." []
subset: pheno_slim
subset: upper_level
synonym: "portion of tissue" EXACT []
synonym: "simple tissue" NARROW []
synonym: "tissue portion" EXACT []
xref: AAO:0000607
xref: AAO:0010054
xref: AEO:0000043
xref: BILA:0000043
xref: birnlex:19
xref: CALOHA:TS-2090
xref: CARO:0000043
xref: EHDAA2:0003043
xref: EMAPA:35868
xref: FBbt:00007003
xref: FMA:9637
xref: galen:Tissue
xref: HAO:0000043
xref: http://linkedlifedata.com/resource/umls/id/C0040300
xref: MA:0003002
xref: MESH:D014024
xref: NCIT:C12801
xref: TAO:0001477
xref: TGMA:0001844
xref: UMLS:C0040300
xref: VHOG:0001757
xref: WBbt:0005729
xref: XAO:0003040
xref: ZFA:0001477
is_a: UBERON:0010000 ! multicellular anatomical structure
property_value: IAO:0000116 "changed label and definition to reflect CARO2" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string
property_value: source ncithesaurus:Tissue xsd:string

[Term]
id: UBERON:0000481
name: multi-tissue structure
namespace: uberon
def: "Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types." []
subset: upper_level
synonym: "multi-tissue structures" RELATED []
xref: AAO:0010048
xref: AEO:0000055
xref: BILA:0000055
xref: CARO:0000055
xref: EHDAA2:0003055
xref: FBbt:00007010
xref: HAO:0000055
xref: http://orcid.org/0000-0001-9114-8737
xref: TAO:0001488
xref: TGMA:0001847
xref: VHOG:0001762
xref: XAO:0003037
xref: ZFA:0001488
is_a: UBERON:0010000 ! multicellular anatomical structure
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string
has_synonym_type: PLURAL

[Term]
id: UBERON:0000945
name: stomach
namespace: uberon
def: "An expanded region of the vertebrate alimentary tract that serves as a food storage compartment and digestive organ. A stomach is lined, in whole or in part by a glandular epithelium." []
subset: efo_slim
subset: major_organ
subset: organ_slim
subset: pheno_slim
subset: uberon_slim
subset: vertebrate_core
synonym: "anterior intestine" RELATED []
synonym: "gaster" RELATED []
synonym: "mesenteron" RELATED []
synonym: "stomach chamber" NARROW []
synonym: "ventriculus" RELATED []
xref: AAO:0000579
xref: ANISEED:1235297
xref: BTO:0001307
xref: CALOHA:TS-0980
xref: EFO:0000837
xref: EHDAA2:0001915
xref: EHDAA:2993
xref: EMAPA:17021
xref: EV:0100070
xref: FMA:7148
xref: GAID:293
xref: galen:Stomach
xref: http://en.wikipedia.org/wiki/Stomach
xref: http://linkedlifedata.com/resource/umls/id/C0038351
xref: http://www.snomedbrowser.com/Codes/Details/181246003
xref: https://orcid.org/0000-0002-6601-2165
xref: ISBN10:0073040584
xref: MA:0000353
xref: MAT:0000051
xref: MESH:A03.492.766
xref: MIAA:0000051
xref: NCIT:C12391
xref: OpenCyc:Mx4rvVjlqpwpEbGdrcN5Y29ycA
xref: TAO:0002121
xref: UMLS:C0038351
xref: VHOG:0000408
xref: XAO:0000128
is_a: UBERON:0004921 ! subdivision of digestive tract
property_value: date_retrieved "2012-06-20" xsd:string
property_value: date_retrieved "2012-09-17" xsd:string
property_value: depicted:by Stomach:diagram.svg
property_value: external_class AAO:0000579 xsd:string
property_value: external_class VHOG:0000408 xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string
property_value: source AAO:EJS xsd:string
property_value: source "DOI:10.1046/j.1525-142x.2000.00076.x Smith DM, Grasty RC, Theodosiou NA, Tabin CJ, Nascone-Yoder NM, Evolutionary relationships between the amphibian, avian, and mammalian stomachs. Evolution and development (2000)" xsd:string
property_value: source http://bgee.unil.ch/
property_value: source ncithesaurus:Stomach xsd:string
property_value: source WP:Stomach#In_other_animals xsd:string
property_value: UBPROP:0000001 "Portion of alimentary canal with increased circular and longitudinal smooth muscle. Bounded posteriorly by the pyloric sphincter. Mucosal lining has increased folding.[AAO]" xsd:string
property_value: UBPROP:0000003 "It appears that the stomach has an ancient origin. The stomach first appears in the fish lineage. The prevertebrate chordates do not have a true stomach, whereas the cartilaginous and bony fish do. Although most fish do have a true stomach, some fish species appear to have lost the stomach secondarily. The remaining vertebrate lineages do have a true stomach (at least in the adult animal), although there is great variation in the size and shape of the stomach.[well established][VHOG]" xsd:string
property_value: UBPROP:0000008 "We restrict this to the vertebrate specific structure - see the grouping class 'food storage organ' for analogous structures in other species. Teleosts: Zebrafish is functionally stomach-less, but may retain ontogenic footprint. Although the precise shape and size of the stomach varies widely among different vertebrates, the relative positions of the oesophageal and duodenal openings remain relatively constant. As a result, the organ always curves somewhat to the left before curving back to meet the pyloric sphincter. However, lampreys, hagfishes, chimaeras, lungfishes, and some teleost fish have no stomach at all, with the oesophagus opening directly into the intestine. The gastric lining is usually divided into two regions, an anterior portion lined by fundic glands, and a posterior with pyloric glands. Cardiac glands are unique to mammals, and even then are absent in a number of species. The distributions of these glands vary between species, and do not always correspond with the same regions as in man. Furthermore, in many non-human mammals, a portion of the stomach anterior to the cardiac glands is lined with epithelium essentially identical to that of the oesophagus. Ruminants, in particular, have a complex stomach, the first three chambers of which are all lined with oesophageal mucosa" xsd:string
has_synonym_type: LATIN
ontology: AAO
ontology: VHOG

[Term]
id: UBERON:0000955
name: brain
namespace: uberon
def: "The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP]." []
subset: cumbo
subset: efo_slim
subset: major_organ
subset: pheno_slim
subset: uberon_slim
subset: vertebrate_core
synonym: "encephalon" RELATED []
synonym: "suprasegmental levels of nervous system" RELATED []
synonym: "suprasegmental structures" RELATED []
synonym: "synganglion" RELATED []
synonym: "the brain" RELATED []
xref: AAO:0010478
xref: ABA:Brain
xref: BAMS:Br
xref: BAMS:Brain
xref: BILA:0000135
xref: birnlex:796
xref: BTO:0000142
xref: CALOHA:TS-0095
xref: DHBA:10155
xref: EFO:0000302
xref: EHDAA2:0000183
xref: EHDAA:2641
xref: EHDAA:6485
xref: EMAPA:16894
xref: EV:0100164
xref: FBbt:00005095
xref: FMA:50801
xref: GAID:571
xref: galen:Brain
xref: HBA:4005
xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=21
xref: http://en.wikipedia.org/wiki/Brain
xref: http://linkedlifedata.com/resource/umls/id/C0006104
xref: http://linkedlifedata.com/resource/umls/id/C1269537
xref: http://www.snomedbrowser.com/Codes/Details/258335003
xref: https://github.com/obophenotype/uberon/issues/300
xref: MA:0000168
xref: MAT:0000098
xref: MBA:8
xref: MBA:997
xref: MESH:D001921
xref: MIAA:0000098
xref: NCIT:C12439
xref: NeuroNames:21
xref: OpenCyc:Mx4rvVjT65wpEbGdrcN5Y29ycA
xref: PBA:3999
xref: TAO:0000008
xref: UMLS:C0006104
xref: UMLS:C1269537
xref: VHOG:0000157
xref: XAO:0000010
xref: ZFA:0000008
is_a: UBERON:0000062 ! organ
property_value: date_retrieved "2012-06-20" xsd:string
property_value: date_retrieved "2012-08-14" xsd:string
property_value: date_retrieved "2012-09-17" xsd:string
property_value: external_class AAO:0010478 xsd:string
property_value: external_class TAO:0000008 xsd:string
property_value: external_class VHOG:0000157 xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor https://github.com/cmungall
property_value: IAO:0000116 "requires review for applicability to invertebrate structures, e.g. synganglion" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string
property_value: source AAO:BJB xsd:string
property_value: source Cumbo:terms
property_value: source http://bgee.unil.ch/
property_value: source "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165" xsd:string
property_value: source ncithesaurus:Brain xsd:string
property_value: source NIFSTD:birnlex_796 xsd:string
property_value: source ZFIN:curator xsd:string
property_value: UBPROP:0000001 "Cavitated compound organ which is comprised of gray and white matter and surrounds the cerebral ventricular system.[TAO]" xsd:string
property_value: UBPROP:0000001 "Part of the central nervous system situated within the cranium and composed of both nerve cell bodies and nerve fibers.[AAO]" xsd:string
property_value: UBPROP:0000001 "The part of the central nervous system contained within the cranium, comprising the forebrain, midbrain, hindbrain, and metencephalon. It is derived from the anterior part of the embryonic neural tube (or the encephalon). Does not include retina. (CUMBO)" xsd:string
property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG]" xsd:string
ontology: AAO
ontology: TAO
ontology: VHOG

[Term]
id: UBERON:0000970
name: eye
namespace: uberon
def: "An organ that detects light." []
subset: efo_slim
subset: functional_classification
subset: major_organ
subset: organ_slim
subset: uberon_slim
synonym: "light-detecting organ" RELATED []
synonym: "visual apparatus" RELATED []
xref: BILA:0000017
xref: BTO:0000439
xref: CALOHA:TS-0309
xref: EFO:0000827
xref: EV:0100336
xref: FBbt:00005162
xref: GAID:69
xref: http://en.wikipedia.org/wiki/Eye
xref: https://orcid.org/0000-0002-6601-2165
xref: MAT:0000140
xref: MESH:D005123
xref: MIAA:0000140
xref: OpenCyc:Mx4rvViTvpwpEbGdrcN5Y29ycA
is_a: UBERON:0000020 ! sense organ
property_value: IAO:0000232 "This class encompasses a variety of light-detecting structures from different phyla with no implication of homology, from the compound insect eye to the vertebrate camera-type eye (distinct classes are provided for each)" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string
property_value: UBPROP:0000007 "ocular" xsd:string
property_value: UBPROP:0000007 "optic" xsd:string
property_value: UBPROP:0000010 "Note that whilst this is classified as an organ, it is in fact more of a unit composed of different structures: in Drosophila, it includes the interommatidial bristle as a part; we consider here the vertebrate eye to include the eyeball/eye proper as a part, with the eye having as parts (when present): eyelids, conjuctiva," xsd:string

[Term]
id: UBERON:0000977
name: pleura
namespace: uberon
def: "The invaginated serous membrane that surrounds the lungs (the visceral portion) and lines the walls of the pleural cavity (parietal portion)." []
subset: efo_slim
subset: pheno_slim
subset: uberon_slim
synonym: "pleura" RELATED []
synonym: "pleural tissue" RELATED []
synonym: "wall of pleural sac" EXACT []
xref: BTO:0001791
xref: CALOHA:TS-2081
xref: EFO:0001980
xref: EMAPA:16775
xref: EV:0100044
xref: FMA:9583
xref: GAID:360
xref: http://en.wikipedia.org/wiki/Pleura
xref: http://linkedlifedata.com/resource/umls/id/C0032225
xref: http://www.snomedbrowser.com/Codes/Details/181609007
xref: https://github.com/obophenotype/uberon/issues/1231
xref: ISBN:0-683-40008-8
xref: MA:0000433
xref: MESH:D010994
xref: MP:0010820
xref: NCIT:C12469
xref: OpenCyc:Mx4rv3zwLZwpEbGdrcN5Y29ycA
xref: Pulmonary:pleurae
xref: UBERON:cjm
xref: UMLS:C0032225
xref: VHOG:0000394
is_a: UBERON:0000042 ! serous membrane
property_value: date_retrieved "2012-09-17" xsd:string
property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/a/ab/Gray965.png
property_value: external_class VHOG:0000394 xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string
property_value: RO:0002175 NCBITaxon:8782
property_value: source BGEE:AN xsd:string
property_value: source http://bgee.unil.ch/
property_value: source ISBN10:0124020607 xsd:string
property_value: source ISBN:978-0030223693 xsd:string
property_value: source ncithesaurus:Pleural_Tissue xsd:string
property_value: UBPROP:0000001 "The serous membrane that covers the lungs and lines the pleural cavity. [Kaufman_MH_and_Bard_JBL, The_anatomical_basis_of_mouse_development_(1999)_San_Diego:_Academic_Press, p.264][VHOG]" xsd:string
property_value: UBPROP:0000007 "pleural" xsd:string
property_value: UBPROP:0000012 "In MA, is_a cavity lining (which we equate to parietal). In FMA, is_a (viscous) serous membrane (which includes mesothelium plus connective tissue). Note the MA structure should probably be associated with the mesothelium of pleura in FMA. JB/EHDAA2 argues the term 'pleura' is best used for the mesothelial lining (thus excluding connective tissue). See https://github.com/obophenotype/uberon/issues/86" xsd:string
ontology: VHOG

[Term]
id: UBERON:0000989
name: penis
namespace: uberon
def: "A intromittent organ in certain biologically male organisms. In placental mammals, this also serves as the organ of urination" []
subset: efo_slim
subset: organ_slim
subset: pheno_slim
subset: uberon_slim
synonym: "penes" RELATED []
synonym: "phallus" RELATED []
xref: BTO:0000405
xref: CALOHA:TS-0758
xref: EFO:0000987
xref: EHDAA2:0001433
xref: EHDAA:9380
xref: EMAPA:18682
xref: EMAPA_RETIRED:18996
xref: EV:0100107
xref: FMA:9707
xref: GAID:389
xref: galen:Penis
xref: http://en.wikipedia.org/wiki/Penis
xref: http://linkedlifedata.com/resource/umls/id/C0030851
xref: http://orcid.org/0000-0002-6601-2165
xref: http://www.snomedbrowser.com/Codes/Details/265793009
xref: ISBN:0-683-40008-8
xref: MA:0000408
xref: MAT:0000186
xref: MESH:D010413
xref: MIAA:0000186
xref: MP:0005187
xref: NCIT:C12409
xref: OpenCyc:Mx4rvVjkCZwpEbGdrcN5Y29ycA
xref: UMLS:C0030851
xref: VHOG:0000727
is_a: UBERON:0008811 ! intromittent organ
property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/8/87/Labelled_flaccid_penis.jpg
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string
property_value: source ncithesaurus:Penis xsd:string
property_value: source "WP" xsd:string
property_value: UBPROP:0000007 "penile" xsd:string
property_value: UBPROP:0000007 "phallic" xsd:string
property_value: UBPROP:0000008 "Most male birds (e.g., roosters and turkeys) have a cloaca (also present on the female), but not a penis. Among bird species with a penis are paleognathes (tinamous and ratites), Anatidae (ducks, geese and swans), and a very few other species (such as flamingoes). A bird penis is different in structure from mammal penises, being an erectile expansion of the cloacal wall and being erected by lymph, not blood. It is usually partially feathered and in some species features spines and brush-like filaments, and in flaccid state curls up inside the cloaca" xsd:string
has_synonym_type: PLURAL

[Term]
id: UBERON:0000991
name: gonad
namespace: uberon
def: "Reproductive organ that produces and releases eggs (ovary) or sperm (testis)." []
subset: major_organ
subset: organ_slim
subset: pheno_slim
subset: uberon_slim
subset: vertebrate_core
synonym: "gonada" EXACT []
synonym: "gonads" RELATED []
xref: AAO:0000213
xref: BILA:0000123
xref: BSA:0000079
xref: BTO:0000534
xref: EMAPA:17383
xref: FBbt:00004858
xref: FMA:18250
xref: GAID:368
xref: HAO:0000379
xref: http://en.wikipedia.org/wiki/Gonad
xref: http://linkedlifedata.com/resource/umls/id/C0018067
xref: http://www.snomedbrowser.com/Codes/Details/304623008
xref: ISBN:0140512888
xref: MA:0002420
xref: MESH:D006066
xref: NCIT:C12725
xref: OpenCyc:Mx4rwQvdiZwpEbGdrcN5Y29ycA
xref: TAO:0000413
xref: UMLS:C0018067
xref: VHOG:0000397
xref: WBbt:0005175
xref: XAO:0003146
xref: ZFA:0000413
xref: ZFIN:curator
is_a: UBERON:0003133 ! reproductive organ
property_value: date_retrieved "2012-06-20" xsd:string
property_value: date_retrieved "2012-08-14" xsd:string
property_value: date_retrieved "2012-09-17" xsd:string
property_value: external_class AAO:0000213 xsd:string
property_value: external_class TAO:0000413 xsd:string
property_value: external_class VHOG:0000397 xsd:string
property_value: external_ontology "FMA" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string
property_value: source AAO:BJB xsd:string
property_value: source "DOI:10.1146/annurev.cellbio.042308.13350 DeFalco T, Capel B, Gonad morphogenesis in vertebrates: divergent means to a convergent end. Annual review of cell and developmental biology (2009)" xsd:string
property_value: source http://bgee.unil.ch/
property_value: source ncithesaurus:Gonad xsd:string
property_value: source ZFIN:curator xsd:string
property_value: UBPROP:0000001 "Anatomical structure which produces gametes as well as certain sex hormones controlled by the pituitary gonadotropins.[AAO]" xsd:string
property_value: UBPROP:0000001 "The part of the reproductive system that produces and releases eggs (ovary) or sperm (testis).[TAO]" xsd:string
property_value: UBPROP:0000003 "Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved.[uncertain][VHOG]" xsd:string
property_value: UBPROP:0000007 "gonadal" xsd:string
property_value: UBPROP:0000012 "FMA xref is a 'general anatomical term'" xsd:string
has_synonym_type: PLURAL
ontology: AAO
ontology: TAO
ontology: VHOG

[Term]
id: UBERON:0000992
name: ovary
namespace: uberon
def: "the gonad of a female organism which contains germ cells" []
subset: efo_slim
subset: organ_slim
subset: pheno_slim
subset: uberon_slim
subset: vertebrate_core
synonym: "animal ovary" EXACT []
synonym: "female gonad" EXACT []
synonym: "female organism genitalia gonad" EXACT []
synonym: "female organism genitalia gonada" EXACT []
synonym: "female organism reproductive system gonad" EXACT []
synonym: "female organism reproductive system gonada" EXACT []
synonym: "female reproductive system gonad" EXACT []
synonym: "female reproductive system gonada" EXACT []
synonym: "genitalia of female organism gonad" EXACT []
synonym: "genitalia of female organism gonada" EXACT []
synonym: "gonad of female organism genitalia" EXACT []
synonym: "gonad of female organism reproductive system" EXACT []
synonym: "gonad of female reproductive system" EXACT []
synonym: "gonad of genitalia of female organism" EXACT []
synonym: "gonad of reproductive system of female organism" EXACT []
synonym: "gonada of female organism genitalia" EXACT []
synonym: "gonada of female organism reproductive system" EXACT []
synonym: "gonada of female reproductive system" EXACT []
synonym: "gonada of genitalia of female organism" EXACT []
synonym: "gonada of reproductive system of female organism" EXACT []
synonym: "ovaries" RELATED []
synonym: "ovarium" RELATED []
synonym: "ovum-producing ovary" EXACT []
synonym: "reproductive system of female organism gonad" EXACT []
synonym: "reproductive system of female organism gonada" EXACT []
xref: AAO:0000371
xref: BILA:0000125
xref: BSA:0000080
xref: BTO:0000975
xref: CALOHA:TS-0730
xref: EFO:0000973
xref: EHDAA2:0001360
xref: EHDAA:8124
xref: EMAPA:17962
xref: EV:0100111
xref: FBbt:00004865
xref: FMA:7209
xref: GAID:367
xref: GO:0061039
xref: http://en.wikipedia.org/wiki/Ovary
xref: http://linkedlifedata.com/resource/umls/id/C0029939
xref: http://www.snomedbrowser.com/Codes/Details/181464007
xref: ISBN:0-683-40008-8
xref: MA:0000384
xref: MESH:D010053
xref: MIAA:0000125
xref: MP:0001126
xref: NCIT:C12404
xref: OBOL:automatic
xref: OpenCyc:Mx4rvVi9QJwpEbGdrcN5Y29ycA
xref: TAO:0000403
xref: UMLS:C0029939
xref: VHOG:0000251
xref: XAO:0000258
xref: ZFA:0000403
is_a: UBERON:0000991 ! gonad
property_value: date_retrieved "2012-06-20" xsd:string
property_value: date_retrieved "2012-08-14" xsd:string
property_value: date_retrieved "2012-09-17" xsd:string
property_value: depicted:by Female:anatomy.png
property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/d/d4/Gray589.png
property_value: external_class AAO:0000371 xsd:string
property_value: external_class TAO:0000403 xsd:string
property_value: external_class VHOG:0000251 xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string
property_value: source AAO:BJB xsd:string
property_value: source "DOI:10.1093/icb/icm052 Extavour CGM, Gray anatomy: phylogenetic patterns of somatic gonad structures and reproductive strategies across the Bilateria. Integrative and Comparative Biology (2007), DOI:10.1146/annurev.cellbio.042308.13350 DeFalco T and Capel B, Gonad morphogenesis in vertebrates: divergent means to a convergent end. Annual review of cell and developmental biology (2009)" xsd:string
property_value: source http://bgee.unil.ch/
property_value: source ncithesaurus:Ovary xsd:string
property_value: source "WP" xsd:string
property_value: source ZFIN:curator xsd:string
property_value: UBPROP:0000001 "Either of paired female reproductive organs involved in production of ova and female sex hormones.[AAO]" xsd:string
property_value: UBPROP:0000001 "Female reproductive organ.[TAO]" xsd:string
property_value: UBPROP:0000003 "(...) while it is likely that Urbilateria lacked a complex somatic reproductive system, it is at present impossible to speculate on whether or not it possessed a true gonad, let alone any other somatic adaptations for reproduction (reference 1); Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved (reference 2).[uncertain][VHOG]" xsd:string
property_value: UBPROP:0000007 "ovarian" xsd:string
property_value: UBPROP:0000008 "Ovaries of some kind are found in the female reproductive system of many animals that employ sexual reproduction, including invertebrates. However, they develop in a very different way in most invertebrates than they do in vertebrates, and are not truly homologous. Many of the features found in human ovaries are common to all vertebrates, including the presence of follicular cells, tunica albuginea, and so on. However, many species produce a far greater number of eggs during their lifetime than do humans, so that, in fish and amphibians, there may be hundreds, or even millions of fertile eggs present in the ovary at any given time. In these species, fresh eggs may be developing from the germinal epithelium throughout life. Corpora lutea are found only in mammals, and in some elasmobranch fish; in other species, the remnants of the follicle are quickly resorbed by the ovary. In birds, reptiles, and monotremes, the egg is relatively large, filling the follicle, and distorting the shape of the ovary at maturity. Amphibians and reptiles have no ovarian medulla; the central part of the ovary is a hollow, lymph-filled space. The ovary of teleosts is also often hollow, but in this case, the eggs are shed into the cavity, which opens into the oviduct. Although most normal female vertebrates have two ovaries, this is not the case in all species. In birds and platypuses, the right ovary never matures, so that only the left is functional. In some elasmobranchs, the reverse is true, with only the right ovary fully developing. In the primitive jawless fish, and some teleosts, there is only one ovary, formed by the fusion of the paired organs in the embryo" xsd:string
has_synonym_type: LATIN
has_synonym_type: PLURAL
has_synonym_type: SENSU
ontology: AAO
ontology: TAO
ontology: VHOG

[Term]
id: UBERON:0000995
name: uterus
namespace: uberon
def: "the female muscular organ of gestation in which the developing embryo or fetus is nourished until birth" []
subset: efo_slim
subset: organ_slim
subset: pheno_slim
subset: uberon_slim
xref: BTO:0001424
xref: CALOHA:TS-1102
xref: EFO:0000975
xref: EMAPA:29915
xref: EV:0100113
xref: FMA:17558
xref: GAID:172
xref: galen:Uterus
xref: http://en.wikipedia.org/wiki/Uterus
xref: http://linkedlifedata.com/resource/umls/id/C0042149
xref: http://www.snomedbrowser.com/Codes/Details/181452004
xref: MA:0000389
xref: MAT:0000127
xref: MESH:D014599
xref: MGI:csmith
xref: MIAA:0000127
xref: MP:0001120
xref: NCIT:C12405
xref: OpenCyc:Mx4rvViojJwpEbGdrcN5Y29ycA
xref: UMLS:C0042149
xref: VHOG:0001137
is_a: UBERON:0013515 ! subdivision of oviduct
property_value: date_retrieved "2012-09-17" xsd:string
property_value: depicted:by Female:anatomy.png
property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/6/6a/Female_reproductive_system_lateral_nolabel.png
property_value: external_class VHOG:0001137 xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string
property_value: source http://bgee.unil.ch/
property_value: source http://medical-dictionary.thefreedictionary.com/uterus
property_value: source "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.678" xsd:string
property_value: source ncithesaurus:Uterus xsd:string
property_value: UBPROP:0000001 "The hollow muscular organ in female mammals in which the blastocyst normally becomes embedded and in which the developing embryo and fetus is nourished. Its cavity opens into the vagina below and into a uterine tube on either side. [TFD][VHOG]" xsd:string
property_value: UBPROP:0000003 "An infundibulum, uterine tube, uterus, and vagina also differentiate along the oviducts of eutherian mammals.[well established][VHOG]" xsd:string
property_value: UBPROP:0000007 "uterine" xsd:string
property_value: UBPROP:0000008 "Most animals that lay eggs, such as birds and reptiles, have an oviduct instead of a uterus. In monotremes, mammals which lay eggs and include the platypus, either the term uterus or oviduct is used to describe the same organ, but the egg does not develop a placenta within the mother and thus does not receive further nourishment after formation and fertilization. Marsupials have two uteruses, each of which connect to a lateral vagina and which both use a third, middle 'vagina' which functions as the birth canal. Marsupial embryos form a choriovitelline 'placenta' (which can be thought of as something between a monotreme egg and a 'true' placenta), in which the egg's yolk sac supplies a large part of the embryo's nutrition but also attaches to the uterine wall and takes nutrients from the mother's bloodstream." xsd:string
property_value: UBPROP:0000011 "Two uteruses usually form initially in a female fetus, and in placental mammals they may partially or completely fuse into a single uterus depending on the species. In many species with two uteruses, only one is functional. Humans and other higher primates such as chimpanzees, along with horses, usually have a single completely fused uterus, although in some individuals the uteruses may not have completely fused [Wikipedia:Uterus]" xsd:string
ontology: VHOG

[Term]
id: UBERON:0000996
name: vagina
namespace: uberon
def: "A fibromuscular tubular tract leading from the uterus to the exterior of the body in female placental mammals and marsupials, or to the cloaca in female birds, monotremes, and some reptiles[WP]." []
subset: efo_slim
subset: pheno_slim
subset: uberon_slim
synonym: "distal oviductal region" RELATED []
synonym: "distal portion of oviduct" RELATED []
synonym: "vaginae" RELATED []
xref: BTO:0000243
xref: CALOHA:TS-1103
xref: EFO:0000976
xref: EMAPA:18986
xref: EV:0100117
xref: FMA:19949
xref: GAID:381
xref: galen:Vagina
xref: http://en.wikipedia.org/wiki/Vagina
xref: http://linkedlifedata.com/resource/umls/id/C0042232
xref: http://orcid.org/0000-0002-6601-2165
xref: http://www.snomedbrowser.com/Codes/Details/181441005
xref: MA:0000394
xref: MAT:0000128
xref: MESH:D014621
xref: MIAA:0000128
xref: NCIT:C12407
xref: OpenCyc:Mx4rvVj1B5wpEbGdrcN5Y29ycA
xref: UMLS:C0042232
xref: VHOG:0001138
is_a: UBERON:0013515 ! subdivision of oviduct
property_value: date_retrieved "2012-09-17" xsd:string
property_value: date_retrieved "2012-11-29" xsd:string
property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/1/1b/Illu_repdt_female.jpg
property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/a/a4/Vaginal_opening_-_english_description.jpg
property_value: external_class FMA:19949 xsd:string
property_value: external_class VHOG:0001138 xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2019-11-22/uberon.owl xsd:string
property_value: source http://bgee.unil.ch/
property_value: source http://medical-dictionary.thefreedictionary.com/vagina
property_value: source "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.688" xsd:string
property_value: source ncithesaurus:Vagina xsd:string
property_value: UBPROP:0000001 "Organ with organ cavity which connects the cervical canal of uterus to the vestibule of vagina.[FMA]" xsd:string
property_value: UBPROP:0000001 "The genital canal in the female, leading from the opening of the vulva to the cervix of the uterus. [TFD][VHOG]" xsd:string
property_value: UBPROP:0000003 "The distal end of the oviducts differentiates as a vagina in Metatheria and Eutheria.[well established][VHOG]" xsd:string
property_value: UBPROP:0000007 "vaginal" xsd:string
property_value: UBPROP:0000011 "'The distal end of the oviducts differentiates as a vagina in Metatheria and Eutheria.' Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective, Third Edition (2001) Orlando Fla.: Harcourt College Publishers, p.688" xsd:string
has_synonym_type: PLURAL
ontology: FMA
ontology: VHOG

[Term]
id: UBERON:0001037
name: strand of hair
namespace: uberon
def: "A filament, mostly protein, that grows from follicles found in the dermis[WP]." []
subset: efo_slim
subset: pheno_slim
subset: uberon_slim
synonym: "coat hair" RELATED []
synonym: "coat/ hair" RELATED []
synonym: "fur" RELATED []
synonym: "hair" EXACT []
synonym: "microchaeta" RELATED []
synonym: "quill" RELATED []
synonym: "setulae" RELATED []
synonym: "vibrissa" RELATED []
synonym: "whisker" RELATED []
xref: BTO:0001501
xref: CALOHA:TS-0430
xref: EFO:0000958
xref: EMAPA:18769
xref: EV:0100157
xref: FMA:53667
xref: GAID:71
xref: http://en.wikipedia.org/wiki/Hair
xref: http://linkedlifedata.com/resource/umls/id/C0018494
xref: http://www.snomedbrowser.com/Codes/Details/361702001
xref: MA:0000155
xref: MAT:0000160
xref: MESH:D006197
xref: MIAA:0000160
xref: NCIT:C32705
xref: OpenCyc:Mx4rvVjOX5wpEbGdrcN5Y29ycA-Mp88EdaAAACgycbRww
xref: UMLS:C0018494
xref: VHOG:0001191
is_a: UBERON:0000021 ! cutaneous appendage
property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/2/25/Gray945.png
property_value: IAO:0000116 "TODO for now we treat vibrissa/whisker as a syonym, but these have different follicles. We could introduce subclasses (see also: Pangolin scales)" xsd:string
property_value: IAO:0000232 "this class defines an individual hair" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string
property_value: source ncithesaurus:Hair xsd:string
has_synonym_type: SENSU

[Term]
id: UBERON:0001052
name: rectum
namespace: uberon
def: "the terminal portion of the intestinal tube, terminating with the anus" []
subset: efo_slim
subset: pheno_slim
subset: uberon_slim
synonym: "intestinum rectum" RELATED []
synonym: "rectal sac" RELATED []
synonym: "terminal portion of intestine" EXACT []
synonym: "terminal portion of large intestine" RELATED []
xref: AAO:0010401
xref: BTO:0001158
xref: CALOHA:TS-1180
xref: EFO:0000848
xref: EHDAA2:0001592
xref: EHDAA:5836
xref: EMAPA:17896
xref: EV:0100081
xref: FMA:14544
xref: GAID:311
xref: galen:Rectum
xref: http://en.wikipedia.org/wiki/Rectum
xref: http://linkedlifedata.com/resource/umls/id/C0034896
xref: http://orcid.org/0000-0002-6601-2165
xref: http://www.snomedbrowser.com/Codes/Details/181261002
xref: ISBN:0-683-40008-8
xref: MA:0000336
xref: MAT:0000050
xref: MESH:A03.492.411.495.767
xref: MIAA:0000050
xref: MP:0000492
xref: NCIT:C12390
xref: OpenCyc:Mx4rvVjaU5wpEbGdrcN5Y29ycA
xref: UMLS:C0034896
xref: VHOG:0001751
xref: XAO:0000238
is_a: UBERON:0004921 ! subdivision of digestive tract
property_value: date_retrieved "2012-09-17" xsd:string
property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/7/75/Anorectum.gif
property_value: external_class VHOG:0001751 xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string
property_value: source http://bgee.unil.ch/
property_value: source ncithesaurus:Rectum xsd:string
property_value: UBPROP:0000001 "The terminal portion of the large intestine between the ileo-pelvic colon and the anus. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]" xsd:string
property_value: UBPROP:0000007 "rectal" xsd:string
property_value: UBPROP:0000008 "In the lungfish, sharks and rays the rectum opens into the cloaca which also receives wastes (urine) from the kidneys and material from the reproductive organs. In bony fish the rectum reaches the outside environment through the anus, which is normally situated just in front the urinary and reproductive openings. However in some fish the digestive tract may be curled back on itself, and in the Electric Eel (Electrophorus electricus) the anus is situated in the fish's throat. -- http://www.earthlife.net/fish/digestion.html" xsd:string
ontology: VHOG

[Term]
id: UBERON:0001062
name: anatomical entity
namespace: uberon
def: "Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species." []
subset: upper_level
xref: AAO:0010841
xref: AEO:0000000
xref: BILA:0000000
xref: birnlex:6
xref: CARO:0000000
xref: EHDAA2:0002229
xref: FBbt:10000000
xref: FBbt_root:00000000
xref: FMA:62955
xref: HAO:0000000
xref: http://linkedlifedata.com/resource/umls/id/C1515976
xref: http://orcid.org/0000-0001-9114-8737
xref: MA:0000001
xref: NCIT:C12219
xref: TAO:0100000
xref: TGMA:0001822
xref: UMLS:C1515976
xref: WBbt:0000100
xref: XAO:0000000
xref: ZFA:0100000
is_a: BFO:0000004 ! independent continuant
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string
property_value: source ncithesaurus:Anatomic_Structure_System_or_Substance xsd:string

[Term]
id: UBERON:0001088
name: urine
namespace: uberon
def: "Excretion that is the output of a kidney" []
subset: efo_slim
subset: pheno_slim
subset: uberon_slim
xref: BTO:0001419
xref: CALOHA:TS-1092
xref: EFO:0001939
xref: EMAPA:36554
xref: ENVO:00002047
xref: FMA:12274
xref: GAID:1189
xref: galen:Urine
xref: http://en.wikipedia.org/wiki/Urine
xref: http://linkedlifedata.com/resource/umls/id/C0042036
xref: https://github.com/geneontology/go-ontology/issues/11025
xref: MA:0002545
xref: MAT:0000058
xref: MESH:D014556
xref: MIAA:0000058
xref: NCIT:C13283
xref: OpenCyc:Mx4rvVjGppwpEbGdrcN5Y29ycA
xref: UMLS:C0042036
is_a: UBERON:0000174 ! excreta
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string
property_value: source ncithesaurus:Urine xsd:string
property_value: UBPROP:0000008 "kidney excreta from some taxa (e.g. in aves) may not be liquid" xsd:string

[Term]
id: UBERON:0001089
name: sweat
namespace: uberon
def: "Secretion produced by a sweat gland." []
subset: pheno_slim
subset: uberon_slim
synonym: "skin exudate" RELATED []
xref: BTO:0001254
xref: ENVO:02000025
xref: FMA:12275
xref: GAID:1172
xref: http://en.wikipedia.org/wiki/Sweat
xref: http://linkedlifedata.com/resource/umls/id/C0038984
xref: MA:0002539
xref: MESH:D013542
xref: NCIT:C13280
xref: OpenCyc:Mx4rvVjJtZwpEbGdrcN5Y29ycA
xref: UMLS:C0038984
is_a: UBERON:0000456 ! secretion of exocrine gland
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string
property_value: source ncithesaurus:Sweat xsd:string

[Term]
id: UBERON:0001155
name: colon
namespace: uberon
def: "Last portion of the large intestine before it becomes the rectum." []
subset: efo_slim
subset: pheno_slim
subset: uberon_slim
subset: vertebrate_core
synonym: "hindgut" RELATED []
synonym: "large bowel" EXACT []
synonym: "posterior intestine" NARROW []
xref: AAO:0010400
xref: BTO:0000269
xref: CALOHA:TS-0158
xref: Colon:(anatomy)
xref: EFO:0000361
xref: EMAPA:18939
xref: EV:0100079
xref: FMA:14543
xref: GAID:309
xref: galen:Colon
xref: http://linkedlifedata.com/resource/umls/id/C0009368
xref: http://orcid.org/0000-0002-6601-2165
xref: http://www.snomedbrowser.com/Codes/Details/302508007
xref: MA:0000335
xref: MAP:0000001
xref: MAT:0000526
xref: MESH:A03.492.411.495.356
xref: NCIT:C12382
xref: OpenCyc:Mx4rvgLEM5wpEbGdrcN5Y29ycA
xref: TAO:0000706
xref: UMLS:C0009368
xref: VHOG:0000648
xref: XAO:0000243
xref: ZFA:0000706
xref: ZFIN:curator
is_a: UBERON:0004921 ! subdivision of digestive tract
property_value: date_retrieved "2012-06-20" xsd:string
property_value: date_retrieved "2012-08-14" xsd:string
property_value: date_retrieved "2012-09-17" xsd:string
property_value: external_class AAO:0010400 xsd:string
property_value: external_class TAO:0000706 xsd:string
property_value: external_class VHOG:0000648 xsd:string
property_value: IAO:0000116 "TODO - abstract this such that it legitimately covers all vertebrates" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string
property_value: source http://bgee.unil.ch/
property_value: source "ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11" xsd:string
property_value: source ncithesaurus:Colon xsd:string
property_value: source UBERON:0001155 xsd:string
property_value: source ZFIN:curator xsd:string
property_value: UBPROP:0000001 "The last portion of the digestive system, it extracts water and salt from solid wastes before they are eliminated from the body.[AAO]" xsd:string
property_value: UBPROP:0000001 "The posterior intestine has short longitudinally arranged epithelial folds which are similar to the colon of higher vertebrates. Wallace et al, 2005.[TAO]" xsd:string
property_value: UBPROP:0000003 "Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG]" xsd:string
property_value: UBPROP:0000007 "colonic" xsd:string
property_value: UBPROP:0000008 "In mammals, the colon consists of four sections: the ascending colon, the transverse colon, the descending colon, and the sigmoid colon[WP]" xsd:string
property_value: UBPROP:0000008 "In zebrafish, the posterior intestine has short longitudinally arranged epithelial folds which are similar to the colon of higher vertebrates[ZFIN]" xsd:string
property_value: UBPROP:0000009 "it extracts water and salt from solid wastes before they are eliminated from the body[WP]" xsd:string
ontology: AAO
ontology: TAO
ontology: VHOG

[Term]
id: UBERON:0001264
name: pancreas
namespace: uberon
def: "An endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating enzymes[GO]." []
subset: efo_slim
subset: major_organ
subset: organ_slim
subset: pheno_slim
subset: uberon_slim
subset: vertebrate_core
xref: AAO:0010112
xref: BTO:0000988
xref: CALOHA:TS-0736
xref: EFO:0000855
xref: EHDAA2:0001367
xref: EHDAA:6893
xref: EMAPA:17503
xref: EV:0100092
xref: FMA:7198
xref: GAID:334
xref: galen:Pancreas
xref: GO:0031016
xref: http://en.wikipedia.org/wiki/Pancreas
xref: http://linkedlifedata.com/resource/umls/id/C0030274
xref: http://www.snomedbrowser.com/Codes/Details/181277001
xref: MA:0000120
xref: MAT:0000075
xref: MESH:D010179
xref: MIAA:0000075
xref: NCIT:C12393
xref: OpenCyc:Mx4rvVimZZwpEbGdrcN5Y29ycA
xref: TAO:0000140
xref: UMLS:C0030274
xref: VHOG:0000050
xref: XAO:0000136
xref: ZFA:0000140
is_a: UBERON:0002075 ! viscus
property_value: date_retrieved "2012-06-20" xsd:string
property_value: date_retrieved "2012-09-17" xsd:string
property_value: depicted:by https://upload.wikimedia.org/wikipedia/commons/7/7e/Blausen_0699_PancreasAnatomy2.png
property_value: external_class AAO:0010112 xsd:string
property_value: external_class VHOG:0000050 xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string
property_value: source AAO:BJB xsd:string
property_value: source "DOI:10.1016/j.crvi.2007.03.006 Madsen OD, Pancreas phylogeny and ontogeny in relation to a 'pancreatic stem cell'. C.R. Biologies (2007)" xsd:string
property_value: source http://bgee.unil.ch/
property_value: source http://www.ncbi.nlm.nih.gov/pubmed/16417468
property_value: source http://www.ncbi.nlm.nih.gov/pubmed/20959416
property_value: source ncithesaurus:Pancreas xsd:string
property_value: UBPROP:0000001 "Organ which secretes a fluid containing enzymes that aid in the digestion of food.[AAO]" xsd:string
property_value: UBPROP:0000003 "In the hagfish and lampreys (our most primitive vertebrate species of today), the first sign of 'a new organ' is found as collections of endocrine cells around the area of the bile duct connection with the duodenum. These endocrine organs are composed of 99% beta cells and 1% somatostatin-producing delta cells. Compared to the more primitive protochordates (e.g. amphioxus), this represents a stage where all previously scattered insulin-producing cells of the intestinal tissue have now quantitatively migrated to found a new organ involved in sensing blood glucose rather than gut glucose. Only later in evolution, the beta cells are joined by exocrine tissue and alpha cells (exemplified by the rat-, rabbit- and elephant-fishes). Finally, from sharks and onwards in evolution, we have the islet PP-cell entering to complete the pancreas.[well established][VHOG]" xsd:string
property_value: UBPROP:0000007 "pancreatic" xsd:string
property_value: UBPROP:0000008 "As a secretory organ serving exocrine and endocrine functions, the pancreas is specific to the vertebrates[PMID:16417468] Hagfishes and lampreys are unique in the complete separation of their endocrine pancreas (islet or- gan) and their exocrine pancreas (50). The endocrine and exocrine pancreas are coassociated in crown gnathostomes (50). In Branchiostoma and Ciona, there is no diverticulum as there is in hagfishes, lampreys, and gnathostomes, only dispersed insulin-secreting cells in the walls of the gastrointestinal tract (51, 52)" xsd:string
property_value: UBPROP:0000008 "The zebrafish does not have a discrete pancreas. Exocrine pancreatic tissue can be found scattered along the intestinal tract. The acinar structure of the exocrine pancreas is very similar to that of mammals and comprises cells with a very dark, basophilic cytoplasm" xsd:string
property_value: UBPROP:0000009 "The mature pancreas of higher vertebrates and mammals comprises two major functional units: the exocrine pancreas, which is responsible for the production of digestive enzymes to be secreted into the gut lumen, and the endocrine pancreas, which has its role in the synthesis of several hormones with key regulatory functions in food uptake and metabolism. The exocrine portion constitutes the majority of the mass of the pancreas, and contains only two different cell types, the secretory acinar cells and the ductular cells. The endocrine portion, which comprises only 1-2% of the total mass, contains five different cell types, which are organized into mixed functional assemblies referred to as the islets of Langerhans" xsd:string
ontology: AAO
ontology: VHOG

[Term]
id: UBERON:0001359
name: cerebrospinal fluid
namespace: uberon
def: "A clear, colorless, bodily fluid, that occupies the subarachnoid space and the ventricular system around and inside the brain and spinal cord." []
subset: efo_slim
subset: pheno_slim
subset: uberon_slim
subset: vertebrate_core
synonym: "cerebral spinal fluid" EXACT []
synonym: "CSF" EXACT []
synonym: "liquor cerebrospinalis" RELATED []
synonym: "spinal fluid" RELATED []
xref: BIRNLEX:1798
xref: BTO:0000237
xref: CALOHA:TS-0130
xref: Cerebrospinal:fluid
xref: EFO:0000329
xref: EHDAA2:0004441
xref: ENVO:02000029
xref: EV:0100311
xref: FMA:20935
xref: GAID:1181
xref: http://linkedlifedata.com/resource/umls/id/C0007806
xref: MA:0002503
xref: MAT:0000499
xref: MESH:A12.207.268
xref: NCIT:C12692
xref: TAO:0002184
xref: UMLS:C0007806
xref: VHOG:0001278
xref: ZFA:0001626
is_a: UBERON:0007779 ! transudate
property_value: date_retrieved "2012-08-14" xsd:string
property_value: date_retrieved "2012-09-17" xsd:string
property_value: external_class TAO:0002184 xsd:string
property_value: external_class VHOG:0001278 xsd:string
property_value: external_ontology "EHDAA2" xsd:string
property_value: external_ontology "FMA" xsd:string
property_value: IAO:0000116 "many sources state the CP as sole producer of CSF, but this is disputed [DOI:10.1007/s11064-015-1581-6]" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2019-11-22/uberon.owl xsd:string
property_value: source BIRNLEX:1798 xsd:string
property_value: source "DOI:10.1021/pr050213t Parada C, Gato A, Bueno D, Mammalian embryonic cerebrospinal fluid proteome has greater apolipoprotein and enzyme pattern complexity than the avian proteome. Journal of Proteome Research (2005)" xsd:string
property_value: source http://bgee.unil.ch/
property_value: source ncithesaurus:Cerebrospinal_Fluid xsd:string
property_value: source ZFIN:curator xsd:string
property_value: UBPROP:0000001 "Portion of organism substance that is a clear fluid that occupies the subarachnoid space and the ventricular system around and inside the brain.[TAO]" xsd:string
property_value: UBPROP:0000003 "In vertebrates, at early stages of Central Nervous System (CNS) development, the architecture of the brain primordium reveals the presence of the cavity of brain vesicles, which is filled by Embryonic Cerebro-Spinal Fluid (E-CSF). (...) Rat and chick E-CSF proteomes are similar, although rat is more complex in certain groups of proteins, e.g., apolipoproteins, which may be involved in the control of neural diversity, and has soluble enzymes present, just like adult human CSF, but unlike chick E-CSF, revealing phylogenetic brain differences between these groups of vertebrates.[uncertain][VHOG]" xsd:string
property_value: UBPROP:0000012 "EHDAA2 models this as developing from CP, which is wrong" xsd:string
property_value: UBPROP:0000012 "the FMA def states that this is subarachnoid spaces only. ZFA def states subarachnoid spaces and brain ventricles, but not SC (and has part_of to brain). Circulation: It circulates from the lateral ventricles to the foramen of Monro (Interventricular foramen), third ventricle, aqueduct of Sylvius (Cerebral aqueduct), fourth ventricle, foramen of Magendie (Median aperture) and foramina of Luschka (Lateral apertures), subarachnoid space over brain and spinal cord. It should be noted that the CSF moves in a pulsatile manner throughout the CSF system with nearly zero net flow. CSF is reabsorbed into venous sinus blood via arachnoid granulations." xsd:string
ontology: TAO
ontology: VHOG

[Term]
id: UBERON:0001560
name: neck of organ
namespace: uberon
subset: non_informative
synonym: "organ neck" EXACT []
xref: FMA:45733
is_a: UBERON:0034944 ! zone of organ
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2019-11-22/uberon.owl xsd:string

[Term]
id: UBERON:0001690
name: ear
namespace: uberon
def: "Sense organ in vertebrates that is specialized for the detection of sound, and the maintenance of balance. Includes the outer ear and middle ear, which collect and transmit sound waves; and the inner ear, which contains the organs of balance and (except in fish) hearing. Also includes the pinna, the visible part of the outer ear, present in some mammals." []
subset: efo_slim
subset: organ_slim
subset: pheno_slim
subset: uberon_slim
synonym: "auditory apparatus" RELATED []
synonym: "auris" RELATED []
xref: AAO:0011014
xref: birnlex:1062
xref: BTO:0000368
xref: CALOHA:TS-1165
xref: EFO:0000826
xref: EHDAA2:0000423
xref: EHDAA:502
xref: EMAPA:16193
xref: EV:0100353
xref: FMA:52780
xref: GAID:62
xref: galen:Ear
xref: GO:0042471
xref: http://en.wikipedia.org/wiki/Ear
xref: http://linkedlifedata.com/resource/umls/id/C0013443
xref: http://linkedlifedata.com/resource/umls/id/C0521421
xref: http://www.snomedbrowser.com/Codes/Details/1910005
xref: MA:0000236
xref: MAT:0000138
xref: MESH:D004423
xref: MIAA:0000138
xref: NCIT:C12394
xref: OpenCyc:Mx4rvViXS5wpEbGdrcN5Y29ycA
xref: OpenCyc:Mx4rvVjL05wpEbGdrcN5Y29ycA
xref: UMLS:C0013443
xref: UMLS:C0521421
xref: VHOG:0000330
xref: XAO:0000189
is_a: UBERON:0000020 ! sense organ
property_value: date_retrieved "2012-09-17" xsd:string
property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/b/b8/Ear.jpg
property_value: external_class VHOG:0000330 xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string
property_value: source "DOI:10.1002/dvdy.20207 Boekhoff-Falk G, Hearing in Drosophila: Development of Johnston's organ and emerging parallels to vertebrate ear development. Developmental Dynamics (2005)" xsd:string
property_value: source http://bgee.unil.ch/
property_value: source http://medical-dictionary.thefreedictionary.com/ear
property_value: source ncithesaurus:Ear xsd:string
property_value: source NIFSTD:birnlex_1062 xsd:string
property_value: UBPROP:0000001 "The organ of hearing and of equilibrium. [TFD][VHOG]" xsd:string
property_value: UBPROP:0000003 "Both vertebrate and invertebrate auditory organs are thought to have evolved from primitive mechanosensors, but the nature of the ancestral structure and the evolutionary trajectories followed in distinct animal lineages remain unknown. In particular, we do not know how many types of mechanosensor existed in the protostome-deuterostome ancestor from which insects and vertebrates evolved or whether the PDA had an auditory organ.[well established][VHOG]" xsd:string
property_value: UBPROP:0000007 "auricular" xsd:string
ontology: VHOG

[Term]
id: UBERON:0001705
name: nail
namespace: uberon
def: "A horn-like keratin structure covering the dorsal aspect of the terminal phalanges of fingers and toes[WP]." []
comment: The nails of humans and the claws are moth are highly similar. Both species have a proximal nail fold, cuticle, nail matrix, nail bed, nail plate, and hyponychium. Distinguishing features are the shape of the nail and the presence of an extended hyponychium in the mouse [PMC3579226]
subset: efo_slim
subset: pheno_slim
subset: uberon_slim
synonym: "claw" NARROW []
synonym: "nail/claw" EXACT []
synonym: "talon" RELATED []
xref: BTO:0001719
xref: CALOHA:TS-2034
xref: EFO:0000956
xref: EMAPA:35580
xref: EV:0100159
xref: FMA:54326
xref: GAID:1320
xref: galen:Nail
xref: http://en.wikipedia.org/wiki/Claw
xref: http://linkedlifedata.com/resource/umls/id/C0027342
xref: http://orcid.org/0000-0002-6601-2165
xref: http://www.snomedbrowser.com/Codes/Details/72651009
xref: https://github.com/obophenotype/uberon/issues/120
xref: MA:0002703
xref: MAT:0000158
xref: MESH:D009262
xref: MIAA:0000158
xref: Nail:(anatomy)
xref: NCIT:C33156
xref: OpenCyc:Mx4rvVjJv5wpEbGdrcN5Y29ycA
xref: UMLS:C0027342
xref: VHOG:0001361
xref: XAO:0003103
is_a: UBERON:0009564 ! distal limb integumentary appendage
property_value: http://purl.org/dc/elements/1.1/contributor https://github.com/cmungall
property_value: http://purl.org/dc/elements/1.1/contributor https://github.com/mellybelly
property_value: IAO:0000232 "Use this class for both the nails of primates and the homologous claws of mammals such as mouse." xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string
property_value: source ncithesaurus:Nail xsd:string
property_value: UBPROP:0000008 "A primate's nail consists of the unguis alone; the subunguis has disappeared" xsd:string
has_synonym_type: SENSU

[Term]
id: UBERON:0001827
name: secretion of lacrimal gland
namespace: uberon
def: "Aqueous substance secreted by the lacrimal gland." []
subset: uberon_slim
synonym: "lacrimal fluid" EXACT []
synonym: "lacrimal gland secretion" EXACT []
synonym: "lacrimal secretion" EXACT []
synonym: "tear" EXACT []
synonym: "tear fluid" RELATED []
synonym: "tears" EXACT []
xref: BTO:0001499
xref: CALOHA:TS-1016
xref: EMAPA:36537
xref: ENVO:02000034
xref: FMA:59756
xref: GAID:1173
xref: galen:Tear
xref: galen:Tears
xref: http://en.wikipedia.org/wiki/Tear
xref: http://linkedlifedata.com/resource/umls/id/C0039409
xref: http://orcid.org/0000-0002-6601-2165
xref: MA:0002508
xref: MESH:D013666
xref: NCIT:C33739
xref: UMLS:C0039409
is_a: UBERON:0000456 ! secretion of exocrine gland
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string
property_value: source ncithesaurus:Tear xsd:string
has_synonym_type: PLURAL

[Term]
id: UBERON:0001836
name: saliva
namespace: uberon
def: "A fluid produced in the oral cavity by salivary glands, typically used in predigestion, but also in other functions." []
subset: uberon_slim
synonym: "sailva normalis" RELATED []
synonym: "saliva atomaris" RELATED []
synonym: "saliva molecularis" RELATED []
synonym: "salivary gland secretion" EXACT []
xref: BTO:0001202
xref: CALOHA:TS-0891
xref: EMAPA:36536
xref: ENVO:02000036
xref: FMA:59862
xref: GAID:1167
xref: galen:Saliva
xref: GO:0046541
xref: http://en.wikipedia.org/wiki/Saliva
xref: http://linkedlifedata.com/resource/umls/id/C0036087
xref: MA:0002507
xref: MAT:0000444
xref: MESH:D012463
xref: NCIT:C13275
xref: OpenCyc:Mx4rvVjJ95wpEbGdrcN5Y29ycA
xref: UMLS:C0036087
is_a: UBERON:0000456 ! secretion of exocrine gland
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string
property_value: source "GO" xsd:string
property_value: source ncithesaurus:Saliva xsd:string
property_value: UBPROP:0000007 "salivary" xsd:string
property_value: UBPROP:0000008 "We classify a wide variety of not necessarily homologous fluids here. In humans, the saliva is a turbid and slightly viscous fluid, generally of an alkaline reaction, and is secreted by the parotid, submaxillary, and sublingual glands. In the mouth the saliva is mixed with the secretion from the buccal glands. In man and many animals, saliva is an important digestive fluid on account of the presence of the peculiar enzyme, ptyalin" xsd:string
has_synonym_type: LATIN

[Term]
id: UBERON:0001913
name: milk
namespace: uberon
def: "An emulsion of fat globules within a fluid that is secreted by the mammary gland during lactation." []
subset: pheno_slim
subset: uberon_slim
synonym: "mammary gland milk" EXACT []
xref: Breast:milk
xref: BTO:0000868
xref: CALOHA:TS-0636
xref: EMAPA:36540
xref: ENVO:02000031
xref: EV:0100126
xref: FMA:62100
xref: GAID:1230
xref: galen:Milk
xref: http://linkedlifedata.com/resource/umls/id/C1511310
xref: http://orcid.org/0000-0002-6601-2165
xref: MA:0002552
xref: MAT:0000056
xref: MESH:A13.622
xref: MIAA:0000056
xref: NCIT:C13401
xref: OpenCyc:Mx4rvVjGZJwpEbGdrcN5Y29ycA
xref: UMLS:C1511310
xref: VHOG:0001263
is_a: UBERON:0006539 ! mammary gland fluid/secretion
property_value: date_retrieved "2012-09-17" xsd:string
property_value: external_class VHOG:0001263 xsd:string
property_value: external_ontology "ncit" xsd:string
property_value: IAO:0000116 "to axiomatize the different forms of mammary gland secretion an ontology of the phases of pregnancy/lactation is required. Using the existing GO def of lactation is circular." xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string
property_value: source http://bgee.unil.ch/
property_value: source "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.224" xsd:string
property_value: source ncithesaurus:Breast_Fluid_or_Secretion xsd:string
property_value: UBPROP:0000003 "The detailed similarities of mammary glands in living monotremes, marsupials, and eutherians argue for a monophyletic origin of these glands, perhaps by the combination of parts of preexisting sebaceous and sweat glands.[well established][VHOG]" xsd:string
property_value: UBPROP:0000012 "ncit:Milk refers specifically to cow milk" xsd:string
ontology: VHOG

[Term]
id: UBERON:0001968
name: semen
namespace: uberon
def: "Organism substance that is composed of sperm cells suspended in seminal fluid." []
subset: pheno_slim
subset: uberon_slim
synonym: "ejaculate" RELATED []
synonym: "sperm" RELATED []
xref: BTO:0001230
xref: CALOHA:TS-0917
xref: EMAPA:31488
xref: FMA:62966
xref: GAID:1169
xref: http://en.wikipedia.org/wiki/Semen
xref: http://linkedlifedata.com/resource/umls/id/C1518159
xref: http://linkedlifedata.com/resource/umls/id/C2756969
xref: http://orcid.org/0000-0002-6601-2165
xref: MA:0002522
xref: MESH:D012661
xref: NCIT:C13277
xref: NCIT:C13713
xref: OpenCyc:Mx4rvgC-zpwpEbGdrcN5Y29ycA
xref: UMLS:C1518159
xref: UMLS:C2756969
is_a: UBERON:0000463 ! organism substance
property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/4/40/Human_semen_in_petri_dish2.jpg
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string
property_value: source ncithesaurus:Male_Genital_System_Fluid_or_Secretion xsd:string
property_value: source ncithesaurus:Semen xsd:string
property_value: UBPROP:0000007 "seminal" xsd:string
property_value: UBPROP:0000008 "Note that in this ontology, semen is defined as the sum of sperm and seminal fluid, where seminal fluid is defined in taxonomically generic way (see comments for UBERON:0006530)." xsd:string

[Term]
id: UBERON:0001969
name: blood plasma
namespace: uberon
def: "The liquid component of blood, in which erythrocytes are suspended." []
subset: efo_slim
subset: pheno_slim
subset: uberon_slim
synonym: "blood plasm" EXACT []
synonym: "plasma" BROAD []
synonym: "portion of blood plasma" EXACT []
synonym: "portion of plasma" BROAD []
xref: Blood:plasma
xref: BTO:0000131
xref: CALOHA:TS-0800
xref: EFO:0001905
xref: EMAPA:35690
xref: FMA:62970
xref: GAID:1178
xref: http://linkedlifedata.com/resource/umls/id/C0032105
xref: http://orcid.org/0000-0002-6601-2165
xref: MA:0002501
xref: MAT:0000052
xref: MESH:D010949
xref: MIAA:0000052
xref: NCIT:C13356
xref: OpenCyc:Mx4rEg4ZYrIbEduAAAAOpmP6tw
xref: UMLS:C0032105
is_a: UBERON:0000179 ! haemolymphatic fluid
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2019-11-22/uberon.owl xsd:string
property_value: source ncithesaurus:Plasma xsd:string

[Term]
id: UBERON:0001970
name: bile
namespace: uberon
def: "vital aqueous secretion of the liver that is formed by hepatocytes and modified down stream by absorptive and secretory properties of the bile duct epithelium." []
subset: pheno_slim
subset: uberon_slim
synonym: "fel" RELATED []
synonym: "gall" RELATED []
xref: BTO:0000121
xref: CALOHA:TS-1172
xref: ENVO:02000023
xref: FMA:62971
xref: GAID:1157
xref: galen:Bile
xref: http://en.wikipedia.org/wiki/Bile
xref: http://linkedlifedata.com/resource/umls/id/C0005388
xref: https://doi.org/10.1002/cphy.c120027
xref: MA:0002513
xref: MESH:D001646
xref: NCIT:C13192
xref: UMLS:C0005388
xref: ZFA:0005857
is_a: UBERON:0000456 ! secretion of exocrine gland
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2019-11-22/uberon.owl xsd:string
property_value: source ncithesaurus:Bile xsd:string
property_value: UBPROP:0000008 "In many species, bile is stored in the gallbladder and upon eating is discharged into the duodenum." xsd:string
property_value: UBPROP:0000009 "aids the process of digestion of lipids in the small intestine" xsd:string
property_value: UBPROP:0000009 "bile salts function to emulsify dietary fats and facilitate their intestinal absorption" xsd:string
property_value: UBPROP:0000009 "elimination of cholesterol" xsd:string
property_value: UBPROP:0000009 "major excretory route for potentially harmful exogenous lipophilic substances" xsd:string
property_value: UBPROP:0000009 "many hormones and pheromones are excreted in bile, and contribute to growth and development of the intestine in some species and provide attractants for the weaning of non-human vertebrates" xsd:string
property_value: UBPROP:0000009 "protects the organism from enteric infections by excreting immune globulin A (IgA), inflammatory cytokines, and stimulating the innate immune system in the intestine" xsd:string

[Term]
id: UBERON:0001977
name: blood serum
namespace: uberon
def: "The portion of blood plasma that excludes clotting factors." []
subset: pheno_slim
subset: uberon_slim
synonym: "serum" EXACT []
xref: BTO:0000133
xref: BTO:0001239
xref: CALOHA:TS-0923
xref: EHDAA2:0004728
xref: EMAPA:35770
xref: FMA:63083
xref: http://linkedlifedata.com/resource/umls/id/C0229671
xref: http://orcid.org/0000-0002-6601-2165
xref: MA:0002502
xref: NCIT:C13325
xref: Serum:(blood)
xref: UMLS:C0229671
is_a: UBERON:0000179 ! haemolymphatic fluid
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string
property_value: source ncithesaurus:Serum xsd:string

[Term]
id: UBERON:0001988
name: feces
namespace: uberon
def: "Portion of semisolid bodily waste discharged through the anus[MW,modified]" []
subset: pheno_slim
subset: uberon_slim
synonym: "cow dung" NARROW []
synonym: "cow pat" NARROW []
synonym: "droppings" RELATED []
synonym: "dung" NARROW []
synonym: "excrement" RELATED []
synonym: "excreta" BROAD []
synonym: "faeces" EXACT []
synonym: "fecal material" EXACT []
synonym: "fecal matter" EXACT []
synonym: "fewmet" NARROW []
synonym: "frass" NARROW []
synonym: "guano" NARROW []
synonym: "matières fécales@fr" EXACT []
synonym: "merde@fr" EXACT []
synonym: "ordure" RELATED []
synonym: "partie de la merde@fr" EXACT []
synonym: "piece of shit" EXACT []
synonym: "porción de mierda@es" EXACT []
synonym: "portion of dung" NARROW []
synonym: "portion of excrement" EXACT []
synonym: "portion of faeces" EXACT []
synonym: "portion of fecal material" EXACT []
synonym: "portion of fecal matter" EXACT []
synonym: "portion of feces" EXACT []
synonym: "portion of guano" NARROW []
synonym: "portion of scat" NARROW []
synonym: "portionem cacas" EXACT []
synonym: "scat" NARROW []
synonym: "spoor" RELATED []
synonym: "spraint" NARROW []
synonym: "stool" EXACT []
synonym: "teil der fäkalien@de" EXACT []
xref: BTO:0000440
xref: CALOHA:TS-2345
xref: Cow:dung
xref: ENVO:00002003
xref: FMA:64183
xref: GAID:1199
xref: galen:Feces
xref: http://en.wikipedia.org/wiki/Feces
xref: http://en.wikipedia.org/wiki/Fewmet
xref: http://en.wikipedia.org/wiki/Frass
xref: http://en.wikipedia.org/wiki/Guano
xref: http://en.wikipedia.org/wiki/Spraint
xref: http://linkedlifedata.com/resource/umls/id/C0015733
xref: http://www.merriam-webster.com/dictionary/feces
xref: http://www.ncbi.nlm.nih.gov/pubmed/23285307
xref: MA:0002509
xref: MAT:0000053
xref: MESH:D005243
xref: MIAA:0000053
xref: NCIT:C13234
xref: OpenCyc:Mx4rvVjJMZwpEbGdrcN5Y29ycA
xref: UMLS:C0015733
is_a: UBERON:0000174 ! excreta
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string
property_value: source FMA:64183 xsd:string
property_value: source ncithesaurus:Feces xsd:string
property_value: UBPROP:0000001 "Excretion in semisolid state processed by the intestine.[FMA]" xsd:string
property_value: UBPROP:0000007 "fecal" xsd:string
has_synonym_type: LATIN

[Term]
id: UBERON:0002046
name: thyroid gland
namespace: uberon
def: "A two-lobed endocrine gland found in all vertebrates, located in front of and on either side of the trachea in humans, and producing various hormones, such as triiodothyronine and calcitonin[BTO]." []
subset: efo_slim
subset: organ_slim
subset: pheno_slim
subset: uberon_slim
synonym: "glandula thyroidea" RELATED []
synonym: "thyroid" EXACT []
xref: AAO:0010544
xref: BTO:0001379
xref: CALOHA:TS-1047
xref: EFO:0000861
xref: EHDAA2:0002028
xref: EHDAA:2148
xref: EHDAA:2975
xref: EMAPA:17068
xref: EV:0100133
xref: FMA:9603
xref: GAID:465
xref: galen:ThyroidGland
xref: http://en.wikipedia.org/wiki/Thyroid
xref: http://linkedlifedata.com/resource/umls/id/C0040132
xref: http://www.snomedbrowser.com/Codes/Details/181117000
xref: MA:0000129
xref: MAT:0000081
xref: MESH:D013961
xref: MIAA:0000081
xref: NCIT:C12400
xref: OpenCyc:Mx4rvVjLT5wpEbGdrcN5Y29ycA
xref: UMLS:C0040132
xref: VHOG:0000418
xref: XAO:0000162
is_a: UBERON:0002368 ! endocrine gland
property_value: date_retrieved "2012-06-20" xsd:string
property_value: date_retrieved "2012-09-17" xsd:string
property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/a/a3/Illu_thyroid_parathyroid.jpg
property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/c/c6/Illu_endocrine_system.jpg
property_value: external_class AAO:0010544 xsd:string
property_value: external_class VHOG:0000418 xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string
property_value: source AAO:BJB xsd:string
property_value: source http://bgee.unil.ch/
property_value: source "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28" xsd:string
property_value: source ncithesaurus:Thyroid_Gland xsd:string
property_value: source "Other_animals"
property_value: source "Romer" xsd:string
property_value: UBPROP:0000001 "Either of paired structures located in the throat which develop from the ventral wall of the pharynx and excretes hormones involved in the morphological and functional changes during metamorphosis as well as influencing other tissues.[AAO]" xsd:string
property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (2) a groove in the pharyngeal floor known as the endostyle, or a thyroid gland derived from part of the endostyle (...).[well established][VHOG]" xsd:string
property_value: UBPROP:0000008 "In fish, it is usually located below the gills and is not always divided into distinct lobes. However, in some teleosts, patches of thyroid tissue are found elsewhere in the body, associated with the kidneys, spleen, heart, or eyes" xsd:string
property_value: UBPROP:0000008 "In larval lampreys, the thyroid originates as an exocrine gland, secreting its hormones into the gut, and associated with the larva's filter-feeding apparatus. In the adult lamprey, the gland separates from the gut, and becomes endocrine, but this path of development may reflect the evolutionary origin of the thyroid. For instance, the closest living relatives of vertebrates, the tunicates and Amphioxus, have a structure very similar to that of larval lampreys, and this also secretes iodine-containing compounds (albeit not thyroxine)" xsd:string
property_value: UBPROP:0000008 "In tetrapods, the thyroid is always found somewhere in the neck region. In most tetrapod species, there are two paired thyroid glands - that is, the right and left lobes are not joined together. However, there is only ever a single thyroid gland in most mammals, and the shape found in humans is common to many other species" xsd:string
scope: NCBITaxon:32443
scope: NCBITaxon:32523
scope: NCBITaxon:7746
has_synonym_type: LATIN
ontology: AAO
ontology: VHOG

[Term]
id: UBERON:0002048
name: lung
namespace: uberon
def: "Respiration organ that develops as an oupocketing of the esophagus." []
comment: Snakes and limbless lizards typically possess only the right lung as a major respiratory organ; the left lung is greatly reduced, or even absent. Amphisbaenians, however, have the opposite arrangement, with a major left lung, and a reduced or absent right lung [WP]
subset: efo_slim
subset: major_organ
subset: organ_slim
subset: pheno_slim
subset: uberon_slim
synonym: "pulmo" EXACT []
xref: AAO:0000275
xref: AAO:0010567
xref: BTO:0000763
xref: CALOHA:TS-0568
xref: EFO:0000934
xref: EHDAA2:0001042
xref: EHDAA:1554
xref: EHDAA:2205
xref: EMAPA:16728
xref: EV:0100042
xref: FMA:7195
xref: GAID:345
xref: galen:Lung
xref: http://en.wikipedia.org/wiki/Lung
xref: http://linkedlifedata.com/resource/umls/id/C0024109
xref: http://orcid.org/0000-0002-6601-2165
xref: http://www.snomedbrowser.com/Codes/Details/181216001
xref: MA:0000415
xref: MAT:0000135
xref: MESH:D008168
xref: MIAA:0000135
xref: NCIT:C12468
xref: OpenCyc:Mx4rvVjKy5wpEbGdrcN5Y29ycA
xref: UMLS:C0024109
xref: VHOG:0000310
xref: XAO:0000119
is_a: UBERON:0005178 ! thoracic cavity element
property_value: date_retrieved "2012-06-20" xsd:string
property_value: date_retrieved "2012-09-17" xsd:string
property_value: external_class AAO:0010567 xsd:string
property_value: external_class VHOG:0000310 xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string
property_value: seeAlso https://github.com/obophenotype/uberon/issues/701
property_value: source AAO:SBH xsd:string
property_value: source http://bgee.unil.ch/
property_value: source "ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.210, DOI:10.1371/journal.pone.0024019 Zheng W, Wang Z, Collins JE, Andrews RM, Stemple D, Gong Z, Comparative transcriptome analyses indicate molecular homology of zebrafish swimbladder and Mammalian lung. PLoS One (2011)" xsd:string
property_value: source ncithesaurus:Lung xsd:string
property_value: UBPROP:0000001 "Either of two organs which allow gas exchange absorbing oxygen from inhaled air and releasing carbon dioxide with exhaled air.[AAO]" xsd:string
property_value: UBPROP:0000003 "Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata. (...) In actinopterygian fishes, apart from Cladistia, the ventral intestinal pocket migrates dorsally and becomes the swim-bladder, a mainly hydrostatical organ (reference 1); Comparative transcriptome analyses indicate molecular homology of zebrafish swimbladder and Mammalian lung (reference 2).[well established][VHOG]" xsd:string
property_value: UBPROP:0000007 "pulmonary" xsd:string
property_value: UBPROP:0000008 "respiration organ in all air-breathing animals, including most tetrapods, a few fish and a few snails. In mammals and the more complex life forms, the two lungs are located in the chest on either side of the heart. Their principal function is to transport oxygen from the atmosphere into the bloodstream, and to release carbon dioxide from the bloodstream into the atmosphere. This exchange of gases is accomplished in the mosaic of specialized cells that form millions of tiny, exceptionally thin-walled air sacs called alveoli. // Avian lungs do not have alveoli as mammalian lungs do, they have Faveolar lungs. They contain millions of tiny passages known as para-bronchi, connected at both ends by the dorsobronchi" xsd:string
has_synonym_type: LATIN
ontology: AAO
ontology: VHOG

[Term]
id: UBERON:0002075
name: viscus
namespace: uberon
def: "An organ that is located within the body cavity (or in its extension, in the scrotum); it consists of organ parts that are embryologically derived from endoderm, splanchnic mesoderm or intermediate mesoderm; together with other organs, the viscus constitutes the respiratory, gastrointestinal, urinary, reproductive and immune systems, or is the central organ of the cardiovascular system. Examples: heart, lung, esophagus, kidney, ovary, spleen." []
subset: organ_slim
subset: pheno_slim
subset: uberon_slim
subset: upper_level
synonym: "Organsystem@de" RELATED []
synonym: "splanchnic tissue" RELATED []
synonym: "viscera" RELATED []
synonym: "visceral organ" EXACT []
synonym: "visceral organ system" EXACT []
synonym: "visceral tissue" RELATED []
xref: AAO:0010386
xref: BTO:0001491
xref: EHDAA:512
xref: EMAPA:16245
xref: FMA:7085
xref: http://en.wikipedia.org/wiki/Viscus
xref: http://linkedlifedata.com/resource/umls/id/C0042779
xref: http://www.snomedbrowser.com/Codes/Details/118760003
xref: https://github.com/obophenotype/mouse-anatomy-ontology/issues/14
xref: MA:0000019
xref: MESH:D014781
xref: NCIT:C28287
xref: RETIRED_EHDAA2:0002201
xref: UMLS:C0042779
xref: XAO:0003034
is_a: UBERON:0005177 ! trunk region element
property_value: date_retrieved "2012-06-20" xsd:string
property_value: external_class AAO:0010386 xsd:string
property_value: external_ontology "FMA" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string
property_value: source BTO:0001491 xsd:string
property_value: source ncithesaurus:Viscera xsd:string
property_value: UBPROP:0000001 "An internal organ of the body; especially: one (as the heart, liver, or intestine) located in the great cavity of the trunk proper.[AAO]" xsd:string
property_value: UBPROP:0000012 "general anatomical term in FMA. Note that we place the MA class here temporarily, although properly systems should be distinguished from organs." xsd:string
ontology: AAO

[Term]
id: UBERON:0002106
name: spleen
namespace: uberon
def: "the organ that functions to filter blood and to store red corpuscles and platelets" []
subset: efo_slim
subset: organ_slim
subset: pheno_slim
subset: uberon_slim
subset: vertebrate_core
synonym: "lien" RELATED []
xref: AAO:0010395
xref: BTO:0001281
xref: CALOHA:TS-0956
xref: EFO:0000869
xref: EMAPA:18767
xref: EV:0100055
xref: FMA:7196
xref: GAID:1289
xref: galen:Spleen
xref: http://en.wikipedia.org/wiki/Spleen
xref: http://linkedlifedata.com/resource/umls/id/C0037993
xref: http://www.snomedbrowser.com/Codes/Details/181279003
xref: ISBN:0-683-40008-8
xref: MA:0000141
xref: MAT:0000085
xref: MESH:A15.382.520.604.713
xref: MIAA:0000085
xref: MP:0000689
xref: NCIT:C12432
xref: OpenCyc:Mx4rvVjgw5wpEbGdrcN5Y29ycA
xref: TAO:0000436
xref: UMLS:C0037993
xref: VHOG:0000120
xref: XAO:0000328
xref: ZFA:0000436
is_a: UBERON:0017672 ! abdominal viscera
property_value: date_retrieved "2012-06-20" xsd:string
property_value: date_retrieved "2012-09-17" xsd:string
property_value: depicted:by Illu:spleen.jpg
property_value: external_class AAO:0010395 xsd:string
property_value: external_class VHOG:0000120 xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string
property_value: source AAO:BMZ xsd:string
property_value: source http://bgee.unil.ch/
property_value: source http://www.ncbi.nlm.nih.gov/pubmed/20959416
property_value: source "ISBN:978-0781765190 Paul WE, Fundamental Immunology (2008) p.94" xsd:string
property_value: source ncithesaurus:Spleen xsd:string
property_value: UBPROP:0000001 "An organ involved in red blood cell filtration and immune response.[AAO]" xsd:string
property_value: UBPROP:0000003 "With the advent of clonal selection, the accumulation and segregation of T and B cells in specialized organs for antigen presentation became necessary, and indeed the spleen is found in all jawed vertebrates, but not in agnathans or invertebrates.[well established][VHOG]" xsd:string
property_value: UBPROP:0000007 "lienal" xsd:string
property_value: UBPROP:0000007 "splenic" xsd:string
property_value: UBPROP:0000008 "In humans, it is located in the left upper quadrant of the abdomen. It removes old red blood cells and holds a reserve in case of hemorrhagic shock, especially in animals like horses (not in humans), while recycling iron" xsd:string
property_value: UBPROP:0000008 "Neither hagfish nor lampreys possess what might be considered a discrete and condensed spleen. Hagfish possess dispersed lymphoid tissue within the submucosa of the intestine (96) associated with the portal vein (97), whereas lymphoid tissue is associated with the typhlosole portion of the intestine in lampreys (96)" xsd:string
property_value: UBPROP:0000009 "It synthesizes antibodies in its white pulp and removes, from blood and lymph node circulation, antibody-coated bacteria along with antibody-coated blood cells" xsd:string
has_synonym_type: LATIN
ontology: AAO
ontology: VHOG

[Term]
id: UBERON:0002107
name: liver
namespace: uberon
def: "An exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO]." []
subset: efo_slim
subset: major_organ
subset: organ_slim
subset: pheno_slim
subset: uberon_slim
subset: vertebrate_core
synonym: "iecur" RELATED []
synonym: "jecur" RELATED []
xref: AAO:0010111
xref: BTO:0000759
xref: CALOHA:TS-0564
xref: EFO:0000887
xref: EHDAA2:0000997
xref: EHDAA:2197
xref: EMAPA:16846
xref: EV:0100089
xref: FMA:7197
xref: GAID:288
xref: galen:Liver
xref: http://en.wikipedia.org/wiki/Liver
xref: http://linkedlifedata.com/resource/umls/id/C0023884
xref: http://www.snomedbrowser.com/Codes/Details/181268008
xref: MA:0000358
xref: MAT:0000097
xref: MESH:D008099
xref: MIAA:0000097
xref: NCIT:C12392
xref: OpenCyc:Mx4rvVimppwpEbGdrcN5Y29ycA
xref: TAO:0000123
xref: UMLS:C0023884
xref: VHOG:0000257
xref: XAO:0000133
xref: ZFA:0000123
is_a: UBERON:0006925 ! digestive system gland
property_value: date_retrieved "2012-06-20" xsd:string
property_value: date_retrieved "2012-09-17" xsd:string
property_value: depicted:by Leber:Schaf.jpg
property_value: external_class AAO:0010111 xsd:string
property_value: external_class VHOG:0000257 xsd:string
property_value: external_ontology "ZFA" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string
property_value: source AAO:BJB xsd:string
property_value: source http://bgee.unil.ch/
property_value: source "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.526, ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43" xsd:string
property_value: source ncithesaurus:Liver xsd:string
property_value: UBPROP:0000001 "Organ which secretes bile and participates in formation of certain blood proteins.[AAO]" xsd:string
property_value: UBPROP:0000002 "relationship type change: differentiates_from endoderm (AAO:0000139) CHANGED TO: develops_from endoderm (UBERON:0000925)[AAO]" xsd:string
property_value: UBPROP:0000003 "All vertebrates possess a liver (reference 1); Later in craniate evolution, an anterior gill arch was transformed into jaws, and many new types of feeding subsequently evolved.(...) A liver evolved that, among its many functions, stores considerable energy as glycogen or lipid (reference 2).[well established][VHOG]" xsd:string
property_value: UBPROP:0000007 "hepatic" xsd:string
property_value: UBPROP:0000008 "An organ sometimes referred to as a liver is found associated with the digestive tract of the primitive chordate Amphioxus. However, this is an enzyme secreting gland, not a metabolic organ, and it is unclear how truly homologous it is to the vertebrate liver. The zebrafish liver differs from the mammalian liver in that the hepatocytes are not clearly organized in cords or lobules and the typical portal triads are not apparent. In addition, the zebrafish liver does not have Kuppfer cells. Furthermore, a clear distinction can be made between the male and female liver in the adult zebrafish. The female hepatocytes are very basophilic (Figure 15c) as a result of the production of vitellogenin (Van der Ven et al. 2003)." xsd:string
property_value: UBPROP:0000008 "The liver is found in all vertebrates, and is typically the largest visceral organ. Its form varies considerably in different species, and is largely determined by the shape and arrangement of the surrounding organs. Nonetheless, in most species it is divided into right and left lobes; exceptions to this general rule include snakes, where the shape of the body necessitates a simple cigar-like form. The internal structure of the liver is broadly similar in all vertebrates." xsd:string
property_value: UBPROP:0000009 "secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO]." xsd:string
property_value: UBPROP:0000012 "Only ZFA considers this part_of immune system - we weaken this to an overlaps relation, as in general it's only a subset of cells that have clear immune function." xsd:string
has_synonym_type: LATIN
ontology: AAO
ontology: VHOG

[Term]
id: UBERON:0002113
name: kidney
namespace: uberon
def: "A paired organ of the urinary tract which has the production of urine as its primary function." []
subset: efo_slim
subset: major_organ
subset: organ_slim
subset: pheno_slim
subset: uberon_slim
subset: vertebrate_core
synonym: "reniculate kidney" NARROW []
xref: AAO:0000250
xref: BTO:0000671
xref: CALOHA:TS-0510
xref: EFO:0000929
xref: EMAPA:17373
xref: EV:0100096
xref: FMA:7203
xref: GAID:423
xref: galen:Kidney
xref: http://anatomy.uams.edu/anatomyhtml/kidney.html
xref: http://en.wikipedia.org/wiki/Kidney
xref: http://linkedlifedata.com/resource/umls/id/C0022646
xref: http://www.snomedbrowser.com/Codes/Details/181414000
xref: MA:0000368
xref: MAT:0000119
xref: MESH:D007668
xref: MIAA:0000119
xref: NCIT:C12415
xref: OpenCyc:Mx4rvVjlYpwpEbGdrcN5Y29ycA
xref: Reniculate:kidney
xref: UMLS:C0022646
xref: XAO:0003267
is_a: UBERON:0005172 ! abdomen element
property_value: date_retrieved "2012-06-20" xsd:string
property_value: external_class AAO:0000250 xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string
property_value: source AAO:BJB xsd:string
property_value: source ncithesaurus:Kidney xsd:string
property_value: UBPROP:0000001 "One of either of a pair of structures lying on either side of the dorsal aorta in which fluid balance is regulated and waste is excreted out in the form of urine.[AAO]" xsd:string
property_value: UBPROP:0000007 "renal" xsd:string
property_value: UBPROP:0000202 FMA:264815
has_synonym_type: SENSU
ontology: AAO

[Term]
id: UBERON:0002268
name: olfactory organ
namespace: uberon
def: "An organ that houses olfactory neurons and is responsible for the sense of smell. Examples include the vertebrate nose and the Drosophila dorsal organ." []
subset: functional_classification
synonym: "main olfactory organ" NARROW []
synonym: "olfactory neuroepithelium" RELATED []
synonym: "olfactory organ" EXACT []
synonym: "olfactory sense organ" EXACT []
synonym: "olfactory sensory organ" EXACT []
synonym: "organ olfactus" RELATED []
synonym: "organum olfactorium" RELATED []
synonym: "primary olfactory organ" NARROW []
xref: AAO:0010180
xref: BTO:0001772
xref: FBbt:00005158
xref: FMA:77659
xref: UBERON:cjm
xref: VHOG:0000287
xref: XAO:0000273
is_a: UBERON:0000020 ! sense organ
property_value: IAO:0000116 "An olfactory organ overlaps with the olfactory system, because some parts of the nose (e.g. nasal skeleton) are parts of the skeletal system, which is spatially disjoint" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string
property_value: UBPROP:0000012 "fma general anatomical term. xao has no subtypes (but Johnstons organ develops from this). An olfactory organ overlaps with the olfactory system, because some parts of the nose (e.g. nasal skeleton) are parts of the skeletal system, which is spatially disjoint" xsd:string

[Term]
id: UBERON:0002358
name: peritoneum
namespace: uberon
def: "A serous membrane that lines the peritoneal cavity[VHOG,modified]." []
subset: pheno_slim
subset: uberon_slim
subset: vertebrate_core
synonym: "peritonaeum" RELATED []
xref: AAO:0010814
xref: BTO:0001472
xref: CALOHA:TS-2072
xref: EV:0100087
xref: FMA:9584
xref: GAID:18
xref: galen:Peritoneum
xref: http://en.wikipedia.org/wiki/Peritoneum
xref: http://linkedlifedata.com/resource/umls/id/C0031153
xref: MA:0000449
xref: MESH:A01.047.025.600
xref: NCIT:C12770
xref: OpenCyc:Mx4rvjJ72ZwpEbGdrcN5Y29ycA
xref: TAO:0005120
xref: UMLS:C0031153
xref: VHOG:0001257
xref: XAO:0000139
xref: ZFA:0005120
is_a: UBERON:0000042 ! serous membrane
property_value: date_retrieved "2012-06-20" xsd:string
property_value: date_retrieved "2012-08-14" xsd:string
property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray1040.png
property_value: external_class AAO:0010814 xsd:string
property_value: external_class TAO:0005120 xsd:string
property_value: external_ontology "MA" xsd:string
property_value: IAO:0000116 "TODO - in ZFA is_a epithelium" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string
property_value: source AAO:JMG xsd:string
property_value: source ncithesaurus:Peritoneum xsd:string
property_value: source ZFIN:curator xsd:string
property_value: UBPROP:0000001 "An epithelium that lines the peritoneal cavity.[TAO]" xsd:string
property_value: UBPROP:0000001 "Serous membrane that forms the lining of the abdominal cavity or the coelom. It covers most of the intra-abdominal organs, supports the abdominal organs, and serves as a conduit for their blood and lymph vessels and nerves. It is composed of a layer of mesothelium.[AAO]" xsd:string
property_value: UBPROP:0000007 "peritoneal" xsd:string
property_value: UBPROP:0000012 "todo: check MA/EMAPA." xsd:string
ontology: AAO
ontology: TAO

[Term]
id: UBERON:0002367
name: prostate gland
namespace: uberon
def: "The prostate gland is a partly muscular, partly glandular body that is situated near the base of the mammalian male urethra and secretes an alkaline viscid fluid which is a major constituent of the ejaculatory fluid." []
subset: efo_slim
subset: major_organ
subset: organ_slim
subset: pheno_slim
subset: uberon_slim
synonym: "male prostate" EXACT []
synonym: "prostata" RELATED []
synonym: "prostate" EXACT []
xref: BTO:0001129
xref: CALOHA:TS-0828
xref: EFO:0000858
xref: EMAPA:19287
xref: EV:0100104
xref: FMA:9600
xref: GAID:392
xref: galen:ProstateGland
xref: GO:0030850
xref: http://en.wikipedia.org/wiki/Prostate
xref: http://linkedlifedata.com/resource/umls/id/C0033572
xref: http://www.ncbi.nlm.nih.gov/pubmed/10668204
xref: http://www.snomedbrowser.com/Codes/Details/181422007
xref: MA:0000404
xref: MAT:0000078
xref: MESH:D011467
xref: MIAA:0000078
xref: NCIT:C12410
xref: OpenCyc:Mx4rv6trqZwpEbGdrcN5Y29ycA
xref: UMLS:C0033572
xref: VHOG:0001261
is_a: UBERON:0010147 ! male accessory sex gland
property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/a/a1/Prostatelead.jpg
property_value: IAO:0000116 "TODO - FMA treats the gland as part of the prostate - see also FMA:74119." xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string
property_value: source ncithesaurus:Prostate_Gland xsd:string
property_value: UBPROP:0000007 "prostatic" xsd:string
has_synonym_type: LATIN

[Term]
id: UBERON:0002368
name: endocrine gland
namespace: uberon
def: "Endocrine glands are glands of the endocrine system that secrete their products directly into the circulatory system rather than through a duct.[WP, modified]." []
subset: organ_slim
subset: pheno_slim
subset: uberon_slim
synonym: "ductless gland" EXACT []
synonym: "ductless gland" RELATED []
synonym: "glandula endocrina" EXACT []
synonym: "glandulae endocrinae" RELATED []
xref: AEO:0000098
xref: BTO:0001488
xref: CALOHA:TS-1300
xref: Ductless:gland
xref: EHDAA2:0003098
xref: EMAPA:35999
xref: Endocrine:gland
xref: FMA:9602
xref: GAID:335
xref: http://linkedlifedata.com/resource/umls/id/C0014133
xref: http://www.snomedbrowser.com/Codes/Details/40818001
xref: MA:0002563
xref: MESH:D004702
xref: NCIT:C12704
xref: OpenCyc:Mx4rvbkiRZwpEbGdrcN5Y29ycA
xref: UMLS:C0014133
is_a: UBERON:0002530 ! gland
property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/d/da/Illu_endocrine_system.png
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string
property_value: source ncithesaurus:Endocrine_Gland xsd:string
has_synonym_type: LATIN

[Term]
id: UBERON:0002369
name: adrenal gland
namespace: uberon
def: "Either of a pair of complex endocrine organs near the anterior medial border of the kidney consisting of a mesodermal cortex that produces glucocorticoid, mineralocorticoid, and androgenic hormones and an ectodermal medulla that produces epinephrine and norepinephrine[BTO]." []
subset: organ_slim
subset: pheno_slim
subset: uberon_slim
synonym: "adrenal" RELATED []
synonym: "adrenal capsule" RELATED []
synonym: "adrenal medulla cell" RELATED []
synonym: "atrabiliary capsule" RELATED []
synonym: "epinephric gland" RELATED []
synonym: "epinephros" RELATED []
synonym: "glandula adrenalis" EXACT []
synonym: "glandula suprarenalis" EXACT []
synonym: "glandula suprarenalis" RELATED []
synonym: "interrenal gland" RELATED []
synonym: "suprarenal capsule" RELATED []
synonym: "suprarenal gland" RELATED []
xref: AAO:0010551
xref: Adrenal:gland
xref: BTO:0000047
xref: CALOHA:TS-0016
xref: EFO:0000238
xref: EMAPA:18426
xref: EV:0100135
xref: FMA:9604
xref: GAID:446
xref: galen:AdrenalGland
xref: GO:0030325
xref: http://linkedlifedata.com/resource/umls/id/C0001625
xref: http://www.snomedbrowser.com/Codes/Details/181127006
xref: MA:0000116
xref: MAT:0000071
xref: MESH:D000311
xref: MIAA:0000071
xref: NCIT:C12666
xref: OpenCyc:Mx4rvXYiz5wpEbGdrcN5Y29ycA
xref: UMLS:C0001625
xref: VHOG:0001141
xref: XAO:0000164
is_a: UBERON:0006858 ! adrenal/interrenal gland
property_value: date_retrieved "2012-06-20" xsd:string
property_value: date_retrieved "2012-09-17" xsd:string
property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/9/9d/Illu_endocrine_system_New.png
property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/c/c6/Illu_endocrine_system.jpg
property_value: external_class AAO:0010551 xsd:string
property_value: external_class VHOG:0001141 xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2019-11-22/uberon.owl xsd:string
property_value: source AAO:BJB xsd:string
property_value: source http://bgee.unil.ch/
property_value: source "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.518 and Figure 15-9" xsd:string
property_value: source ncithesaurus:Adrenal_Gland xsd:string
property_value: UBPROP:0000001 "Anatomical structure which is found on the surface of the kidney and secretes various hormones including epinephrine, norephinephrine, aldosterone, corticosterone, and cortisol.[AAO]" xsd:string
property_value: UBPROP:0000003 "All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues, but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG]" xsd:string
property_value: UBPROP:0000008 "The origin of the adrenal gland is still controversial. It is thought to share the same origin as the kidney and gonads, derived from coelomic epithelium of the urogenital ridge and/or the underlying mesenchyme (Keegan and Hammer, 2002; Morohashi, 1997). We follow Kardong and state homology at the level of the cortex and medulla rather than gland as a whole" xsd:string
property_value: UBPROP:0000009 "suprarenal cortex manufactures corticosteroids; suprarenal medulla manufactures epinephrine and norepinephrine; suprarenal medulla receives preganglionic sympathetic innervation from the greater thoracic splanchnic n." xsd:string
has_synonym_type: HOMOLOGY
has_synonym_type: LATIN
ontology: AAO
ontology: VHOG

[Term]
id: UBERON:0002371
name: bone marrow
namespace: uberon
def: "the soft tissue that fills the cavities of bones" []
subset: efo_slim
subset: pheno_slim
subset: uberon_slim
synonym: "medulla of bone" RELATED []
synonym: "medulla ossea" EXACT []
synonym: "medulla ossium" EXACT []
synonym: "medullary bone" RELATED []
xref: AAO:0011007
xref: Bone:marrow
xref: BTO:0000141
xref: BTO:0000829
xref: CALOHA:TS-0087
xref: EFO:0000868
xref: EMAPA:32760
xref: EV:0100046
xref: FMA:9608
xref: GAID:1287
xref: galen:BoneMarrow
xref: http://linkedlifedata.com/resource/umls/id/C0005953
xref: http://www.snomedbrowser.com/Codes/Details/421320006
xref: MA:0000134
xref: MAT:0000084
xref: MESH:D001853
xref: MGI:cwg
xref: MIAA:0000084
xref: MP:0002397
xref: NCIT:C12431
xref: OpenCyc:Mx4rvVm-FpwpEbGdrcN5Y29ycA
xref: UMLS:C0005953
xref: VHOG:0001218
xref: XAO:0000123
is_a: UBERON:0000479 ! tissue
property_value: date_retrieved "2012-09-17" xsd:string
property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/7/74/Gray72-en.svg
property_value: external_class VHOG:0001218 xsd:string
property_value: IAO:0000116 "consider placement of NCIT:C53466 medullary bone" xsd:string
property_value: IAO:0000116 "TODO - create superclass for bone marrow / head kidney. both are portions of tissue in the hematopoetic system. also consider adding as subclass of zone of bone organ for consistency with FMA. See also: Leydig and epigonal organs" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2019-11-22/uberon.owl xsd:string
property_value: source "DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood Cells and Blood Cell Development in the Animal Kingdom. Annual Review of Cell and Developmental Biology (2006)" xsd:string
property_value: source http://bgee.unil.ch/
property_value: source ncithesaurus:Bone_Marrow xsd:string
property_value: UBPROP:0000003 "The bone marrow is the hematopoietic organ in all vertebrates but fishes, in which hematopoiesis occurs in the kidney.[well established][VHOG]" xsd:string
property_value: UBPROP:0000009 "In adults, marrow in large bones produces new blood cells[Wikipedia:Bone_marrow]" xsd:string
has_synonym_type: LATIN
ontology: VHOG

[Term]
id: UBERON:0002409
name: pericardial fluid
namespace: uberon
def: "Transudate contained in the pericardial cavity.[FMA]" []
subset: uberon_slim
xref: BTO:0001016
xref: FMA:9887
xref: MA:0002530
xref: Pericardial:fluid
is_a: UBERON:0007794 ! secretion of serous gland
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2019-11-22/uberon.owl xsd:string

[Term]
id: UBERON:0002530
name: gland
namespace: uberon
alt_id: UBERON:MIAA_0000021
def: "an organ that functions as a secretory or excretory organ" []
subset: efo_slim
subset: pheno_slim
subset: uberon_slim
synonym: "Druese" RELATED []
synonym: "glandula" RELATED []
synonym: "glandular organ" EXACT []
xref: AAO:0000212
xref: AEO:0000096
xref: BTO:0000522
xref: EFO:0000797
xref: EHDAA2:0003096
xref: EHDAA:2161
xref: EHDAA:4475
xref: EHDAA:6522
xref: EMAPA:18425
xref: FBbt:00100317
xref: FMA:7146
xref: FMA:86294
xref: galen:Gland
xref: HAO:0000375
xref: http://en.wikipedia.org/wiki/Gland
xref: http://linkedlifedata.com/resource/umls/id/C1285092
xref: http://orcid.org/0000-0002-6601-2165
xref: http://www.snomedbrowser.com/Codes/Details/134358001
xref: MA:0003038
xref: MAT:0000021
xref: MGI:csmith
xref: MIAA:0000021
xref: MP:0002163
xref: NCIT:C13319
xref: OpenCyc:Mx4rwP3vyJwpEbGdrcN5Y29ycA
xref: UMLS:C1285092
xref: WikipediaCategory:Glands
is_a: UBERON:0000062 ! organ
property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/a/a1/Gray1026.png
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string
property_value: source ncithesaurus:Gland xsd:string
property_value: UBPROP:0000007 "glandular" xsd:string
has_synonym_type: LATIN

[Term]
id: UBERON:0003133
name: reproductive organ
namespace: uberon
def: "An organ involved in reproduction" []
subset: functional_classification
subset: organ_slim
subset: pheno_slim
synonym: "genital organ" EXACT []
synonym: "genitalia" RELATED []
synonym: "reproductive system organ" EXACT []
synonym: "sex organ" EXACT []
xref: EMAPA:17381
xref: EMAPA:37731
xref: http://linkedlifedata.com/resource/umls/id/C0017420
xref: http://www.snomedbrowser.com/Codes/Details/128181006
xref: MA:0001752
xref: MESH:D005835
xref: NCIT:C25177
xref: OpenCyc:Mx4rwO39aJwpEbGdrcN5Y29ycA
xref: TGMA:0000591
xref: UBERON:xp
xref: UMLS:C0017420
xref: WBbt:0008422
is_a: UBERON:0000062 ! organ
property_value: external_ontology "GO" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string
property_value: source MA:th xsd:string
property_value: source ncithesaurus:Genitalia xsd:string
property_value: UBPROP:0000012 "GO uses genitalia for the singular organ" xsd:string
has_synonym_type: PLURAL

[Term]
id: UBERON:0003937
name: reproductive gland
namespace: uberon
def: "Any of the organized aggregations of cells that function as secretory or excretory organs and are associated with reproduction." []
subset: organ_slim
subset: pheno_slim
synonym: "genitalia gland" EXACT []
synonym: "gland of genitalia" EXACT []
synonym: "gland of reproductive system" EXACT []
synonym: "reproductive gland" EXACT []
synonym: "reproductive system gland" EXACT []
synonym: "sex gland" EXACT []
xref: MA:0001751
xref: MP:0000653
xref: OBOL:automatic
is_a: UBERON:0002530 ! gland
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string

[Term]
id: UBERON:0004921
name: subdivision of digestive tract
namespace: uberon
def: "A proximal-distal subdivision of the digestive tract." []
subset: non_informative
synonym: "alimentary system subdivision" RELATED []
synonym: "intestinal tract" RELATED []
synonym: "segment of intestinal tract" RELATED []
synonym: "subdivision of alimentary system" RELATED []
xref: FBbt:00100315
xref: FMA:71131
xref: http://orcid.org/0000-0002-6601-2165
is_a: UBERON:0013522 ! subdivision of tube
property_value: IAO:0000232 "intended to denote both embryonic and adult structures. Note the FMA grouping here is not quite correct." xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string

[Term]
id: UBERON:0005172
name: abdomen element
namespace: uberon
def: "An organ or element that is in the abdomen. Examples: spleen, intestine, kidney, abdominal mammary gland." []
subset: non_informative
synonym: "abdomen organ" EXACT []
xref: http://orcid.org/0000-0002-6601-2165
xref: http://www.snomedbrowser.com/Codes/Details/272631008
xref: MA:0000522
is_a: UBERON:0005173 ! abdominal segment element
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string

[Term]
id: UBERON:0005173
name: abdominal segment element
namespace: uberon
def: "An organ or element that is part of the adbominal segment of the organism. This region can be further subdivided into the abdominal cavity and the pelvic region." []
subset: non_informative
synonym: "abdominal segment organ" EXACT []
xref: EMAPA:37062
xref: http://orcid.org/0000-0002-6601-2165
xref: MA:0000529
is_a: UBERON:0005177 ! trunk region element
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string
property_value: source MA:th xsd:string

[Term]
id: UBERON:0005177
name: trunk region element
namespace: uberon
def: "An organ or element that part of the trunk region. The trunk region can be further subdividied into thoracic (including chest and thoracic cavity) and abdominal (including abdomen and pelbis) regions." []
subset: non_informative
subset: organ_slim
synonym: "trunk organ" EXACT []
xref: EMAPA:37270
xref: http://orcid.org/0000-0002-6601-2165
xref: MA:0000516
is_a: UBERON:0000062 ! organ
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string
property_value: source MA:th xsd:string

[Term]
id: UBERON:0005178
name: thoracic cavity element
namespace: uberon
def: "An organ or element that is in the thoracic cavity. Examples: lung, heart, longus colli." []
subset: non_informative
subset: pheno_slim
synonym: "thoracic cavity organ" EXACT []
xref: EMAPA:37273
xref: http://orcid.org/0000-0002-6601-2165
xref: MA:0000557
is_a: UBERON:0005181 ! thoracic segment organ
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string
property_value: source MA:th xsd:string

[Term]
id: UBERON:0005181
name: thoracic segment organ
namespace: uberon
def: "An organ that part of the thoracic segment region. This region can be further subdividied chest and thoracic cavity regions." []
subset: non_informative
synonym: "upper body organ" RELATED []
xref: EMAPA:37271
xref: http://orcid.org/0000-0002-6601-2165
xref: MA:0000563
is_a: UBERON:0005177 ! trunk region element
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string
property_value: source MA:th xsd:string

[Term]
id: UBERON:0005399
name: male reproductive gland
namespace: uberon
def: "A sex gland that is part of a male reproductive system." []
subset: organ_slim
subset: pheno_slim
synonym: "accessory sex gland" RELATED []
xref: BTO:0000080
xref: EMAPA:19285
xref: MA:0000399
xref: OBOL:automatic
is_a: UBERON:0003937 ! reproductive gland
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string

[Term]
id: UBERON:0006003
name: integumentary adnexa
namespace: uberon
def: "Anatomical structure embedded in or located in the integument that is part of the integumental system. Examples: hair, follicles, skin glands, claws, nails, feathers." []
subset: pheno_slim
synonym: "adnexae cutis" RELATED []
synonym: "body hair or bristle" NARROW []
synonym: "skin adnexa" RELATED []
synonym: "skin adnexal structure" RELATED []
synonym: "skin appendage" RELATED []
xref: EMAPA:37883
xref: GO:GO
xref: http://code.google.com/p/caro2/issues/detail?id=5
xref: http://orcid.org/0000-0002-6601-2165
xref: Skin:appendage
is_a: UBERON:0000064 ! organ part
property_value: IAO:0000116 "add subclasses based on resolution of CARO tracker item. Also check: adnexal gland. Note that MP implicitly includes hypodermis." xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string
property_value: source MA:th xsd:string
property_value: source MP:0010678 xsd:string
property_value: UBPROP:0000001 "the tissue or structures associated with or embedded in the skin such as hair and hair follicles, sweat glands, sebaceous glands and claws or nails[MP:0010678]" xsd:string
has_synonym_type: LATIN

[Term]
id: UBERON:0006314
name: bodily fluid
namespace: uberon
def: "Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not." []
subset: pheno_slim
synonym: "body fluid" EXACT []
synonym: "fluid" BROAD []
xref: birnlex:20
xref: Body:fluid
xref: EMAPA:37441
xref: FMA:280556
xref: GAID:266
xref: galen:BodyFluid
xref: MESH:A12.207
xref: MESH:D001826
is_a: UBERON:0000463 ! organism substance
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string
property_value: source MA:th xsd:string

[Term]
id: UBERON:0006538
name: respiratory system fluid/secretion
namespace: uberon
def: "A portion of organism substance that secreted_by a respiratory system." []
synonym: "respiratory system fluid" RELATED []
synonym: "respiratory system secretion" RELATED []
xref: EMAPA:36550
xref: http://linkedlifedata.com/resource/umls/id/C1514899
xref: MA:0002533
xref: NCIT:C13722
xref: OBOL:automatic
xref: UMLS:C1514899
is_a: UBERON:0000463 ! organism substance
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string
property_value: source ncithesaurus:Respiratory_System_Fluid_or_Secretion xsd:string

[Term]
id: UBERON:0006539
name: mammary gland fluid/secretion
namespace: uberon
def: "A substance that is secreted by a mammary gland. The substance may differ depending on phase, with colostrum produced during pregancy/early lactation, and milk produced afterwards." []
synonym: "lactiferous gland fluid" RELATED []
synonym: "lactiferous gland secretion" RELATED []
synonym: "mammary gland fluid" RELATED []
synonym: "mammary gland secreted fluid" RELATED []
synonym: "mammary gland secretion" RELATED []
synonym: "secretion of mammary gland" RELATED []
xref: EMAPA:36538
xref: http://orcid.org/0000-0002-6601-2165
xref: MA:0002505
is_a: UBERON:0000456 ! secretion of exocrine gland
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string

[Term]
id: UBERON:0006562
name: pharynx
namespace: uberon
def: "The pharynx is the part of the digestive system immediately posterior to the mouth[GO]." []
subset: grouping_class
subset: uberon_slim
synonym: "anterior part of foregut" RELATED []
synonym: "pharyngeal tube" RELATED []
xref: FBbt:00005380
xref: GO:0060465
xref: MAT:0000049
xref: MIAA:0000049
is_a: UBERON:0004921 ! subdivision of digestive tract
property_value: IAO:0000232 "currently this is an extremely generic class, encompassing both protostomes and deuterostomes." xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string
property_value: UBPROP:0000007 "branchial" xsd:string
property_value: UBPROP:0000007 "pharyngeal" xsd:string

[Term]
id: UBERON:0006858
name: adrenal/interrenal gland
namespace: uberon
def: "This gland can either be a discrete structure located bilaterally above each kidney, or a cluster of cells in the head kidney that perform the functions of the adrenal gland. In either case, this organ consists of two cells types, aminergic chromaffin cells and steroidogenic cortical cells[GO]" []
subset: homology_grouping
subset: organ_slim
synonym: "adrenal - interrenal gland" RELATED []
synonym: "adrenal gland - interrenal gland" EXACT []
synonym: "adrenal gland/interrenal tissue" EXACT []
synonym: "suprarenal gland - interrenal gland" RELATED []
xref: GO:0030325
xref: VHOG:0001141
is_a: UBERON:0002368 ! endocrine gland
property_value: date_retrieved "2012-09-17" xsd:string
property_value: external_class VHOG:0001141 xsd:string
property_value: IAO:0000116 "keep this grouping class so long as it is required for GO" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2019-11-22/uberon.owl xsd:string
property_value: source http://bgee.unil.ch/
property_value: source "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.518 and Figure 15-9" xsd:string
property_value: UBPROP:0000003 "All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues, but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG]" xsd:string
ontology: VHOG

[Term]
id: UBERON:0006925
name: digestive system gland
namespace: uberon
def: "Any gland that is part of the digestive system." []
subset: organ_slim
synonym: "digestive gland" RELATED []
xref: AAO:0000130
xref: BTO:0000345
xref: UBERON:cjm
is_a: UBERON:0002368 ! endocrine gland
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string

[Term]
id: UBERON:0007109
name: meconium
namespace: uberon
def: "A dark greenish mass that accumulates in the bowel during fetal life and is discharged shortly after birth." []
xref: BTO:0000838
xref: ncithesaurus:Meconium
is_a: UBERON:0001988 ! feces
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string

[Term]
id: UBERON:0007221
name: neonate stage
namespace: uberon
def: "Of or pertaining to the period of time immediately following birth, or to the newborn." []
synonym: "fledgling stage" NARROW []
synonym: "hatchling" NARROW []
synonym: "hatchling stage" NARROW []
synonym: "infant stage" NARROW []
synonym: "neonatal stage" EXACT []
synonym: "nestling stage" NARROW []
synonym: "newborn stage" RELATED []
synonym: "pouch stage" NARROW []
synonym: "puggle" NARROW []
synonym: "puggle stage" NARROW []
xref: BTO:0001762
xref: Category:Infant\:organism
xref: Category:Newborn\:organism
xref: EV:0300037
xref: HsapDv:0000082
xref: http://en.wikipedia.org/wiki/Infant
xref: MmusDv:0000096
xref: NIF_Organism:birnlex_695
xref: OGES:000025
is_a: UBERON:0000105 ! life cycle stage
property_value: IAO:0000116 "consider splitting infant/newborn" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl xsd:string
property_value: seeAlso https://github.com/obophenotype/uberon/issues/350

[Term]
id: UBERON:0007311
name: sputum
namespace: uberon
def: "Matter ejected from the lungs, bronchi, and trachea, through the mouth." []
synonym: "expectoration" RELATED []
xref: BTO:0001297
xref: CALOHA:TS-0963
xref: Dorlands_Medical_Dictionary:MerckSource
xref: EMAPA:36553
xref: FMA:312401
xref: GAID:1171
xref: http://linkedlifedata.com/resource/umls/id/C0038056
xref: MA:0002536
xref: MESH:D013183
xref: NCIT:C13278
xref: UMLS:C0038056
is_a: UBERON:0006538 ! respiratory system fluid/secretion
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string
property_value: source ncithesaurus:Sputum xsd:string

[Term]
id: UBERON:0007779
name: transudate
namespace: uberon
def: "Any bodily fluid that has passed through a membrane such as the capillary wall, as a result of unbalanced hydrostatic and osmotic forces" []
synonym: "plasma ultrafiltrate" RELATED []
xref: FMA:12276
xref: GAID:1195
xref: http://medical-dictionary.thefreedictionary.com/transudate
xref: MESH:D005122
xref: ncithesaurus:Transudate
is_a: UBERON:0006314 ! bodily fluid
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2019-11-22/uberon.owl xsd:string
property_value: UBPROP:0000007 "transudative" xsd:string
property_value: UBPROP:0000010 "characteristically low in protein and cellular content (unless there has been secondary concentration)" xsd:string

[Term]
id: UBERON:0007794
name: secretion of serous gland
namespace: uberon
def: "Any fluid produced by a serous gland." []
synonym: "serosal fluid" EXACT []
synonym: "serous fluid" BROAD []
synonym: "serous gland fluid" EXACT []
xref: Serous:fluid
xref: UBERON:cjm
is_a: UBERON:0006314 ! bodily fluid
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2019-11-22/uberon.owl xsd:string

[Term]
id: UBERON:0008811
name: intromittent organ
namespace: uberon
def: "An external organ of a male organism that is specialized to deliver sperm during copulation. Intromittent organs are found most often in terrestrial species, as most aquatic species fertilize their eggs externally, although there are exceptions[WP]." []
subset: grouping_class
subset: organ_slim
synonym: "aedeagus" NARROW []
synonym: "copulatory organ" RELATED []
synonym: "penis" NARROW []
xref: AAO:0010255
xref: FBbt:00004850
xref: HAO:0000091
xref: Intromittent:organ
xref: TAO:0002036
xref: TGMA:0000585
is_a: UBERON:0000079 ! male reproductive system
property_value: date_retrieved "2012-08-14" xsd:string
property_value: external_class TAO:0002036 xsd:string
property_value: IAO:0000232 "this is a broad grouping class connecting a number of different analagous organs by their function. We place the insect aedeagus here rather than penis, although this is somewhat arbitrary given the broadness of the current definition" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string
property_value: source TAO:wd xsd:string
property_value: UBPROP:0000001 "Surface structure that is an external structure of a male organism through which sperm is transferred to a female organism during mating.[TAO]" xsd:string
has_synonym_type: SENSU
ontology: TAO

[Term]
id: UBERON:0009564
name: distal limb integumentary appendage
namespace: uberon
def: "A nail, hoof or claw." []
synonym: "hoof or claw" RELATED []
synonym: "hoof, claw or nail" RELATED []
synonym: "keratin plate" RELATED []
synonym: "keratin sheath" RELATED []
synonym: "unguis" RELATED []
xref: http://www.ncbi.nlm.nih.gov/pubmed/11710767
xref: MESH:D006724
is_a: UBERON:0013703 ! integumentary projection
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string

[Term]
id: UBERON:0010000
name: multicellular anatomical structure
namespace: uberon
def: "An anatomical structure that has more than one cell as a part." []
subset: upper_level
synonym: "multicellular structure" EXACT []
xref: CARO:0010000
xref: FBbt:00100313
is_a: UBERON:0000061 ! anatomical structure
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string

[Term]
id: UBERON:0010147
name: male accessory sex gland
namespace: uberon
def: "Any gland, other than the gonad, associated with the genital tract, such as the ampulla of the ductus deferens and the bulbourethral, prostate and vesicular glands of the male." []
subset: pheno_slim
synonym: "male accessory gland" RELATED []
synonym: "male accessory reproductive gland" RELATED []
xref: BTO:0004798
is_a: UBERON:0005399 ! male reproductive gland
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string

[Term]
id: UBERON:0010172
name: bulb of aorta
namespace: uberon
def: "The portion of the left ventricular outflow tract delineated by the sinotubular ridge superiorly and the bases of the valve leaflets inferiorly; it comprises the aortic sinuses, the aortic valve leaflets, the commissures, and the interleaflet triangles" []
subset: pheno_slim
synonym: "aorta bulb" EXACT []
synonym: "aortic bulb" EXACT []
synonym: "aortic root" EXACT []
synonym: "bulb of ascending aorta" EXACT []
synonym: "bulbus aortae" EXACT []
synonym: "root of aorta" EXACT []
synonym: "supraaortic valve area" EXACT []
xref: BTO:0004695
xref: FMA:3740
xref: FMA:TA
xref: http://www.snomedbrowser.com/Codes/Details/362032000
xref: MP:0011572
xref: MP:0011575
is_a: UBERON:0000064 ! organ part
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2019-11-22/uberon.owl xsd:string
property_value: source http://medical-dictionary.thefreedictionary.com/aortic+bulb
property_value: UBPROP:0000001 "The dilated first part of the aorta containing the aortic semilunar valves and the aortic sinuses." xsd:string
has_synonym_type: LATIN

[Term]
id: UBERON:0012168
name: umbilical cord blood
namespace: uberon
def: "blood that remains in the placenta and in the attached umbilical cord after childbirth[WP]." []
comment: Cord blood is collected because it contains stem cells, which can be used to treat hematopoietic and genetic disorders.[WP]
subset: efo_slim
synonym: "cord blood" RELATED []
synonym: "fetal blood" RELATED []
synonym: "umbilical cord blood" RELATED []
xref: BTO:0004053
xref: CALOHA:TS-1079
xref: Cord:blood
xref: EFO:0001942
xref: MESH:A12.207.152.200
xref: MESH:D005312
is_a: UBERON:0000178 ! blood
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2019-11-22/uberon.owl xsd:string

[Term]
id: UBERON:0013515
name: subdivision of oviduct
namespace: uberon
def: "A section through the tube or network of tubes that connects the ovaries to the outside of the body." []
subset: non_informative
synonym: "subdivision of fallopian tube" NARROW []
synonym: "subdivision of oviduct" EXACT []
synonym: "subdivision of uterine tube" EXACT []
synonym: "uterine tube zone" EXACT []
synonym: "zone of uterine tube" EXACT []
xref: FMA:18302
xref: http://orcid.org/0000-0002-6601-2165
is_a: UBERON:0013522 ! subdivision of tube
property_value: external_ontology "FMA" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string
property_value: UBPROP:0000012 "FMA class may only represent the uterine portion" xsd:string

[Term]
id: UBERON:0013522
name: subdivision of tube
namespace: uberon
is_a: UBERON:0000064 ! organ part
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string

[Term]
id: UBERON:0013703
name: integumentary projection
namespace: uberon
def: "Anatomical projection that is part of the integumentl system." []
synonym: "skin projection" NARROW []
xref: http://orcid.org/0000-0002-6601-2165
is_a: UBERON:0006003 ! integumentary adnexa
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string

[Term]
id: UBERON:0013755
name: arterial blood
namespace: uberon
def: "A blood that is part of a artery." []
subset: pheno_slim
synonym: "arterial blood" EXACT []
synonym: "blood in artery" EXACT []
synonym: "portion of arterial blood" EXACT []
xref: FMA:83066
xref: OBOL:automatic
is_a: UBERON:0000178 ! blood
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2019-11-22/uberon.owl xsd:string

[Term]
id: UBERON:0013756
name: venous blood
namespace: uberon
def: "A blood that is part of a vein." []
synonym: "blood in vein" EXACT []
synonym: "portion of venous blood" EXACT []
synonym: "venous blood" EXACT []
xref: FMA:83067
xref: OBOL:automatic
is_a: UBERON:0000178 ! blood
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2019-11-22/uberon.owl xsd:string

[Term]
id: UBERON:0017672
name: abdominal viscera
namespace: uberon
def: "A viscus that is part of a abdomen." []
subset: pheno_slim
synonym: "abdominal viscera" EXACT []
synonym: "abdominal viscera set" EXACT []
synonym: "set of abdominal viscera" EXACT []
xref: FMA:32413
xref: FMA:67355
xref: OBOL:automatic
is_a: UBERON:0005172 ! abdomen element
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string

[Term]
id: UBERON:0034873
name: bodily gas
namespace: uberon
def: "Any substance in the body or expelled from the body that is in a gaseous state." []
synonym: "gas in anatomical space" EXACT []
synonym: "portion of gas in anatomical space" EXACT []
xref: FMA:84580
xref: http://orcid.org/0000-0002-6601-2165
is_a: UBERON:0000463 ! organism substance
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2019-11-22/uberon.owl xsd:string

[Term]
id: UBERON:0034929
name: external soft tissue zone
namespace: uberon
def: "A region or zone on the surface of an organism that encompasses skin and any adnexa, down through muscles and bounded by underlying skeletal support structures." []
xref: http://orcid.org/0000-0002-6601-2165
is_a: UBERON:0010000 ! multicellular anatomical structure
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string

[Term]
id: UBERON:0034944
name: zone of organ
namespace: uberon
synonym: "organ region with floating fiat boundary" RELATED []
synonym: "organ sector" EXACT []
synonym: "organ zonal region" EXACT []
synonym: "organ zone" EXACT []
xref: FMA:55268
is_a: UBERON:0000064 ! organ part
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string

[Term]
id: UBERON:0034947
name: gas in respiratory system
namespace: uberon
def: "Any portion of gas located in a part of the respiratory system." []
synonym: "respiratory gas" EXACT []
synonym: "respiratory system gas" EXACT []
xref: http://orcid.org/0000-0002-6601-2165
is_a: UBERON:0034873 ! bodily gas
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2019-11-22/uberon.owl xsd:string

[Term]
id: UBERON:0035943
name: life cycle temporal boundary
namespace: uberon
def: "A temporal boundary connecting two life cycle stages that follow in immediate succession. A temporal boundary is an abstract, instantaneous entity." []
subset: upper_level
is_a: BFO:0000035 ! process boundary

[Term]
id: UBERON:0035944
name: life-death temporal boundary
namespace: uberon
def: "A life cycle temporal boundary that marks the end of the life cycle of the organism." []
synonym: "death" RELATED []
synonym: "end of life" RELATED []
synonym: "end of life cycle" EXACT []
synonym: "moment of death" EXACT []
synonym: "time of death" EXACT []
is_a: UBERON:0035943 ! life cycle temporal boundary

[Term]
id: UBERON:0035946
name: start of neonate stage
namespace: uberon
def: "A life cycle temporal boundary that marks the start of the neonate stage of the organism." []
synonym: "birth" RELATED []
synonym: "moment of birth" EXACT []
synonym: "time of birth" EXACT []
is_a: UBERON:0035943 ! life cycle temporal boundary

[Term]
id: UBERON:0036017
name: regurgitated substance
namespace: uberon
def: "A bodily fluid consisting of the contents of the digestive tract expulsed through the anterior portion of the digestive tract." []
synonym: "regurgitate" RELATED []
xref: UBERON:cjm
is_a: UBERON:0000463 ! organism substance
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl xsd:string

[Term]
id: UO:0000001
name: length unit
def: "A unit which is a standard measure of the distance between two points." []
is_a: IAO:0000003 ! measurement unit label
property_value: IAO:0000111 "length unit" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl

[Term]
id: UO:0000002
name: mass unit
def: "A unit which is a standard measure of the amount of matter/energy of a physical object." []
is_a: IAO:0000003 ! measurement unit label
property_value: IAO:0000111 "mass unit" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl

[Term]
id: UO:0000003
name: time unit
def: "A unit which is a standard measure of the dimension in which events occur in sequence." []
is_a: IAO:0000003 ! measurement unit label
property_value: IAO:0000111 "time unit" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl

[Term]
id: obligee_role
name: obsolete obligee role
def: "A role that is either the specified output of an obligation generating social act or the concretization of a transferable obligation and that is realized by it's bearer being the receiving part of a process that fulfills the previously agreed upon requirements." []
is_a: ObsoleteClass ! Obsolete Class
property_value: IAO:0000117 "Sarah Bost" xsd:string
is_obsolete: true

[Term]
id: obligor_role
name: obsolete obligor role
def: "A role that is either the specified output of an obligation generating social act or the concretization of a transferable obligation and that is realized by it's bearer being the providing part of a process that fulfills the previously agreed upon requirements." []
is_a: ObsoleteClass ! Obsolete Class
property_value: IAO:0000117 "Sarah Bost" xsd:string
is_obsolete: true

[Typedef]
id: BFO:0000050
name: part of
def: "a core relation that holds between a part and its whole" []
subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension
subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term
subset: http://purl.obolibrary.org/obo/valid_for_go_ontology
subset: http://purl.obolibrary.org/obo/valid_for_gocam
property_value: IAO:0000111 "is part of" xsd:string
property_value: IAO:0000112 "my brain is part of my body (continuant parthood, two material entities)" xsd:string
property_value: IAO:0000112 "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" xsd:string
property_value: IAO:0000112 "this day is part of this year (occurrent parthood)" xsd:string
property_value: IAO:0000116 "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." xsd:string
property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string
property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string
property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." xsd:string
property_value: IAO:0000118 "part_of" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/ido.owl
property_value: IAO:0000412 http://purl.obolibrary.org/obo/omrse.owl
property_value: RO:0001900 RO:0001901
property_value: RO:0040042 BFO:0000002
property_value: RO:0040042 BFO:0000003
property_value: RO:0040042 BFO:0000004
property_value: RO:0040042 BFO:0000017
property_value: RO:0040042 BFO:0000019
property_value: RO:0040042 BFO:0000020
property_value: RO:0040042 BFO:0000031
property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections
property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf
property_value: seeAlso http://www.obofoundry.org/ro/#OBO_REL:part_of xsd:string
is_transitive: true
is_a: RO:0002131 ! overlaps
inverse_of: BFO:0000051 ! has part

[Typedef]
id: BFO:0000051
name: has part
def: "a core relation that holds between a whole and its part" []
subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension
subset: http://purl.obolibrary.org/obo/valid_for_go_ontology
subset: http://purl.obolibrary.org/obo/valid_for_gocam
property_value: IAO:0000111 "has part" xsd:string
property_value: IAO:0000112 "my body has part my brain (continuant parthood, two material entities)" xsd:string
property_value: IAO:0000112 "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" xsd:string
property_value: IAO:0000112 "this year has part this day (occurrent parthood)" xsd:string
property_value: IAO:0000116 "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." xsd:string
property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string
property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string
property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." xsd:string
property_value: IAO:0000118 "has_part" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/ido.owl
property_value: IAO:0000412 http://purl.obolibrary.org/obo/omrse.owl
property_value: RO:0001900 RO:0001901
is_transitive: true
is_a: RO:0002131 ! overlaps

[Typedef]
id: BFO:0000054
name: realized in
comment: Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process
property_value: IAO:0000111 "realized in" xsd:string
property_value: IAO:0000112 "this disease is realized in this disease course" xsd:string
property_value: IAO:0000112 "this fragility is realized in this shattering" xsd:string
property_value: IAO:0000112 "this investigator role is realized in this investigation" xsd:string
property_value: IAO:0000118 "is realized by" xsd:string
property_value: IAO:0000118 "realized_in" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/ido.owl
property_value: IAO:0000412 http://purl.obolibrary.org/obo/omrse.owl
property_value: IAO:0000412 http://purl.obolibrary.org/obo/ro.owl xsd:string
property_value: IAO:0000600 "[copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
domain: BFO:0000017 ! realizable entity
range: BFO:0000015 ! process
inverse_of: BFO:0000055 ! realizes

[Typedef]
id: BFO:0000055
name: realizes
comment: Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process
property_value: IAO:0000111 "realizes" xsd:string
property_value: IAO:0000112 "this disease course realizes this disease" xsd:string
property_value: IAO:0000112 "this investigation realizes this investigator role" xsd:string
property_value: IAO:0000112 "this shattering realizes this fragility" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/ido.owl
property_value: IAO:0000412 http://purl.obolibrary.org/obo/omrse.owl
property_value: IAO:0000600 "to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/iao.owl
domain: BFO:0000015 ! process
range: BFO:0000017 ! realizable entity

[Typedef]
id: BFO:0000060
name: obsolete preceded by
comment: accidentally included in BFO 1.2 proposal\n        - should have been BFO_0000062
is_transitive: true
is_obsolete: true

[Typedef]
id: BFO:0000062
name: preceded by
def: "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." []
subset: ro-eco
property_value: http://purl.org/dc/elements/1.1/source http://www.obofoundry.org/ro/#OBO_REL:preceded_by xsd:string
property_value: IAO:0000111 "preceded by" xsd:string
property_value: IAO:0000116 "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C.    The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string
property_value: IAO:0000118 "is preceded by" xsd:string
property_value: IAO:0000118 "preceded_by" xsd:string
domain: BFO:0000003 ! occurrent
range: BFO:0000003 ! occurrent
holds_over_chain: BFO:0000050 BFO:0000062
holds_over_chain: RO:0002091 BFO:0000062
holds_over_chain: RO:0002092 BFO:0000062
is_transitive: true
is_a: RO:0002086 ! ends after
inverse_of: BFO:0000063 ! precedes

[Typedef]
id: BFO:0000063
name: precedes
def: "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." []
subset: ro-eco
property_value: IAO:0000111 "precedes" xsd:string
domain: BFO:0000003 ! occurrent
range: BFO:0000003 ! occurrent
holds_over_chain: BFO:0000050 BFO:0000063
is_transitive: true
is_a: RO:0002222 ! temporally related to

[Typedef]
id: BFO:0000066
name: occurs in
def: "b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" []
comment: Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant
subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension
subset: http://purl.obolibrary.org/obo/valid_for_go_ontology
subset: http://purl.obolibrary.org/obo/valid_for_gocam
property_value: IAO:0000111 "occurs in" xsd:string
property_value: IAO:0000118 "occurs_in" xsd:string
property_value: IAO:0000118 "unfolds in" xsd:string
property_value: IAO:0000118 "unfolds_in" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
domain: BFO:0000003 ! occurrent
range: BFO:0000004 ! independent continuant
holds_over_chain: BFO:0000050 BFO:0000066
inverse_of: BFO:0000067 ! contains process
transitive_over: BFO:0000050 ! part of

[Typedef]
id: BFO:0000067
name: contains process
def: "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" []
comment: Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant
property_value: IAO:0000111 "site of" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl

[Typedef]
id: BFO:0000108
name: exists at
property_value: BFO:0000179 "exists-at" xsd:string
property_value: BFO:0000180 "existsAt" xsd:string
property_value: IAO:0000116 "BFO2 Reference: entity" xsd:string
property_value: IAO:0000116 "BFO2 Reference: temporal region" xsd:string
property_value: IAO:0000600 "b exists_at t means: b is an entity which exists at some temporal region t. (axiom label in BFO2 Reference: [118-002])" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
domain: BFO:0000001 ! entity
range: BFO:0000008 ! temporal region
inverse_of: BFO:0000157 ! during which exists

[Typedef]
id: BFO:0000117
name: has occurrent part
def: "b has_occurrent_part c = Def. c occurrent_part_of b. (axiom label in BFO2 Reference: [007-001])" []
property_value: BFO:0000179 "o-has-part" xsd:string
property_value: BFO:0000180 "hasOccurrentPart" xsd:string
property_value: IAO:0000112 "[copied from inverse property 'part of occurrent'] Mary’s 5th birthday occurrent_part_of Mary’s life" xsd:string
property_value: IAO:0000112 "[copied from inverse property 'part of occurrent'] the first set of the tennis match occurrent_part_of the tennis match." xsd:string
property_value: IAO:0000112 "[copied from inverse property 'part of occurrent'] The process of a footballer’s heart beating once is an occurrent part but not a temporal_part of a game of football." xsd:string
property_value: IAO:0000116 "[copied from inverse property 'part of occurrent'] BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion." xsd:string
property_value: IAO:0000116 "[copied from inverse property 'part of occurrent'] BFO2 Reference: occurrent" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/vo.owl xsd:string
property_value: IAO:0000600 "[copied from inverse property 'part of occurrent'] b occurrent_part_of c =Def. b is a part of c & b and c are occurrents. (axiom label in BFO2 Reference: [003-002])" xsd:string
property_value: IAO:0000602 "(iff (hasOccurrentPart a b) (occurrentPartOf b a)) // axiom label in BFO2 CLIF: [007-001] " xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
domain: BFO:0000003 ! occurrent
range: BFO:0000003 ! occurrent
is_transitive: true
inverse_of: BFO:0000132 ! part of occurrent

[Typedef]
id: BFO:0000118
name: has proper occurrent part
def: "[copied from inverse property 'proper part of occurrent'] b proper_occurrent_part_of c =Def. b occurrent_part_of c & b and c are not identical. (axiom label in BFO2 Reference: [005-001])" []
def: "b has_proper_occurrent_part c = Def. c proper_occurrent_part_of b. [XXX-001" []
property_value: BFO:0000179 "o-has-ppart" xsd:string
property_value: BFO:0000180 "hasProperOccurrentPart" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/vo.owl xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
domain: BFO:0000003 ! occurrent
range: BFO:0000003 ! occurrent
is_transitive: true
is_a: BFO:0000117 ! has occurrent part
inverse_of: BFO:0000138 ! proper part of occurrent

[Typedef]
id: BFO:0000121
name: has temporal part
def: "[copied from inverse property 'temporal part of'] b proper_temporal_part_of c =Def. b temporal_part_of c & not (b = c). (axiom label in BFO2 Reference: [116-001])" []
def: "[copied from inverse property 'temporal part of'] b temporal_part_of c =Def.b occurrent_part_of c & & for some temporal region t, b occupies_temporal_region t & for all occurrents d, t (if d occupies_temporal_region t  & t? occurrent_part_of t then (d occurrent_part_of a iff d occurrent_part_of b)). (axiom label in BFO2 Reference: [078-003])" []
property_value: BFO:0000179 "has-t-part" xsd:string
property_value: IAO:0000112 "[copied from inverse property 'temporal part of'] the 4th year of your life is a temporal part of your life\\. The first quarter of a game of football is a temporal part of the whole game\\. The process of your heart beating from 4pm to 5pm today is a temporal part of the entire process of your heart beating.\\ The 4th year of your life is a temporal part of your life" xsd:string
property_value: IAO:0000112 "[copied from inverse property 'temporal part of'] the process boundary which separates the 3rd and 4th years of your life." xsd:string
property_value: IAO:0000112 "[copied from inverse property 'temporal part of'] your heart beating from 4pm to 5pm today is a temporal part of the process of your heart beating" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/vo.owl xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
domain: BFO:0000003 ! occurrent
range: BFO:0000003 ! occurrent
is_transitive: true
is_a: BFO:0000117 ! has occurrent part
inverse_of: BFO:0000139 ! temporal part of

[Typedef]
id: BFO:0000132
name: part of occurrent
def: "[copied from inverse property 'has occurrent part'] b has_occurrent_part c = Def. c occurrent_part_of b. (axiom label in BFO2 Reference: [007-001])" []
property_value: BFO:0000179 "o-part-of" xsd:string
property_value: BFO:0000180 "occurrentPartOf" xsd:string
property_value: IAO:0000112 "Mary’s 5th birthday occurrent_part_of Mary’s life" xsd:string
property_value: IAO:0000112 "the first set of the tennis match occurrent_part_of the tennis match." xsd:string
property_value: IAO:0000112 "The process of a footballer’s heart beating once is an occurrent part but not a temporal_part of a game of football." xsd:string
property_value: IAO:0000116 "BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion." xsd:string
property_value: IAO:0000116 "BFO2 Reference: occurrent" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/vo.owl xsd:string
property_value: IAO:0000600 "b occurrent_part_of c =Def. b is a part of c & b and c are occurrents. (axiom label in BFO2 Reference: [003-002])" xsd:string
property_value: IAO:0000601 "occurrent_part_of is antisymmetric. (axiom label in BFO2 Reference: [123-001])" xsd:string
property_value: IAO:0000601 "occurrent_part_of is reflexive (every occurrent entity is an occurrent_part_of itself). (axiom label in BFO2 Reference: [113-002])" xsd:string
property_value: IAO:0000601 "occurrent_part_of is transitive. (axiom label in BFO2 Reference: [112-001])" xsd:string
property_value: IAO:0000601 "occurrent_part_of satisfies unique product. (axiom label in BFO2 Reference: [125-001])" xsd:string
property_value: IAO:0000601 "occurrent_part_of satisfies weak supplementation. (axiom label in BFO2 Reference: [124-001])" xsd:string
property_value: IAO:0000602 "(forall (x y t) (if (and (occurrentPartOf x y t) (not (= x y))) (exists (z) (and (occurrentPartOf z y t) (not (exists (w) (and (occurrentPartOf w x t) (occurrentPartOf w z t)))))))) // axiom label in BFO2 CLIF: [124-001] " xsd:string
property_value: IAO:0000602 "(forall (x y t) (if (and (occurrentPartOf x y t) (occurrentPartOf y x t)) (= x y))) // axiom label in BFO2 CLIF: [123-001] " xsd:string
property_value: IAO:0000602 "(forall (x y t) (if (exists (v) (and (occurrentPartOf v x t) (occurrentPartOf v y t))) (exists (z) (forall (u w) (iff (iff (occurrentPartOf w u t) (and (occurrentPartOf w x t) (occurrentPartOf w y t))) (= z u)))))) // axiom label in BFO2 CLIF: [125-001] " xsd:string
property_value: IAO:0000602 "(forall (x y z) (if (and (occurrentPartOf x y) (occurrentPartOf y z)) (occurrentPartOf x z))) // axiom label in BFO2 CLIF: [112-001] " xsd:string
property_value: IAO:0000602 "(forall (x) (if (Occurrent x) (occurrentPartOf x x))) // axiom label in BFO2 CLIF: [113-002] " xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
domain: BFO:0000003 ! occurrent
range: BFO:0000003 ! occurrent
is_transitive: true

[Typedef]
id: BFO:0000138
name: proper part of occurrent
def: "[copied from inverse property 'has proper occurrent part'] b has_proper_occurrent_part c = Def. c proper_occurrent_part_of b. [XXX-001" []
def: "b proper_occurrent_part_of c =Def. b occurrent_part_of c & b and c are not identical. (axiom label in BFO2 Reference: [005-001])" []
property_value: BFO:0000179 "o-ppart-of" xsd:string
property_value: BFO:0000180 "properOccurrentPartOf" xsd:string
property_value: IAO:0000602 "(iff (properOccurrentPartOf a b) (and (occurrentPartOf a b) (not (= a b)))) // axiom label in BFO2 CLIF: [005-001] " xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
domain: BFO:0000003 ! occurrent
range: BFO:0000003 ! occurrent
is_transitive: true
is_a: BFO:0000132 ! part of occurrent

[Typedef]
id: BFO:0000139
name: temporal part of
def: "b proper_temporal_part_of c =Def. b temporal_part_of c & not (b = c). (axiom label in BFO2 Reference: [116-001])" []
def: "b temporal_part_of c =Def.b occurrent_part_of c & & for some temporal region t, b occupies_temporal_region t & for all occurrents d, t (if d occupies_temporal_region t  & t? occurrent_part_of t then (d occurrent_part_of a iff d occurrent_part_of b)). (axiom label in BFO2 Reference: [078-003])" []
property_value: BFO:0000179 "t-part-of" xsd:string
property_value: BFO:0000180 "temporalPartOf" xsd:string
property_value: IAO:0000112 "the 4th year of your life is a temporal part of your life\\. The first quarter of a game of football is a temporal part of the whole game\\. The process of your heart beating from 4pm to 5pm today is a temporal part of the entire process of your heart beating.\\ The 4th year of your life is a temporal part of your life" xsd:string
property_value: IAO:0000112 "the process boundary which separates the 3rd and 4th years of your life." xsd:string
property_value: IAO:0000112 "your heart beating from 4pm to 5pm today is a temporal part of the process of your heart beating" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/vo.owl xsd:string
property_value: IAO:0000601 "if b proper_temporal_part_of c, then there is some d which is a proper_temporal_part_of c and which shares no parts with b. (axiom label in BFO2 Reference: [117-002])" xsd:string
property_value: IAO:0000602 "(forall (x y) (if (properTemporalPartOf x y) (exists (z) (and (properTemporalPartOf z y) (not (exists (w) (and (temporalPartOf w x) (temporalPartOf w z)))))))) // axiom label in BFO2 CLIF: [117-002] " xsd:string
property_value: IAO:0000602 "(iff (properTemporalPartOf a b) (and (temporalPartOf a b) (not (= a b)))) // axiom label in BFO2 CLIF: [116-001] " xsd:string
property_value: IAO:0000602 "(iff (temporalPartOf a b) (and (occurrentPartOf a b) (exists (t) (and (TemporalRegion t) (occupiesSpatioTemporalRegion a t))) (forall (c t_1) (if (and (Occurrent c) (occupiesSpatioTemporalRegion c t_1) (occurrentPartOf t_1 r)) (iff (occurrentPartOf c a) (occurrentPartOf c b)))))) // axiom label in BFO2 CLIF: [078-003] " xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
domain: BFO:0000003 ! occurrent
range: BFO:0000003 ! occurrent
is_transitive: true
is_a: BFO:0000132 ! part of occurrent

[Typedef]
id: BFO:0000155
name: occupies temporal region
property_value: BFO:0000179 "spans" xsd:string
property_value: BFO:0000180 "occupiesTemporalRegion" xsd:string
property_value: IAO:0000600 "p occupies_temporal_region t. This is a primitive relation between an occurrent p and the temporal region t upon which the spatiotemporal region p occupies_spatiotemporal_region projects. (axiom label in BFO2 Reference: [132-001])" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
domain: BFO:0000003 ! occurrent
range: BFO:0000008 ! temporal region
is_a: BFO:0000108 ! exists at
inverse_of: BFO:0000156 ! has temporal occupant

[Typedef]
id: BFO:0000156
name: has temporal occupant
property_value: BFO:0000179 "span-of" xsd:string
property_value: BFO:0000180 "spanOf" xsd:string
property_value: IAO:0000600 "[copied from inverse property 'occupies temporal region'] p occupies_temporal_region t. This is a primitive relation between an occurrent p and the temporal region t upon which the spatiotemporal region p occupies_spatiotemporal_region projects. (axiom label in BFO2 Reference: [132-001])" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
domain: BFO:0000008 ! temporal region
range: BFO:0000003 ! occurrent
is_a: BFO:0000157 ! during which exists

[Typedef]
id: BFO:0000157
name: during which exists
property_value: BFO:0000179 "during-which-exists" xsd:string
property_value: IAO:0000116 "[copied from inverse property 'exists at'] BFO2 Reference: entity" xsd:string
property_value: IAO:0000116 "[copied from inverse property 'exists at'] BFO2 Reference: temporal region" xsd:string
property_value: IAO:0000600 "[copied from inverse property 'exists at'] b exists_at t means: b is an entity which exists at some temporal region t. (axiom label in BFO2 Reference: [118-002])" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
domain: BFO:0000008 ! temporal region
range: BFO:0000001 ! entity

[Typedef]
id: BFO:0000184
name: history of
property_value: definition "(Elucidation) b history of c if c is a material entity and b is a history that is the unique history of c" xsd:string
property_value: example "This life is the history of this organism. " xsd:string
property_value: http://purl.org/dc/elements/1.1/identifier "144-BFO" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/bfo/2020/bfo.owl xsd:string
property_value: prefLabel "history of" xsd:string
domain: BFO:0000182 ! history
range: BFO:0000040 ! material entity
inverse_of: BFO:0000185 ! has history

[Typedef]
id: BFO:0000185
name: has history
property_value: definition "b has history c =Def c history of b" xsd:string
property_value: example "This organism has history this life. " xsd:string
property_value: http://purl.org/dc/elements/1.1/identifier "145-BFO" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/bfo/2020/bfo.owl xsd:string
property_value: prefLabel "has history" xsd:string
domain: BFO:0000040 ! material entity
range: BFO:0000182 ! history

[Typedef]
id: IAO:0000039
name: has measurement unit label
range: IAO:0000003 ! measurement unit label
is_functional: true
is_a: BFO:0000051 ! has part

[Typedef]
id: IAO:0000135
name: obsolete_specifically denotes
def: "c specifically denotes r =def \nr is a portion of reality\n& c is a particular quality\n& c depends specifically on some independent continuant b \n& b acquired c as the result of the achievement of an objective to enable pointing to r repeatedly. \n\nMarked means there is a changed or additional quality of the bearer - the  quality is the information carrier.\n\nCase 1\nMemory trace as mark created when reading some description of some friend. The trace can denote.\n\nCase 2\nPattern of ink arrayed on paper as mark when writing down a friend's name\n\nCase 3\nPattern of magnetic domains on scattered pieces of a hard disk platter as mark when saving a file." []
property_value: IAO:0000112 "The process of creation is, for example,  writing down on paper the name of a friend by deliberately creating a certain pattern using ink.\n\nHere the ink + paper is the independent continuant and the carrier is the pattern in the ink.\n\nc = pattern in the ink\nb = paper + ink\nr = friend" xsd:string
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000116 "8/6/2009 Alan Ruttenberg: The suggestions is to deprecate specific and generically denotes in favor of a single denote relationship that corresponds to the generic sense" xsd:string
property_value: IAO:0000116 "see https://github.com/information-artifact-ontology/IAO/issues/25&q=denote" xsd:string
property_value: IAO:0000117 "Alan Ruttenberg" xsd:string
property_value: IAO:0000119 "Smith, Ceusters, Ruttenberg, 2000 years of philosophy" xsd:string
property_value: IAO:0000231 IAO:0000103
is_a: ObsoleteProperty
is_obsolete: true

[Typedef]
id: IAO:0000136
name: is about
def: "A (currently) primitive relation that relates an information artifact to an entity." []
property_value: IAO:0000112 "This document is about information artifacts and their representations" xsd:string
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000116 "7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of \"mentions\" relation. Weaken the is_about relationship to be primitive. \n\nWe will try to build it back up by elaborating the various subproperties that are more precisely defined.\n\nSome currently missing phenomena that should be considered \"about\" are predications - \"The only person who knows the answer is sitting beside me\" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic." xsd:string
property_value: IAO:0000117 "person:Alan Ruttenberg" xsd:string
property_value: IAO:0000119 "Smith, Ceusters, Ruttenberg, 2000 years of philosophy" xsd:string
domain: IAO:0000030 ! information content entity

[Typedef]
id: IAO:0000142
name: mentions
def: "An information artifact IA mentions an entity E exactly when it has a component/part that denotes E" []
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000116 "7/6/2009 Alan Ruttenberg. P4 RC1 munges our GCI so remove it for now: mentions some entity equivalentTo has_part some ('generically denotes' some entity)" xsd:string
property_value: IAO:0000116 "7/6/2009 Alan Ruttenberg: Add this relation following conversation with Jonathan Rees that N&S GCI for is_about was too strong. Really it was simply sufficient. To effect this change we introduce this relation, which is subproperty of is_about, and have previous GCI use this relation \"mentions\" in it's (logical) definition" xsd:string
property_value: IAO:0000117 "Person: Alan Ruttenberg" xsd:string
property_value: IAO:0000117 "PERSON: Jonathan Rees" xsd:string
is_a: IAO:0000136 ! is about

[Typedef]
id: IAO:0000219
name: denotes
def: "A primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically" []
property_value: IAO:0000112 "A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance \"Alan\" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between \"Alan\" and the person that is being named." xsd:string
property_value: IAO:0000116 "2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive.\ng denotes r =def \nr is a portion of reality\nthere is some c that is a concretization of g \nevery c that is a concretization of g specifically denotes r" xsd:string
property_value: IAO:0000117 "person:Alan Ruttenberg" xsd:string
property_value: IAO:0000119 "Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan" xsd:string
domain: IAO:0000030 ! information content entity
range: BFO:0000001 ! entity
is_a: IAO:0000136 ! is about
inverse_of: IAO:0000235 ! denoted by

[Typedef]
id: IAO:0000220
name: obsolete_materially denotes
property_value: IAO:0000116 "see https://github.com/information-artifact-ontology/IAO/issues/25&q=denote" xsd:string
property_value: IAO:0000231 IAO:0000103
is_a: ObsoleteProperty
is_obsolete: true

[Typedef]
id: IAO:0000221
name: is quality measurement of
def: "m is a quality measurement of q at t. When q is a quality, there is a measurement process p that has specified output m, a measurement datum, that is about q" []
property_value: IAO:0000116 "8/6/2009 Alan Ruttenberg: The strategy is to be rather specific with this relationship. There are other kinds of measurements that are not of qualities, such as those that measure time. We will add these as separate properties for the moment and see about generalizing later" xsd:string
property_value: IAO:0000116 "From the second IAO workshop [Alan Ruttenberg 8/6/2009: not completely current, though bringing in comparison is probably important]\n\nThis one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it \"measuring\" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail.\n\nWerner suggests a solution based on \"Magnitudes\" a proposal for which we are awaiting details.\n--\nFrom the second IAO workshop, various comments, [commented on by Alan Ruttenberg 8/6/2009]\n\nunit of measure is a quality, e.g. the length of a ruler.\n\n[We decided to hedge on what units of measure are, instead talking about measurement unit labels, which are the information content entities that are about whatever measurement units are. For IAO we need that information entity in any case. See the term measurement unit label]\n\n[Some struggling with the various subflavors of is_about. We subsequently removed the relation represents, and describes until and only when we have a better theory]\n\na represents b means either a denotes b or a describes\n\ndescribe:\na describes b means a is about b and a allows an inference of at least one quality of b\n\nWe have had a long discussion about denotes versus describes." xsd:string
property_value: IAO:0000116 "From the second IAO workshop: An attempt at tieing the quality to the measurement datum more carefully.\n\na is a magnitude means a is a determinate quality particular inhering in some bearer b existing at a time t that can be represented/denoted by an information content entity e that has parts denoting a unit of measure, a number, and b. The unit of measure is an instance of the determinable quality." xsd:string
property_value: IAO:0000116 "From the second meeting on IAO:\n\nAn attempt at defining assay using Barry's \"reliability\" wording\n\nassay:\nprocess and has_input some material entity\nand has_output some information content entity \nand which is such that instances of this process type reliably generate \noutputs that describes the input." xsd:string
property_value: IAO:0000116 "This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it \"measuring\" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail.\n\nWerner suggests a solution based on \"Magnitudes\" a proposal for which we are awaiting details." xsd:string
property_value: IAO:0000117 "Alan Ruttenberg" xsd:string
domain: IAO:0000109 ! measurement datum
range: BFO:0000019 ! quality
is_a: IAO:0000136 ! is about
inverse_of: IAO:0000417 ! is quality measured as

[Typedef]
id: IAO:0000222
name: obsolete_describes
property_value: IAO:0000231 IAO:0000103
is_a: ObsoleteProperty
is_obsolete: true

[Typedef]
id: IAO:0000223
name: obsolete_represents
property_value: IAO:0000231 IAO:0000103
is_a: ObsoleteProperty
is_obsolete: true

[Typedef]
id: IAO:0000235
name: denoted by
def: "inverse of the relation 'denotes'" []
property_value: IAO:0000117 "Person: Jie Zheng, Chris Stoeckert, Mike Conlon" xsd:string
property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/206
domain: BFO:0000001 ! entity
range: IAO:0000030 ! information content entity

[Typedef]
id: IAO:0000407
name: has coordinate unit label
comment: relating a cartesian spatial coordinate datum to a unit label that together with the values represent a point
domain: IAO:0000400 ! cartesian spatial coordinate datum
range: UO:0000001 ! length unit
is_functional: true
is_a: BFO:0000051 ! has part

[Typedef]
id: IAO:0000413
name: is duration of
def: "relates a process to a time-measurement-datum that represents the duration of the process" []
property_value: IAO:0000114 IAO:0000120
property_value: IAO:0000117 "Person:Alan Ruttenberg" xsd:string
domain: IAO:0000416 ! time measurement datum
range: BFO:0000015 ! process
is_a: IAO:0000136 ! is about

[Typedef]
id: IAO:0000417
name: is quality measured as
def: "inverse of the relation of is quality measurement of" []
property_value: IAO:0000114 IAO:0000120
property_value: IAO:0000116 "2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship" xsd:string
property_value: IAO:0000117 "Person:Alan Ruttenberg" xsd:string

[Typedef]
id: IAO:0000418
name: is quality specification of
def: "A relation between a data item and a quality of a material entity where the material entity is the specified output of a material transformation which achieves an objective specification that indicates the intended value of the specified quality." []
property_value: IAO:0000114 IAO:0000120
property_value: IAO:0000117 "Person:Alan Ruttenberg" xsd:string
property_value: IAO:0000117 "Person:Bjoern Peters" xsd:string
is_a: IAO:0000136 ! is about
inverse_of: IAO:0000419 ! quality is specified as

[Typedef]
id: IAO:0000419
name: quality is specified as
def: "inverse of the relation of is quality specification of" []
property_value: IAO:0000114 IAO:0000120
property_value: IAO:0000116 "2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship" xsd:string
property_value: IAO:0000117 "Person:Alan Ruttenberg" xsd:string
property_value: IAO:0000117 "Person:Bjoern Peters" xsd:string

[Typedef]
id: IAO:0000581
name: has time stamp
def: "relates a time stamped measurement datum to the time measurement datum that denotes the time when the measurement was taken" []
property_value: IAO:0000114 IAO:0000123
property_value: IAO:0000117 "Alan Ruttenberg" xsd:string
domain: IAO:0000582 ! time stamped measurement datum
range: IAO:0000416 ! time measurement datum
is_functional: true
is_a: BFO:0000051 ! has part

[Typedef]
id: IAO:0000583
name: has measurement datum
def: "relates a time stamped measurement datum to the measurement datum that was measured" []
property_value: IAO:0000114 IAO:0000123
property_value: IAO:0000117 "Alan Ruttenberg" xsd:string
domain: IAO:0000582 ! time stamped measurement datum
is_a: BFO:0000051 ! has part

[Typedef]
id: IAO:0020012
name: obsolete_designates
def: "x designates y, if for any given group of language users, x is an information content entity, is about y, and represents y in a linguistic context.." []
property_value: http://purl.org/dc/elements/1.1/creator "Mathias Brochhausen" xsd:string
property_value: IAO:0000231 IAO:0000228
is_a: ObsoleteProperty
is_obsolete: true
replaced_by: IAO:0000219

[Typedef]
id: IAO:0020013
name: is_borrowed_reference_to
def: "x is_borrowed_reference_for y, if x is a proper name that is used to refer to one individual among a specific group after the dubbing process took place." []
property_value: http://purl.org/dc/elements/1.1/creator "Mathias Brochhausen" xsd:string
domain: IAO:0020000 ! identifier
range: BFO:0000001 ! entity
is_asymmetric: true

[Typedef]
id: IAO:0020014
name: is_fixing_reference_to
def: "x is_fixed_reference_for y, if x is an utterance or graphemes concretized as writing quality inhering in some independent continuant that is used to single out one individual and refer to the latter among a specific group after the." []
property_value: http://purl.org/dc/elements/1.1/creator "Mathias Brochhausen" xsd:string
is_asymmetric: true

[Typedef]
id: IAO:0020018
name: is designated by
def: "p1 is designated by p2, if p2 is an information content entity that represents p1 in a linguistic context." []
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
is_asymmetric: true

[Typedef]
id: IAO:0021011
name: legally revokes
def: "d socio-legally revokes s if s participates in d and at the end of d s no longer exists.\nIt is important to note that this going out of existence of s is complete and unlike the going out of existence for material entities which basically always are transformed into something else. After the declaration nothing is left of the socio-legal generically dependent continuant in question." []
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
domain: IAO:0021009 ! deontic declaration
range: IAO:0021008 ! deontic role
is_functional: true
is_a: RO:0000057 ! has_participant
is_asymmetric: true

[Typedef]
id: IAO:0021012
name: obsolete_legally transfers
def: "d socio-legally transfers l if l participates in d and d has specified input  (concretization of l)1 and specified output  (concretization of l)2, where (concretization of l)1 and (concretization of l)2 are not identical." []
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
property_value: IAO:0000231 IAO:0000103
is_functional: true
is_a: ObsoleteProperty
is_obsolete: true
is_asymmetric: true

[Typedef]
id: OBI:0000293
name: has_specified_input
def: "A relation between a planned process and a continuant participating in that process that is not created during  the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of." []
property_value: IAO:0000111 "has_specified_input" xsd:string
property_value: IAO:0000111 "has_specified_input" xsd:string
property_value: IAO:0000112 "see is_input_of example_of_usage" xsd:string
property_value: IAO:0000114 IAO:0000122
property_value: IAO:0000116 "8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works." xsd:string
property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string
property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string
property_value: IAO:0000117 "PERSON: Larry Hunter" xsd:string
property_value: IAO:0000117 "PERSON: Melanie Coutot" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl
domain: OBI:0000011 ! planned process
is_a: RO:0000057 ! has_participant
inverse_of: OBI:0000295 ! is_specified_input_of

[Typedef]
id: OBI:0000295
name: is_specified_input_of
def: "A relation between a planned process and a continuant participating in that process that is not created during  the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of." []
property_value: IAO:0000111 "is_specified_input_of" xsd:string
property_value: IAO:0000112 "some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay" xsd:string
property_value: IAO:0000114 IAO:0000122
property_value: IAO:0000117 "Alan Ruttenberg" xsd:string
property_value: IAO:0000117 "PERSON:Bjoern Peters" xsd:string
range: OBI:0000011 ! planned process
is_a: RO:0000056 ! participates in

[Typedef]
id: OBI:0000299
name: has_specified_output
def: "A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of." []
property_value: IAO:0000111 "has_specified_output" xsd:string
property_value: IAO:0000111 "has_specified_output" xsd:string
property_value: IAO:0000114 IAO:0000122
property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string
property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string
property_value: IAO:0000117 "PERSON: Larry Hunter" xsd:string
property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl
domain: OBI:0000011 ! planned process
is_a: RO:0000057 ! has_participant
inverse_of: OBI:0000312 ! is_specified_output_of

[Typedef]
id: OBI:0000312
name: is_specified_output_of
def: "A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of." []
property_value: IAO:0000111 "is_specified_output_of" xsd:string
property_value: IAO:0000111 "is_specified_output_of" xsd:string
property_value: IAO:0000114 IAO:0000122
property_value: IAO:0000117 "Alan Ruttenberg" xsd:string
property_value: IAO:0000117 "PERSON:Bjoern Peters" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl
range: OBI:0000011 ! planned process
is_a: RO:0000056 ! participates in

[Typedef]
id: OBI:0000846
name: is member of organization
def: "Relating a legal person or organization to an organization in the case where the legal person or organization has a role as member of the organization." []
property_value: IAO:0000111 "is member of organization" xsd:string
property_value: IAO:0000114 IAO:0000120
property_value: IAO:0000116 "2009/10/01 Alan Ruttenberg. Barry prefers generic is-member-of. Question of what the range should be. For now organization. Is organization a population? Would the same relation be used to record members of a population" xsd:string
property_value: IAO:0000116 "JZ: Discussed on May 7, 2012 OBI dev call. Bjoern points out that we need to allow for organizations to be members of organizations. And agreed by the other OBI developers. So, human and organization were specified in 'Domains'. The textual definition was updated based on it." xsd:string
property_value: IAO:0000117 "Person:Alan Ruttenberg" xsd:string
property_value: IAO:0000117 "Person:Helen Parkinson" xsd:string
property_value: IAO:0000119 "Person:Alan Ruttenberg" xsd:string
property_value: IAO:0000119 "Person:Helen Parkinson" xsd:string
property_value: IAO:0000232 "2009/09/28 Alan Ruttenberg. Fucoidan-use-case" xsd:string

[Typedef]
id: OBI:0001688
name: has organization member
def: "Relating an organization to a legal person or organization." []
property_value: IAO:0000111 "has organization member" xsd:string
property_value: IAO:0000114 IAO:0000123
property_value: IAO:0000116 "See tracker:\nhttps://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_id=177891&atid=886178" xsd:string
property_value: IAO:0000117 "Person: Jie Zheng" xsd:string

[Typedef]
id: OMIABIS:0000008
name: owns
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
property_value: IAO:0000600 "This is a primitive relation. This relation is the foundation to the owners right to have the owned entity at his/her full disposal." xsd:string

[Typedef]
id: OMIABIS:0000009
name: administrates
def: "a administrates b if c owns b and some rights and obligations grounded in the owning relation regarding b are transferred  from c to a." []
comment: A definition of "tranfers" object property can be found in d-acts: http:purl.obolibrary.org/iao/d-acts.owl
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
inverse_of: OMRSE:00000068 ! is administered by

[Typedef]
id: OMIABIS:0000048
name: is owned by
def: "a is owned by b if b has complete power over a. All rights and obligations of ownership are grounded in this (primitive) relation. The claims and obligations of ownership can be partially transferred to a third party by the owner, b." []
property_value: IAO:0000119 "Reinach, A. Sämtliche Werke. Texkritische Ausgabe, München: Philosophia Verlag, 1989, p.189-204." xsd:string

[Typedef]
id: OMRSE:00000020
name: is-aggregate-of
name: obsolete is-aggregate-of
comment: We anticipate BFO 2.0 including and defining this relation.  When it does, we will obsolete this property and declare it equivalent to the BFO 2.0 relation.\n
property_value: IAO:0000231 "BFO relation takes precedence." xsd:string
is_a: ObsoleteProperty
is_obsolete: true

[Typedef]
id: OMRSE:00000021
name: obsolete is-component-of-aggregate
comment: At the instance level, this relation is the named inverse of is-aggregate-of.\n\nAt the type level, however, not so.\n\nWe expect BFO 2.0 to have this relation as well, and we will obsolete this property and declare it equivalent to BFO's version when BFO 2.0 comes out.
is_a: ObsoleteProperty
is_obsolete: true

[Typedef]
id: OMRSE:00000068
name: is administered by
is_asymmetric: true

[Typedef]
id: OMRSE:00000070
name: is enrolled in school
range: OMRSE:00000057 ! school organization
is_asymmetric: true

[Typedef]
id: OMRSE:00000071
name: is admitted to hospital
range: OMRSE:00000056 ! hospital organization

[Typedef]
id: OMRSE:00000167
name: provides service

[Typedef]
id: RO:0000052
name: characteristic of
name: inheres in
def: "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." []
def: "a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence" []
comment: Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing.
property_value: IAO:0000111 "inheres in" xsd:string
property_value: IAO:0000112 "this fragility inheres in this vase" xsd:string
property_value: IAO:0000112 "this fragility is a characteristic of this vase" xsd:string
property_value: IAO:0000112 "this red color inheres in this apple" xsd:string
property_value: IAO:0000112 "this red color is a characteristic of this apple" xsd:string
property_value: IAO:0000116 "A dependent inheres in its bearer at all times for which the dependent exists." xsd:string
property_value: IAO:0000118 "inheres_in" xsd:string
property_value: RO:0001900 RO:0001901
is_functional: true
is_a: RO:0002314 ! inheres in part of
inverse_of: RO:0000053 ! bearer of

[Typedef]
id: RO:0000053
name: bearer of
name: bearer_of
name: has characteristic
def: "a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence" []
def: "Inverse of characteristic_of" []
property_value: IAO:0000111 "bearer of" xsd:string
property_value: IAO:0000112 "this apple is bearer of this red color" xsd:string
property_value: IAO:0000112 "this vase is bearer of this fragility" xsd:string
property_value: IAO:0000116 "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." xsd:string
property_value: IAO:0000118 "bearer_of" xsd:string
property_value: IAO:0000118 "is bearer of" xsd:string
property_value: RO:0001900 RO:0001901
range: BFO:0000020 ! specifically dependent continuant
is_inverse_functional: true

[Typedef]
id: RO:0000056
name: participates in
def: "a relation between a continuant and a process, in which the continuant is somehow involved in the process" []
property_value: IAO:0000111 "participates in" xsd:string
property_value: IAO:0000112 "this blood clot participates in this blood coagulation" xsd:string
property_value: IAO:0000112 "this input material (or this output material) participates in this process" xsd:string
property_value: IAO:0000112 "this investigator participates in this investigation" xsd:string
property_value: IAO:0000118 "participates_in" xsd:string
domain: BFO:0000002 ! continuant
range: BFO:0000003 ! occurrent
inverse_of: RO:0000057 ! has_participant

[Typedef]
id: RO:0000057
name: has participant
name: has_participant
def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" []
property_value: http://purl.org/dc/elements/1.1/source http://www.obofoundry.org/ro/#OBO_REL:has_participant xsd:string
property_value: IAO:0000111 "has participant" xsd:string
property_value: IAO:0000112 "this blood coagulation has participant this blood clot" xsd:string
property_value: IAO:0000112 "this investigation has participant this investigator" xsd:string
property_value: IAO:0000112 "this process has participant this input material (or this output material)" xsd:string
property_value: IAO:0000116 "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string
property_value: IAO:0000118 "has_participant" xsd:string
domain: BFO:0000003 ! occurrent
range: BFO:0000002 ! continuant
holds_over_chain: BFO:0000051 RO:0000057

[Typedef]
id: RO:0000058
name: is concretized as
def: "A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants." []
property_value: IAO:0000111 "is concretized as" xsd:string
property_value: IAO:0000112 "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)." xsd:string
property_value: IAO:0000112 "An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process)." xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl xsd:string
domain: BFO:0000031 ! generically dependent continuant
range: BFO:0000020 ! specifically dependent continuant
inverse_of: RO:0000059 ! concretizes

[Typedef]
id: RO:0000059
name: concretizes
def: "A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant." []
property_value: IAO:0000111 "concretizes" xsd:string
property_value: IAO:0000112 "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)." xsd:string
property_value: IAO:0000112 "An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process)." xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl xsd:string
domain: BFO:0000020 ! specifically dependent continuant
range: BFO:0000031 ! generically dependent continuant

[Typedef]
id: RO:0000079
name: function of
def: "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence" []
comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
property_value: IAO:0000112 "this catalysis function is a function of this enzyme" xsd:string
property_value: IAO:0000116 "A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists." xsd:string
property_value: IAO:0000118 "function_of" xsd:string
property_value: IAO:0000118 "is function of" xsd:string
domain: BFO:0000034 ! function
is_a: RO:0000052 ! inheres in
inverse_of: RO:0000085 ! has function

[Typedef]
id: RO:0000080
name: quality of
def: "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" []
comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
property_value: IAO:0000112 "this red color is a quality of this apple" xsd:string
property_value: IAO:0000116 "A quality inheres in its bearer at all times for which the quality exists." xsd:string
property_value: IAO:0000118 "is quality of" xsd:string
property_value: IAO:0000118 "quality_of" xsd:string
is_a: RO:0000052 ! inheres in
inverse_of: RO:0000086 ! has quality

[Typedef]
id: RO:0000081
name: role of
def: "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence" []
comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
property_value: IAO:0000112 "this investigator role is a role of this person" xsd:string
property_value: IAO:0000116 "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists." xsd:string
property_value: IAO:0000118 "is role of" xsd:string
property_value: IAO:0000118 "role_of" xsd:string
is_a: RO:0000052 ! inheres in
inverse_of: RO:0000087 ! has role

[Typedef]
id: RO:0000085
name: has function
def: "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence" []
property_value: IAO:0000112 "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)" xsd:string
property_value: IAO:0000116 "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists." xsd:string
property_value: IAO:0000118 "has_function" xsd:string
domain: BFO:0000004 ! independent continuant
range: BFO:0000034 ! function
is_a: RO:0000053 ! bearer of

[Typedef]
id: RO:0000086
name: has quality
def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" []
property_value: IAO:0000112 "this apple has quality this red color" xsd:string
property_value: IAO:0000116 "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." xsd:string
property_value: IAO:0000118 "has_quality" xsd:string
range: BFO:0000019 ! quality
is_a: RO:0000053 ! bearer of

[Typedef]
id: RO:0000087
name: has role
def: "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence" []
property_value: IAO:0000112 "this person has role this investigator role (more colloquially: this person has this role of investigator)" xsd:string
property_value: IAO:0000116 "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists." xsd:string
property_value: IAO:0000118 "has_role" xsd:string
domain: BFO:0000004 ! independent continuant
range: BFO:0000023 ! role
is_a: RO:0000053 ! bearer of

[Typedef]
id: RO:0000091
name: has disposition
def: "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence" []
domain: BFO:0000004 ! independent continuant
range: BFO:0000016 ! disposition
is_a: RO:0000053 ! bearer of
inverse_of: RO:0000092 ! disposition of

[Typedef]
id: RO:0000092
name: disposition of
def: "inverse of has disposition" []
comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
subset: RO:0002259
is_a: RO:0000052 ! inheres in

[Typedef]
id: RO:0001000
name: derives from
def: "a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" []
subset: ro-eco
property_value: IAO:0000112 "this cell derives from this parent cell (cell division)" xsd:string
property_value: IAO:0000112 "this nucleus derives from this parent nucleus (nuclear division)" xsd:string
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000116 "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'." xsd:string
property_value: IAO:0000118 "derives_from" xsd:string
property_value: IAO:0000232 "This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations." xsd:string
inverse_of: RO:0001001 ! derives into

[Typedef]
id: RO:0001001
name: derives into
def: "a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" []
subset: ro-eco
property_value: IAO:0000112 "this parent cell derives into this cell (cell division)" xsd:string
property_value: IAO:0000112 "this parent nucleus derives into this nucleus (nuclear division)" xsd:string
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000116 "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'." xsd:string
property_value: IAO:0000118 "derives_into" xsd:string

[Typedef]
id: RO:0001015
name: location of
def: "a relation between two independent continuants, the location and the target, in which the target is entirely within the location" []
property_value: IAO:0000111 "is location of" xsd:string
property_value: IAO:0000112 "my head is the location of my brain" xsd:string
property_value: IAO:0000112 "this cage is the location of this rat" xsd:string
property_value: IAO:0000116 "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string
property_value: IAO:0000116 "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string
property_value: IAO:0000118 "location_of" xsd:string
property_value: RO:0001900 RO:0001901
is_transitive: true
inverse_of: RO:0001025 ! located in

[Typedef]
id: RO:0001018
name: contained in
subset: ro-eco
property_value: IAO:0000111 "contained in" xsd:string
property_value: IAO:0000116 "Containment is location not involving parthood, and arises only where some immaterial continuant is involved." xsd:string
property_value: IAO:0000116 "Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation.    If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows:    c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition):" xsd:string
property_value: IAO:0000116 "Intended meaning:\ndomain: material entity\nrange: spatial region or site (immaterial continuant)\n        " xsd:string
property_value: IAO:0000118 "contained_in" xsd:string
property_value: RO:0001900 RO:0001901
domain: BFO:0000040 ! material entity
range: BFO:0000004 ! independent continuant
holds_over_chain: RO:0001025 BFO:0000050
inverse_of: RO:0001019 ! contains

[Typedef]
id: RO:0001019
name: contains
subset: ro-eco
property_value: IAO:0000111 "contains" xsd:string
property_value: RO:0001900 RO:0001901

[Typedef]
id: RO:0001020
name: is allergic trigger for
def: "A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." []
property_value: IAO:0000112 "penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520)" xsd:string
domain: BFO:0000040 ! material entity
is_a: RO:0003302 ! causes or contributes to condition
inverse_of: RO:0001022 ! has allergic trigger

[Typedef]
id: RO:0001021
name: is autoimmune trigger for
def: "A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." []
domain: BFO:0000040 ! material entity
is_a: RO:0003302 ! causes or contributes to condition
inverse_of: RO:0001023 ! has autoimmune trigger

[Typedef]
id: RO:0001022
name: has allergic trigger
def: "A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." []
property_value: IAO:0000112 "penicillin allergy (DOID:0060520) has allergic trigger penicillin (CHEBI:17334)" xsd:string
range: BFO:0000040 ! material entity
is_a: RO:0003302 ! causes or contributes to condition

[Typedef]
id: RO:0001023
name: has autoimmune trigger
def: "A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." []
range: BFO:0000040 ! material entity
is_a: RO:0003302 ! causes or contributes to condition

[Typedef]
id: RO:0001025
name: located in
def: "a relation between two independent continuants, the target and the location, in which the target is entirely within the location" []
property_value: http://purl.org/dc/elements/1.1/source http://www.obofoundry.org/ro/#OBO_REL:located_in xsd:string
property_value: IAO:0000111 "located in" xsd:string
property_value: IAO:0000112 "my brain is located in my head" xsd:string
property_value: IAO:0000112 "this rat is located in this cage" xsd:string
property_value: IAO:0000116 "Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1.    Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus" xsd:string
property_value: IAO:0000116 "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string
property_value: IAO:0000116 "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string
property_value: IAO:0000118 "located_in" xsd:string
property_value: RO:0001900 RO:0001901
domain: BFO:0000004 {http://purl.obolibrary.org/obo/IAO_0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant
range: BFO:0000004 {http://purl.obolibrary.org/obo/IAO_0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant
is_transitive: true

[Typedef]
id: RO:0002000
name: 2D boundary of
def: "a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity" []
property_value: IAO:0000112 "the surface of my skin is a 2D boundary of my body" xsd:string
property_value: IAO:0000116 "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string
property_value: IAO:0000116 "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string
property_value: IAO:0000118 "2D_boundary_of" xsd:string
property_value: IAO:0000118 "boundary of" xsd:string
property_value: IAO:0000118 "is 2D boundary of" xsd:string
property_value: IAO:0000118 "is boundary of" xsd:string
property_value: RO:0001900 RO:0001901
is_a: RO:0002323 ! mereotopologically related to
inverse_of: RO:0002002 ! has 2D boundary

[Typedef]
id: RO:0002002
name: has 2D boundary
def: "a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity" []
property_value: IAO:0000112 "my body has 2D boundary the surface of my skin" xsd:string
property_value: IAO:0000116 "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string
property_value: IAO:0000116 "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string
property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string
property_value: IAO:0000118 "has boundary" xsd:string
property_value: IAO:0000118 "has_2D_boundary" xsd:string
property_value: RO:0001900 RO:0001901
domain: BFO:0000040 ! material entity
range: BFO:0000141 ! immaterial entity
is_a: RO:0002323 ! mereotopologically related to

[Typedef]
id: RO:0002007
name: bounding layer of
def: "X outer_layer_of Y iff:\n. X :continuant that bearer_of some PATO:laminar\n. X part_of Y\n. exists Z :surface\n. X has_boundary Z\n. Z boundary_of Y\n\nhas_boundary: http://purl.obolibrary.org/obo/RO_0002002\nboundary_of: http://purl.obolibrary.org/obo/RO_0002000" []
comment: A relationship that applies between a continuant and its outer, bounding layer.  Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane.
subset: ro-eco
property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string
range: BFO:0000040 ! material entity
is_a: BFO:0000050 ! part of

[Typedef]
id: RO:0002008
name: coincident with
def: "A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other." []
comment: Example: if we define region of chromosome as any subdivision of a chromosome along its long axis, then we can define a region of chromosome that contains only gene x as 'chromosome region' that coincident_with some 'gene x', where the term gene X corresponds to a genomic sequence.
subset: ro-eco
property_value: IAO:0000116 "Note from NCEAS meeting: consider changing primary label" xsd:string
property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string
is_a: RO:0002323 ! mereotopologically related to

[Typedef]
id: RO:0002010
name: regulates in other organism
def: "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." []
property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string
domain: BFO:0000015 ! process
range: BFO:0000015 ! process
is_a: RO:0002418 ! causally upstream of or within

[Typedef]
id: RO:0002011
name: regulates transport of
def: "A relationship that holds between a  process that regulates a transport process and the entity transported by that process." []
subset: ro-eco
property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string

[Typedef]
id: RO:0002012
name: occurent part of
def: "A part of relation that applies only between occurents." []
domain: BFO:0000003 ! occurrent
range: BFO:0000003 ! occurrent
is_a: BFO:0000050 ! part of
is_a: RO:0002418 ! causally upstream of or within

[Typedef]
id: RO:0002013
name: has regulatory component activity
def: "A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B." []
is_a: RO:0002017 ! has component activity
is_a: RO:0002334 ! regulated by
created_by: dos
creation_date: 2017-05-24T09:30:46Z

[Typedef]
id: RO:0002014
name: has negative regulatory component activity
def: "A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole.  More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B." []
comment: By convention GO molecular functions are classified by their effector function.  Internal regulatory functions are treated as components.  For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'.
is_a: RO:0002013 ! has regulatory component activity
is_a: RO:0002335 ! negatively regulated by
created_by: dos
creation_date: 2017-05-24T09:31:01Z

[Typedef]
id: RO:0002015
name: has positive regulatory component activity
def: "A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole.  More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B." []
comment: By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components.  So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'.
is_a: RO:0002013 ! has regulatory component activity
is_a: RO:0002336 ! positively regulated by
created_by: dos
creation_date: 2017-05-24T09:31:17Z

[Typedef]
id: RO:0002016
name: has necessary component activity
comment: A has necessary component activity B if A and B are GO molecular functions  (GO_0003674), A has_component B and B is necessary for A.  For example,  ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity.
is_a: RO:0002017 ! has component activity
is_a: RO:0002336 ! positively regulated by
created_by: dos
creation_date: 2017-05-24T09:36:08Z

[Typedef]
id: RO:0002017
name: has component activity
comment: A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B.
is_a: RO:0002018 ! has component process
created_by: dos
creation_date: 2017-05-24T09:44:33Z

[Typedef]
id: RO:0002018
name: has component process
def: "w 'has process component' p if p and w are processes,  w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." []
domain: BFO:0000015 ! process
range: BFO:0000015 ! process
is_a: RO:0002180 ! has component
created_by: dos
creation_date: 2017-05-24T09:49:21Z

[Typedef]
id: RO:0002019
name: has ligand
def: "A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function." []
is_a: RO:0002233 ! has input
created_by: dos
creation_date: 2017-07-19T17:30:36Z

[Typedef]
id: RO:0002021
name: occurs across
def: "A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization." []
is_a: RO:0002479 ! has part that occurs in
created_by: dos
creation_date: 2017-07-20T17:19:37Z

[Typedef]
id: RO:0002022
name: directly regulated by
comment: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2).  For example, if protein A has protein binding activity(P1) that targets protein B and this binding  regulates the kinase activity (P2) of protein B then P1 directly regulates P2. {xref="GOC:dos"}
is_a: RO:0002334 ! regulated by
inverse_of: RO:0002578 ! directly regulates
created_by: dos
creation_date: 2017-09-17T13:52:24Z

[Typedef]
id: RO:0002023
name: directly negatively regulated by
def: "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2).  For example, if protein A has protein binding activity(P1) that targets protein B and this binding  negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1." [GOC:dos]
is_a: RO:0002022 ! directly regulated by
inverse_of: RO:0002630 ! directly negatively regulates
created_by: dos
creation_date: 2017-09-17T13:52:38Z

[Typedef]
id: RO:0002024
name: directly positively regulated by
def: "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2).  For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1." [GOC:dos]
is_a: RO:0002022 ! directly regulated by
inverse_of: RO:0002629 ! directly positively regulates
created_by: dos
creation_date: 2017-09-17T13:52:47Z

[Typedef]
id: RO:0002025
name: has effector activity
def: "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674),  A 'has component activity' B and B is the effector (output function) of B.  Each compound function has only one effector activity." [GOC:dos]
comment: This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations.
is_functional: true
is_a: RO:0002017 ! has component activity
is_a: RO:0002211 ! regulates
created_by: dos
creation_date: 2017-09-22T14:14:36Z

[Typedef]
id: RO:0002026
name: in register with
def: "A relationship that holds between two images, A and B, where:\nA depicts X;\nB depicts Y;\nX and Y are both of type T'\nC is a 2 layer image consiting of layers A and B;\nA and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other.\nNote: A and B may be 2D or 3D.\nExamples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software." [GOC:dos]
property_value: created_by "dos" xsd:string
is_a: RO:0002323 ! mereotopologically related to
creation_date: 2017-12-07T12:58:06Z

[Typedef]
id: RO:0002081
name: before or simultaneous with
comment: Primitive instance level timing relation between events
subset: ro-eco
property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string
property_value: IAO:0000118 "<=" xsd:string
is_a: RO:0002222 ! temporally related to

[Typedef]
id: RO:0002082
name: simultaneous with
comment: t1 simultaneous_with t2 iff:=  t1 before_or_simultaneous_with t2  and not (t1 before t2)
subset: ro-eco
property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string
is_transitive: true
is_a: RO:0002081 ! before or simultaneous with

[Typedef]
id: RO:0002083
name: before
comment: t1 before t2 iff:=  t1 before_or_simulataneous_with t2  and not (t1 simultaeous_with t2)
subset: ro-eco
property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string
is_transitive: true
is_a: RO:0002081 ! before or simultaneous with

[Typedef]
id: RO:0002084
name: during which ends
comment: Previously had ID  http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point.  No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line.  Official ID now chosen from DOS ID range.
subset: ro-eco
property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string
is_a: RO:0002222 ! temporally related to
inverse_of: RO:0002093 ! ends during

[Typedef]
id: RO:0002085
name: encompasses
comment: Previously had ID  http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point.  No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line.  Official ID now chosen from DOS ID range.
property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string
property_value: IAO:0000118 "di" xsd:string
is_transitive: true
is_a: RO:0002088 ! during which starts
inverse_of: RO:0002092 ! happens during

[Typedef]
id: RO:0002086
name: ends after
comment: X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)
subset: ro-eco
property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string
holds_over_chain: RO:0002093 BFO:0000062
is_transitive: true
is_a: RO:0002222 ! temporally related to

[Typedef]
id: RO:0002087
name: immediately preceded by
comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string
property_value: IAO:0000118 "starts_at_end_of" xsd:string
holds_over_chain: RO:0002224 RO:0002230
is_a: BFO:0000062 ! preceded by
inverse_of: RO:0002090 ! immediately precedes

[Typedef]
id: RO:0002088
name: during which starts
comment: Previously had ID  http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point.  No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line.  Official ID now chosen from DOS ID range.
subset: ro-eco
property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string
is_a: RO:0002222 ! temporally related to
inverse_of: RO:0002091 ! starts during

[Typedef]
id: RO:0002089
name: starts before
subset: ro-eco
property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string
holds_over_chain: RO:0002091 BFO:0000060
is_transitive: true
is_a: RO:0002222 ! temporally related to

[Typedef]
id: RO:0002090
name: immediately precedes
comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)
subset: ro-eco
property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string
property_value: IAO:0000118 "ends_at_start_of" xsd:string
property_value: IAO:0000118 "meets" xsd:string
property_value: RO:0002575 BFO:0000063
holds_over_chain: RO:0002230 RO:0002224
is_a: BFO:0000063 ! precedes

[Typedef]
id: RO:0002091
name: starts during
comment: X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y))
subset: ro-eco
property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string
property_value: IAO:0000118 "io" xsd:string
domain: BFO:0000003 ! occurrent
range: BFO:0000003 ! occurrent
is_a: RO:0002222 ! temporally related to

[Typedef]
id: RO:0002092
name: happens during
comment: X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y))
subset: ro-eco
property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string
property_value: IAO:0000118 "d" xsd:string
property_value: IAO:0000118 "during" xsd:string
is_transitive: true
is_a: RO:0002093 ! ends during

[Typedef]
id: RO:0002093
name: ends during
comment: X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). 
subset: ro-eco
property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string
property_value: IAO:0000118 "o" xsd:string
property_value: IAO:0000118 "overlaps" xsd:string
is_a: RO:0002222 ! temporally related to

[Typedef]
id: RO:0002131
name: overlaps
def: "x overlaps y if and only if there exists some z such that x has part z and z part of y" []
subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension
subset: http://purl.obolibrary.org/obo/valid_for_gocam
subset: ro-eco
property_value: IAO:0000114 IAO:0000125
property_value: RO:0001900 RO:0001901
holds_over_chain: BFO:0000050 BFO:0000050
holds_over_chain: BFO:0000051 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"}
holds_over_chain: BFO:0000051 RO:0002131
is_a: RO:0002323 ! mereotopologically related to
transitive_over: BFO:0000050 ! part of
expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)" []

[Typedef]
id: RO:0002150
name: continuous with
def: "X continuous_with Y if and only if X and Y share a fiat boundary." []
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string
property_value: IAO:0000118 "connected to" xsd:string
property_value: IAO:0000232 "The label for this relation was previously connected to. I relabeled this to \"continuous with\". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)" xsd:string
property_value: RO:0001900 RO:0001901
property_value: seeAlso FMA:85972 xsd:string
domain: BFO:0000004 ! independent continuant
range: BFO:0000004 ! independent continuant
is_a: RO:0002323 ! mereotopologically related to

[Typedef]
id: RO:0002151
name: partially overlaps
def: "x partially overlaps y iff there exists some z such that z is part of x and z is part of y, and it is also the case that neither x is part of y or y is part of x" []
subset: ro-eco
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000116 "We would like to include disjointness axioms with part_of and has_part, however this is not possible in OWL2 as these are non-simple properties and hence cannot appear in a disjointness axiom" xsd:string
property_value: IAO:0000118 "proper overlaps" xsd:string
property_value: IAO:0000426 "(forall (?x ?y) \n	(iff \n		(proper_overlaps ?x ?y)\n		(and \n			(overlaps ?x ?y)\n			(not (part_of ?x ?y)) \n			(not (part_of ?y ?x)))))" xsd:string
property_value: RO:0001900 RO:0001901
is_a: RO:0002131 ! overlaps

[Typedef]
id: RO:0002163
name: spatially disjoint from
def: "A is spatially_disjoint_from B if and only if they have no parts in common" []
subset: ro-eco
property_value: http://xmlns.com/foaf/0.1/page https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern xsd:anyURI
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000116 "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552
property_value: IAO:0000232 "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy" xsd:string
property_value: RO:0001900 RO:0001901
is_a: RO:0002323 ! mereotopologically related to
expand_expression_to: "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)" []

[Typedef]
id: RO:0002170
name: connected to
def: "a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b" []
property_value: http://xmlns.com/foaf/0.1/page https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern xsd:anyURI
property_value: http://xmlns.com/foaf/0.1/page https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern xsd:anyURI
property_value: IAO:0000112 "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." xsd:string
property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552
is_a: RO:0002323 ! mereotopologically related to

[Typedef]
id: RO:0002176
name: connects
def: "c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system." []
property_value: http://xmlns.com/foaf/0.1/page https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern xsd:anyURI
property_value: http://xmlns.com/foaf/0.1/page https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern xsd:anyURI
property_value: IAO:0000112 "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." xsd:string
property_value: IAO:0000112 "The M8 connects Glasgow and Edinburgh" xsd:string
property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552
domain: BFO:0000004 ! independent continuant
is_a: RO:0002323 ! mereotopologically related to

[Typedef]
id: RO:0002178
name: supplies
def: "Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy." []
property_value: IAO:0000116 "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure" xsd:string
property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205
is_a: RO:0002170 ! connected to

[Typedef]
id: RO:0002180
name: has component
def: "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." []
subset: ro-eco
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000116 "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." xsd:string
property_value: IAO:0000232 "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." xsd:string
property_value: RO:0001900 RO:0001901
property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:Componency
is_a: BFO:0000051 ! has part

[Typedef]
id: RO:0002201
name: phenotype of
def: "inverse of has phenotype" []
subset: ro-eco
subset: RO:0002259
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_functional: true

[Typedef]
id: RO:0002205
name: has gene product
def: "x has gene product y if and only if x is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from y" []
property_value: IAO:0000112 "every HOTAIR lncRNA is the gene product of some HOXC gene" xsd:string
property_value: IAO:0000112 "every sonic hedgehog protein (PR:000014841) is the gene product of some sonic hedgehog gene" xsd:string
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "Chris Mungall" xsd:string
domain: BFO:0000002 ! continuant
range: BFO:0000004 ! independent continuant

[Typedef]
id: RO:0002211
name: regulates
def: "process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2." []
subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension
subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term
subset: http://purl.obolibrary.org/obo/valid_for_go_ontology
subset: http://purl.obolibrary.org/obo/valid_for_gocam
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000116 "We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000117 "David Hill" xsd:string
property_value: IAO:0000117 "Tanya Berardini" xsd:string
property_value: IAO:0000119 "GO" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: IAO:0000232 "Regulation precludes parthood; the regulatory process may not be within the regulated process." xsd:string
property_value: IAO:0000589 "regulates (processual)" xsd:string
property_value: IAO:0000600 "false" xsd:boolean
domain: BFO:0000015 ! process
range: BFO:0000015 ! process
holds_over_chain: RO:0002230 RO:0002211
holds_over_chain: RO:0002578 RO:0002578
is_transitive: true
is_a: RO:0002411 ! causally upstream of
inverse_of: RO:0002334 ! regulated by
transitive_over: RO:0002025 ! has effector activity

[Typedef]
id: RO:0002212
name: negatively regulates
def: "Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2." []
subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension
subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term
subset: http://purl.obolibrary.org/obo/valid_for_go_ontology
subset: http://purl.obolibrary.org/obo/valid_for_gocam
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: IAO:0000589 "negatively regulates (process to process)" xsd:string
property_value: RO:0004050 RO:0002211
holds_over_chain: RO:0002230 RO:0002212
is_a: RO:0002211 ! regulates
is_a: RO:0002305 ! causally upstream of, negative effect
inverse_of: RO:0002335 ! negatively regulated by

[Typedef]
id: RO:0002213
name: positively regulates
def: "Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2." []
subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension
subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term
subset: http://purl.obolibrary.org/obo/valid_for_go_ontology
subset: http://purl.obolibrary.org/obo/valid_for_gocam
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: IAO:0000589 "positively regulates (process to process)" xsd:string
property_value: RO:0004049 RO:0002211
holds_over_chain: RO:0002212 RO:0002212
holds_over_chain: RO:0002230 RO:0002213
is_transitive: true
is_a: RO:0002211 ! regulates
is_a: RO:0002304 ! causally upstream of, positive effect
inverse_of: RO:0002336 ! positively regulated by

[Typedef]
id: RO:0002214
name: has prototype
def: "x has prototype y if and only if x is an instance of C and y is a prototypical instance of C. For example, every instance of heart, both normal and abnormal is related by the has prototype relation to some instance of a \"canonical\" heart, which participates in blood circulation." []
property_value: IAO:0000112 "'human p53 protein' SubClassOf some ('has prototype' some ('participates in' some 'DNA repair'))" xsd:string
property_value: IAO:0000112 "heart SubClassOf 'has prototype' some ('participates in' some 'blood circulation')" xsd:string
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000116 "Experimental. In future there may be a formalization in which this relation is treated as a shortcut to some modal logic axiom. We may decide to obsolete this and adopt a more specific evolutionary relationship (e.g. evolved from)" xsd:string
property_value: IAO:0000116 "This property can be used to make weaker forms of certain relations by chaining an additional property. For example, we may say: retina SubClassOf has_prototype some 'detection of light'. i.e. every retina is related to a prototypical retina instance which is detecting some light. Note that this is very similar to 'capable of', but this relation affords a wider flexibility. E.g. we can make a relation between continuants." xsd:string
property_value: IAO:0000116 "TODO: add homeomorphy axiom" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string

[Typedef]
id: RO:0002215
name: capable of
def: "A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. " []
subset: ro-eco
property_value: IAO:0000112 "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" xsd:string
property_value: IAO:0000112 "osteoclast SubClassOf 'capable of' some 'bone resorption'" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "has function realized in" xsd:string
property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20123131
property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/21208450
property_value: IAO:0000232 "For compatibility with BFO, this relation has a shortcut definition in which the expression \"capable of some P\" expands to \"bearer_of (some realized_by only P)\"." xsd:string
domain: BFO:0000004 ! independent continuant
range: BFO:0000015 ! process
is_a: RO:0002216 ! capable of part of
expand_expression_to: "RO_0000053 some (RO_0000054 only ?Y)" []

[Typedef]
id: RO:0002216
name: capable of part of
def: "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." []
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "has function in" xsd:string
property_value: seeAlso "defining-property-chains-involving-reflexivity"
holds_over_chain: RO:0002215 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"}
is_a: RO:0002328 ! functionally related to
is_a: RO:0002500 ! causal agent in process
expand_expression_to: "RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y))" []

[Typedef]
id: RO:0002217
name: actively participates in
name: obsolete actively participates in
def: "OBSOLETE x actively participates in y if and only if x participates in y and x realizes some active role" []
def: "x actively participates in y if and only if x participates in y and x realizes some active role" []
comment: Obsoleted as the inverse property was obsoleted.
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "agent in" xsd:string
is_a: ObsoleteProperty
is_a: RO:0000056 ! participates in
inverse_of: RO:0002218 ! has active participant
is_obsolete: true

[Typedef]
id: RO:0002218
name: has active participant
name: obsolete has active participant
def: "x has participant y if and only if x realizes some active role that inheres in y" []
subset: ro-eco
property_value: IAO:0000112 "'heart development' has active participant some Shh protein" xsd:string
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000116 "This may be obsoleted and replaced by the original 'has agent' relation" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "has agent" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/ro.owl xsd:string
is_a: RO:0000057 ! has_participant
is_obsolete: true

[Typedef]
id: RO:0002219
name: surrounded by
def: "x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x" []
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: RO:0001900 RO:0001901
is_a: RO:0002220 ! adjacent to
inverse_of: RO:0002221 ! surrounds

[Typedef]
id: RO:0002220
name: adjacent to
def: "x adjacent to y if and only if x and y share a boundary." []
property_value: IAO:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="issuecomment-218584934"}
property_value: IAO:0000112 "The epidermis layer of a vertebrate is adjacent to the dermis." xsd:string
property_value: IAO:0000112 "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." xsd:string
property_value: IAO:0000112 "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." xsd:string
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000116 "This relation acts as a join point with BSPO" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: RO:0001900 RO:0001901
domain: BFO:0000004 ! independent continuant
range: BFO:0000004 ! independent continuant
is_a: RO:0002163 ! spatially disjoint from

[Typedef]
id: RO:0002221
name: surrounds
def: "inverse of surrounded by" []
subset: RO:0002259
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: RO:0001900 RO:0001901
is_a: RO:0002220 ! adjacent to

[Typedef]
id: RO:0002222
name: temporally related to
comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.
subset: ro-eco
property_value: http://purl.org/dc/elements/1.1/source https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 xsd:anyURI
property_value: http://purl.org/dc/terms/source https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 xsd:anyURI
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 https://en.wikipedia.org/wiki/Allen%27s_interval_algebra
property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." xsd:string
domain: BFO:0000003 ! occurrent
range: BFO:0000003 ! occurrent

[Typedef]
id: RO:0002223
name: starts
def: "inverse of starts with" []
subset: ro-eco
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 "Allen" xsd:string
is_a: BFO:0000050 ! part of
is_a: RO:0002222 ! temporally related to
inverse_of: RO:0002224 ! starts with

[Typedef]
id: RO:0002224
name: starts with
def: "x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." []
subset: ro-eco
property_value: IAO:0000112 "Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor" xsd:string
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "started by" xsd:string
is_transitive: true
is_a: BFO:0000051 ! has part
is_a: RO:0002222 ! temporally related to

[Typedef]
id: RO:0002229
name: ends
def: "inverse of ends with" []
subset: ro-eco
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: BFO:0000050 ! part of
is_a: RO:0002222 ! temporally related to
inverse_of: RO:0002230 ! ends with

[Typedef]
id: RO:0002230
name: ends with
def: "x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." []
subset: ro-eco
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "finished by" xsd:string
is_transitive: true
is_a: BFO:0000051 ! has part
is_a: RO:0002222 ! temporally related to

[Typedef]
id: RO:0002231
name: has start location
def: "x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y" []
subset: ro-eco
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "starts with process that occurs in" xsd:string
domain: BFO:0000015 ! process
range: BFO:0000004 ! independent continuant
holds_over_chain: RO:0002224 BFO:0000066
is_a: RO:0002479 ! has part that occurs in

[Typedef]
id: RO:0002232
name: has end location
def: "x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y" []
subset: ro-eco
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "ends with process that occurs in" xsd:string
domain: BFO:0000015 ! process
range: BFO:0000004 ! independent continuant
holds_over_chain: RO:0002230 BFO:0000066
is_a: RO:0002479 ! has part that occurs in

[Typedef]
id: RO:0002233
name: has input
def: "p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p." []
subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension
subset: http://purl.obolibrary.org/obo/valid_for_go_ontology
subset: http://purl.obolibrary.org/obo/valid_for_gocam
subset: ro-eco
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "consumes" xsd:string
domain: BFO:0000015 ! process
range: BFO:0000040 ! material entity
holds_over_chain: RO:0002224 RO:0002233
is_a: RO:0000057 ! has_participant
inverse_of: RO:0002352 ! input of

[Typedef]
id: RO:0002234
name: has output
def: "p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p." []
subset: ro-eco
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "produces" xsd:string
is_a: RO:0000057 ! has_participant
inverse_of: RO:0002353 ! output of

[Typedef]
id: RO:0002240
name: has exposure receptor
def: "A broad relationship between an exposure event or process and any entity (e.g., an organism, organism population, or an organism part) that interacts with an exposure stimulus during the exposure event." []
property_value: IAO:0000119 ExO:0000001 xsd:string
is_a: RO:0002244 ! related via exposure to

[Typedef]
id: RO:0002241
name: has exposure stressor
def: "A broad relationship between an exposure event or process and any agent, stimulus, activity, or event that causes stress or tension on an organism and interacts with an exposure receptor during an exposure event." []
property_value: IAO:0000119 ExO:0000000 xsd:string
is_a: RO:0002309 ! has exposure stimulus

[Typedef]
id: RO:0002242
name: has exposure route
def: "A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor" []
property_value: IAO:0000119 ExO:0000055 xsd:string
is_a: RO:0002244 ! related via exposure to

[Typedef]
id: RO:0002243
name: has exposure transport path
def: "A broad relationship between an exposure event or process and the course takes from the source to the target." []
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ExO_0000004 xsd:anyURI
is_a: RO:0002244 ! related via exposure to

[Typedef]
id: RO:0002244
name: related via exposure to
def: "Any relationship between an exposure event or process and any other entity." []
property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes." xsd:string
is_a: RO:0002410 ! causally related to

[Typedef]
id: RO:0002248
name: has active ingredient
def: "A relationship that holds between a substance and a chemical entity, if the chemical entity is part of the substance, and the chemical entity forms the biologically active component of the substance." []
synonym: "has active pharmaceutical ingredient" RELATED []
synonym: "has active substance" EXACT []
property_value: IAO:0000112 "Any portion of roundup 'has active ingredient' some glyphosate" xsd:string
domain: BFO:0000040 ! material entity
range: BFO:0000040 ! material entity
is_a: BFO:0000051 ! has part
inverse_of: RO:0002249 ! active ingredient in'

[Typedef]
id: RO:0002249
name: active ingredient in'
def: "inverse of has active ingredient" []
subset: RO:0002259
is_a: BFO:0000050 ! part of

[Typedef]
id: RO:0002252
name: connecting branch of
def: "b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t." []
is_a: RO:0002375 ! in branching relationship with
inverse_of: RO:0002253 ! has connecting branch

[Typedef]
id: RO:0002253
name: has connecting branch
def: "inverse of connecting branch of" []
subset: RO:0002259
is_a: RO:0002375 ! in branching relationship with

[Typedef]
id: RO:0002263
name: acts upstream of
def: "c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes." []
subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term
property_value: IAO:0000112 "A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision." xsd:string
property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of
holds_over_chain: RO:0002327 RO:0002411
is_a: RO:0002264 ! acts upstream of or within

[Typedef]
id: RO:0002264
name: acts upstream of or within
def: "c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process." []
subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term
synonym: "affects" RELATED []
property_value: IAO:0000112 "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." xsd:string
property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within
holds_over_chain: RO:0002327 RO:0002418
is_a: RO:0002500 ! causal agent in process

[Typedef]
id: RO:0002302
name: is treated by substance
def: "Inverse of 'is substance that treats'" []
subset: RO:0002259
property_value: http://purl.org/dc/elements/1.1/creator "cjm" xsd:string
is_a: RO:0002410 ! causally related to
inverse_of: RO:0002606 ! is substance that treats

[Typedef]
id: RO:0002304
name: causally upstream of, positive effect
comment: holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y
subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension
subset: http://purl.obolibrary.org/obo/valid_for_gocam
property_value: http://purl.org/dc/elements/1.1/creator "cjm" xsd:string
property_value: http://purl.org/dc/terms/creator "cjm" xsd:string
property_value: RO:0004049 RO:0002411
is_a: RO:0002411 ! causally upstream of
is_a: RO:0004047 ! causally upstream of or within, positive effect

[Typedef]
id: RO:0002305
name: causally upstream of, negative effect
comment: holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y
property_value: http://purl.org/dc/elements/1.1/creator "cjm" xsd:string
property_value: http://purl.org/dc/terms/creator "cjm" xsd:string
property_value: RO:0004050 RO:0002411
is_a: RO:0002411 ! causally upstream of
is_a: RO:0004046 ! causally upstream of or within, negative effect

[Typedef]
id: RO:0002309
name: has exposure stimulus
def: "A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event." []
property_value: http://purl.org/dc/elements/1.1/contributor "Austin Meier" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Chris Mungall" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Marie Angelique Laporte" xsd:string
is_a: RO:0002244 ! related via exposure to
created_by: cjm
creation_date: 2017-06-05T17:35:04Z

[Typedef]
id: RO:0002314
name: inheres in part of
def: "q inheres in part of w if and only if there exists some p such that q inheres in p and p part of w." []
property_value: IAO:0000116 "Because part_of is transitive, inheres in is a sub-relation of inheres in part of" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205
property_value: RO:0001900 RO:0001901
property_value: seeAlso "defining-property-chains-involving-reflexivity"
holds_over_chain: RO:0000052 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"}
is_a: RO:0002502 ! depends on
transitive_over: BFO:0000050 ! part of

[Typedef]
id: RO:0002323
name: mereotopologically related to
def: "A mereological relationship or a topological relationship" []
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" xsd:string
property_value: RO:0001900 RO:0001901

[Typedef]
id: RO:0002325
name: colocalizes with
def: "a colocalizes_with b if and only if  a is transiently or peripherally associated with b[GO]." []
property_value: http://purl.org/dc/elements/1.1/creator "Gene Ontology Consortium" xsd:string
property_value: IAO:0000112 "Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826)" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://www.geneontology.org/GO.annotation.conventions.shtml#colocalizes_with xsd:string
property_value: IAO:0000232 "In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO]" xsd:string
domain: BFO:0000040 ! material entity
range: BFO:0000040 ! material entity
is_a: RO:0002323 ! mereotopologically related to

[Typedef]
id: RO:0002326
name: contributes to
property_value: IAO:0000112 "ATP citrate lyase (ACL) in Arabidopsis: it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity." xsd:string
property_value: IAO:0000112 "eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to \"ribosome binding\". And all three are part_of an eIF2 complex" xsd:string
property_value: IAO:0000112 "Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity." xsd:string
property_value: IAO:0000116 "We would like to say\n\nif and only if\n exists c', p'\n  c part_of c' and c' capable_of p\n   and\n  c capable_of p' and p' part_of p\nthen\n c contributes_to p\n\nHowever, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction." xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://www.geneontology.org/GO.annotation.conventions.shtml#contributes_to xsd:string
property_value: IAO:0000232 "In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. " xsd:string
is_a: RO:0002216 ! capable of part of
is_a: RO:0002329 ! part of structure that is capable of

[Typedef]
id: RO:0002327
name: enables
subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term
property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "catalyzes" xsd:string
property_value: IAO:0000118 "executes" xsd:string
property_value: IAO:0000118 "has" xsd:string
property_value: IAO:0000118 "is catalyzing" xsd:string
property_value: IAO:0000118 "is executing" xsd:string
property_value: IAO:0000232 "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." xsd:string
property_value: IAO:0000232 "This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time." xsd:string
is_a: RO:0002215 ! capable of
inverse_of: RO:0002333 ! enabled by
transitive_over: BFO:0000051 ! has part
transitive_over: RO:0002017 ! has component activity

[Typedef]
id: RO:0002328
name: functionally related to
def: "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." []
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000232 "This is a grouping relation that collects relations used for the purpose of connecting structure and function" xsd:string

[Typedef]
id: RO:0002329
name: part of structure that is capable of
def: "this relation holds between c and p when c is part of some c', and c' is capable of p." []
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "false" xsd:boolean
holds_over_chain: BFO:0000050 RO:0002215 {http://purl.obolibrary.org/obo/RO_0002581="true"}
is_a: RO:0002328 ! functionally related to

[Typedef]
id: RO:0002331
name: involved in
def: "c involved_in p if and only if c enables some process p', and p' is part of p" []
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "actively involved in" xsd:string
property_value: IAO:0000118 "enables part of" xsd:string
property_value: seeAlso Involved:in
holds_over_chain: RO:0002327 BFO:0000050
is_a: RO:0000056 ! participates in
is_a: RO:0002217 ! obsolete actively participates in
is_a: RO:0002431 ! involved in or involved in regulation of
transitive_over: BFO:0000050 ! part of

[Typedef]
id: RO:0002332
name: regulates levels of
def: "p regulates levels of c if p regulates some amount (PATO:0000070) of c" []
property_value: IAO:0000112 "every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: IAO:0000589 "regulates levels of (process to entity)" xsd:string
domain: BFO:0000015 ! process
range: BFO:0000040 ! material entity
is_a: RO:0002328 ! functionally related to

[Typedef]
id: RO:0002333
name: enabled by
def: "inverse of enables" []
subset: http://purl.obolibrary.org/obo/valid_for_gocam
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: RO:0000057 ! has_participant
is_a: RO:0002328 ! functionally related to

[Typedef]
id: RO:0002334
name: regulated by
def: "inverse of regulates" []
subset: RO:0002259
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000589 "regulated by (processual)" xsd:string
domain: BFO:0000015 ! process
range: BFO:0000015 ! process
is_transitive: true
is_a: RO:0002427 ! causally downstream of or within

[Typedef]
id: RO:0002335
name: negatively regulated by
def: "inverse of negatively regulates" []
subset: RO:0002259
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: RO:0002334 ! regulated by

[Typedef]
id: RO:0002336
name: positively regulated by
def: "inverse of positively regulates" []
subset: RO:0002259
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: RO:0002334 ! regulated by

[Typedef]
id: RO:0002337
name: related via localization to
def: "A relationship that holds via some process of localization" []
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000232 "Do not use this relation directly. It is a grouping relation." xsd:string
domain: BFO:0000015 ! process
range: BFO:0000002 ! continuant

[Typedef]
id: RO:0002338
name: has target start location
def: "This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination." []
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: RO:0002344 ! results in transport to from or in

[Typedef]
id: RO:0002339
name: has target end location
def: "This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l." []
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: RO:0002344 ! results in transport to from or in

[Typedef]
id: RO:0002341
name: results in transport along
def: "Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l " []
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: RO:0002337 ! related via localization to

[Typedef]
id: RO:0002342
name: results in transport across
def: "Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m." []
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: RO:0002021 ! occurs across
is_a: RO:0002344 ! results in transport to from or in

[Typedef]
id: RO:0002344
name: results in transport to from or in
property_value: IAO:0000112 "'mitochondrial transport' results_in_transport_to_from_or_in some  mitochondrion (GO:0005739)" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: RO:0002337 ! related via localization to

[Typedef]
id: RO:0002350
name: member of
def: "is member of is a mereological relation between a item and a collection." []
property_value: IAO:0000112 "An organism that is a member of a population of organisms" xsd:string
property_value: IAO:0000118 "is member of" xsd:string
property_value: IAO:0000118 "member part of" xsd:string
property_value: IAO:0000119 "SIO" xsd:string
property_value: RO:0001900 RO:0001901
is_a: BFO:0000050 ! part of
inverse_of: RO:0002351 ! has member

[Typedef]
id: RO:0002351
name: has member
def: "has member is a mereological relation between a collection and an item." []
property_value: IAO:0000119 "SIO" xsd:string
property_value: RO:0001900 RO:0001901
is_a: BFO:0000051 ! has part

[Typedef]
id: RO:0002352
name: input of
def: "inverse of has input" []
subset: ro-eco
subset: RO:0002259
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: RO:0000056 ! participates in
is_a: RO:0002328 ! functionally related to

[Typedef]
id: RO:0002353
name: output of
def: "inverse of has output" []
subset: ro-eco
subset: RO:0002259
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: RO:0000056 ! participates in
is_a: RO:0002328 ! functionally related to

[Typedef]
id: RO:0002354
name: formed as result of
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: RO:0002353 ! output of

[Typedef]
id: RO:0002360
name: has dendrite location
property_value: http://purl.org/dc/elements/1.1/source http://neurolex.org/wiki/Property:DendriteLocation xsd:anyURI
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: RO:0002131 ! overlaps

[Typedef]
id: RO:0002375
name: in branching relationship with
def: "A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network." []
property_value: http://xmlns.com/foaf/0.1/page https://github.com/obophenotype/uberon/issues/170 xsd:anyURI
property_value: IAO:0000114 IAO:0000428
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships" xsd:string
property_value: IAO:0000232 "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)" xsd:string
property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png
domain: BFO:0000040 ! material entity
range: BFO:0000040 ! material entity
is_a: BFO:0000050 ! part of
is_a: RO:0002323 ! mereotopologically related to

[Typedef]
id: RO:0002376
name: tributary of
def: "x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein." []
subset: ro-eco
property_value: IAO:0000112 "Deschutes River tributary_of Columbia River" xsd:string
property_value: IAO:0000112 "inferior epigastric vein tributary_of external iliac vein" xsd:string
property_value: IAO:0000114 IAO:0000428
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "drains into" xsd:string
property_value: IAO:0000118 "drains to" xsd:string
property_value: IAO:0000118 "tributary channel of" xsd:string
property_value: IAO:0000119 http://en.wikipedia.org/wiki/Tributary xsd:string
property_value: IAO:0000119 http://www.medindia.net/glossary/venous_tributary.htm xsd:string
property_value: IAO:0000232 "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)" xsd:anyURI
property_value: seeAlso http://dbpedia.org/ontology/drainsTo
property_value: seeAlso http://en.wikipedia.org/wiki/Tributary xsd:anyURI
is_a: RO:0002375 ! in branching relationship with

[Typedef]
id: RO:0002377
name: distributary of
def: "x distributary_of y if and only if x is capable of channeling the flow of a substance to y, where y channels less of the substance than x" []
comment: This is both a mereotopological relationship and a relationship defined in connection to processes. It concerns both the connecting structure, and how this structure is disposed to causally affect flow processes
subset: ro-eco
property_value: IAO:0000112 "Deschutes River distributary_of Little Lava Lake" xsd:string
property_value: IAO:0000114 IAO:0000428
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "branch of" xsd:string
property_value: IAO:0000118 "distributary channel of" xsd:string
property_value: IAO:0000119 http://en.wikipedia.org/wiki/Distributary xsd:string
is_a: RO:0002375 ! in branching relationship with

[Typedef]
id: RO:0002378
name: anabranch of
def: "x anabranch_of y if x is a distributary of y (i.e. it channels a from a larger flow from y) and x ultimately channels the flow back into y." []
subset: ro-eco
property_value: IAO:0000114 IAO:0000428
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "anastomoses with" xsd:string
is_a: RO:0002377 ! distributary of
disjoint_from: RO:0002382 ! proper distributary of
disjoint_from: RO:0002383 ! proper tributary of

[Typedef]
id: RO:0002379
name: spatially coextensive with
def: "x spatially_coextensive_with y if and inly if x and y have the same location" []
property_value: IAO:0000112 "A lump of clay and a statue" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000232 "This relation is added for formal completeness. It is unlikely to be used in many practical scenarios" xsd:string
is_a: RO:0002131 ! overlaps

[Typedef]
id: RO:0002380
name: branching part of
def: "x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y" []
subset: ro-eco
property_value: IAO:0000114 IAO:0000428
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: seeAlso FMA:85994 xsd:string
is_a: BFO:0000050 ! part of
is_a: RO:0002375 ! in branching relationship with
inverse_of: RO:0002569 ! has branching part

[Typedef]
id: RO:0002381
name: main stem of
def: "x main_stem_of y if y is a branching structure and x is a channel that traces a linear path through y, such that x has higher capacity than any other such path." []
subset: ro-eco
property_value: IAO:0000114 IAO:0000428
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: RO:0002375 ! in branching relationship with

[Typedef]
id: RO:0002382
name: proper distributary of
def: "x proper_distributary_of y iff x distributary_of y and x does not flow back into y" []
subset: ro-eco
property_value: IAO:0000114 IAO:0000428
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: RO:0002377 ! distributary of

[Typedef]
id: RO:0002383
name: proper tributary of
def: "x proper_tributary_of y iff x tributary_of y and x does not originate from y" []
subset: ro-eco
property_value: IAO:0000114 IAO:0000428
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: RO:0002376 ! tributary of

[Typedef]
id: RO:0002400
name: has direct input
def: "p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p." []
property_value: IAO:0000112 "'protein catabolic process' SubClassOf has_direct_input some protein" xsd:string
property_value: IAO:0000114 IAO:0000428
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "directly consumes" xsd:string
property_value: IAO:0000232 "This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate'" xsd:string
is_a: RO:0002233 ! has input

[Typedef]
id: RO:0002401
name: obsolete has indirect input
comment: Likely to be obsoleted. See:\nhttps://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit
property_value: IAO:0000114 IAO:0000428
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_obsolete: true

[Typedef]
id: RO:0002402
name: obsolete has direct output
def: "p has direct input c iff c is a participanti n p, c is present at the end of p, and c is not present at the beginning of c. " []
property_value: IAO:0000112 "translation SubClassOf has_direct_output some protein" xsd:string
property_value: IAO:0000114 IAO:0000428
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "directly produces" xsd:string
is_obsolete: true

[Typedef]
id: RO:0002403
name: obsolete has indirect output
comment: Likely to be obsoleted. See:\nhttps://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit
property_value: IAO:0000114 IAO:0000428
property_value: IAO:0000117 "Chris Mungall" xsd:string
holds_over_chain: RO:0002411 RO:0002402
is_obsolete: true

[Typedef]
id: RO:0002404
name: causally downstream of
def: "inverse of upstream of" []
property_value: IAO:0000114 IAO:0000428
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: BFO:0000062 ! preceded by
is_a: RO:0002427 ! causally downstream of or within
inverse_of: RO:0002411 ! causally upstream of

[Typedef]
id: RO:0002405
name: immediately causally downstream of
property_value: IAO:0000114 IAO:0000428
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: RO:0002087 ! immediately preceded by
is_a: RO:0002404 ! causally downstream of
inverse_of: RO:0002412 ! immediately causally upstream of

[Typedef]
id: RO:0002406
name: directly activates
def: "p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q" []
property_value: IAO:0000114 IAO:0000428
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "directly positively regulates" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: IAO:0000589 "directly activates (process to process)" xsd:string
is_a: RO:0002629 ! directly positively regulates

[Typedef]
id: RO:0002407
name: indirectly activates
def: "p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q" []
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "indirectly positively regulates" xsd:string
property_value: RO:0002579 RO:0002213
is_transitive: true
is_a: RO:0002213 ! positively regulates

[Typedef]
id: RO:0002408
name: directly inhibits
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "directly negatively regulates" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: IAO:0000589 "directly inhibits (process to process)" xsd:string
is_a: RO:0002630 ! directly negatively regulates

[Typedef]
id: RO:0002409
name: indirectly inhibits
property_value: IAO:0000114 IAO:0000428
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "indirectly negatively regulates" xsd:string
property_value: RO:0002579 RO:0002212
is_transitive: true
is_a: RO:0002212 ! negatively regulates

[Typedef]
id: RO:0002410
name: causally related to
def: "This relation groups causal relations between material entities and causal relations between processes" []
property_value: IAO:0000114 IAO:0000428
property_value: IAO:0000116 "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string

[Typedef]
id: RO:0002411
name: causally upstream of
def: "p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain" []
subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension
subset: http://purl.obolibrary.org/obo/valid_for_gocam
property_value: IAO:0000114 IAO:0000428
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_transitive: true
is_a: BFO:0000063 ! precedes
is_a: RO:0002418 ! causally upstream of or within

[Typedef]
id: RO:0002412
name: immediately causally upstream of
def: "p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p  must be an input of q." []
property_value: IAO:0000114 IAO:0000428
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: RO:0002575 RO:0002411
is_a: RO:0002090 ! immediately precedes
is_a: RO:0002411 ! causally upstream of

[Typedef]
id: RO:0002413
name: directly provides input for
def: "p1 directly provides input for p2 iff there exists some c such that p1 has_output c and p2 has_input c" []
property_value: IAO:0000114 IAO:0000428
property_value: IAO:0000116 "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: IAO:0000589 "directly provides input for (process to process)" xsd:string
is_a: RO:0002412 ! immediately causally upstream of
is_a: RO:0002414 ! transitively provides input for

[Typedef]
id: RO:0002414
name: transitively provides input for
def: "transitive form of directly_provides_input_for" []
property_value: IAO:0000114 IAO:0000428
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000232 "This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'directly provides input for' (which may later be relabeled simply to 'provides input for')" xsd:string
property_value: IAO:0000589 "transitively provides input for (process to process)" xsd:string
domain: BFO:0000015 ! process
range: BFO:0000015 ! process
is_transitive: true
is_a: RO:0002411 ! causally upstream of

[Typedef]
id: RO:0002418
name: causally upstream of or within
def: "p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q." []
synonym: "affects" RELATED []
property_value: IAO:0000116 "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "influences (processual)" xsd:string
is_transitive: true
is_a: RO:0002501 ! causal relation between processes
inverse_of: RO:0002427 ! causally downstream of or within

[Typedef]
id: RO:0002424
name: differs in
comment: This is an exploratory relation
property_value: IAO:0000116 "false" xsd:boolean
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: seeAlso https://code.google.com/p/phenotype-ontologies/w/edit/PhenotypeModelCompetencyQuestions xsd:anyURI

[Typedef]
id: RO:0002425
name: differs in attribute of
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: RO:0002424 ! differs in

[Typedef]
id: RO:0002426
name: differs in attribute
property_value: IAO:0000117 "Chris Mungall" xsd:string
range: BFO:0000020 ! specifically dependent continuant
is_a: RO:0002424 ! differs in

[Typedef]
id: RO:0002427
name: causally downstream of or within
def: "inverse of causally upstream of or within" []
subset: RO:0002259
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
is_transitive: true
is_a: RO:0002501 ! causal relation between processes

[Typedef]
id: RO:0002428
name: involved in regulation of
def: "c involved in regulation of p if c is involved in some p' and p' regulates some p" []
property_value: IAO:0000117 "Chris Mungall" xsd:string
holds_over_chain: RO:0002327 RO:0002211
holds_over_chain: RO:0002331 RO:0002211
is_a: RO:0002263 ! acts upstream of
is_a: RO:0002431 ! involved in or involved in regulation of

[Typedef]
id: RO:0002429
name: involved in positive regulation of
def: "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" []
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: RO:0004049 RO:0002428
holds_over_chain: RO:0002327 RO:0002213
holds_over_chain: RO:0002331 RO:0002213
is_a: RO:0002428 ! involved in regulation of

[Typedef]
id: RO:0002430
name: involved in negative regulation of
def: "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" []
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: RO:0004050 RO:0002428
holds_over_chain: RO:0002327 RO:0002212
holds_over_chain: RO:0002331 RO:0002212
is_a: RO:0002428 ! involved in regulation of

[Typedef]
id: RO:0002431
name: involved in or involved in regulation of
def: "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" []
property_value: IAO:0000116 "OWL does not allow defining object properties via a Union" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "involved in or reguates" xsd:string
is_a: RO:0002264 ! acts upstream of or within
is_a: RO:0002328 ! functionally related to
is_a: RO:0002500 ! causal agent in process

[Typedef]
id: RO:0002432
name: is active in
def: "c executes activity in d if and only if c enables p and p occurs_in d.  Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure." [GOC:cjm, GOC:dos]
synonym: "enables activity in" EXACT []
property_value: IAO:0000112 "A protein that enables activity in a cytosol." xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "executes activity in" xsd:string
holds_over_chain: RO:0002327 BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"}
is_a: RO:0002131 ! overlaps
is_a: RO:0002328 ! functionally related to

[Typedef]
id: RO:0002433
name: contributes to morphology of
def: "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm." []
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: RO:0002131 ! overlaps

[Typedef]
id: RO:0002434
name: interacts with
def: "A relationship that holds between two entities in which the processes executed by the two entities are causally connected." []
subset: ro-eco
synonym: "in pairwise interaction with" EXACT []
property_value: http://xmlns.com/foaf/0.1/page https://github.com/oborel/obo-relations/wiki/InteractionRelations xsd:anyURI
property_value: IAO:0000116 "Considering relabeling as 'pairwise interacts with'" xsd:anyURI
property_value: IAO:0000116 "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000232 "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." xsd:string
property_value: seeAlso http://purl.obolibrary.org/obo/MI_0914 xsd:anyURI
domain: BFO:0000040 ! material entity
range: BFO:0000040 ! material entity
is_symmetric: true

[Typedef]
id: RO:0002436
name: molecularly interacts with
def: "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other." []
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "binds" xsd:string
property_value: IAO:0000118 "molecularly binds with" xsd:string
property_value: seeAlso ECO:0000353
property_value: seeAlso http://purl.obolibrary.org/obo/MI_0915 xsd:anyURI
is_symmetric: true
is_a: RO:0002434 ! interacts with

[Typedef]
id: RO:0002437
name: biotically interacts with
def: "An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts." []
subset: ro-eco
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "interacts with on organism level" xsd:string
property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005
property_value: seeAlso http://eol.org/schema/terms/interactsWith xsd:string
domain: BFO:0000040 ! material entity
range: BFO:0000040 ! material entity
is_symmetric: true
is_a: RO:0002434 ! interacts with

[Typedef]
id: RO:0002446
name: participates in a abiotic-biotic interaction with
def: "A biotic interaction relationship in which one partner is an organism and the other partner is inorganic. For example, the relationship between a sponge and the substrate to which is it anchored." []
subset: ro-eco
synonym: "semibiotically interacts with" RELATED []
property_value: IAO:0000112 "Porifiera attaches to substrate" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005
is_a: RO:0002437 ! biotically interacts with

[Typedef]
id: RO:0002447
name: phosphorylates
property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y." xsd:string
is_a: RO:0002436 ! molecularly interacts with

[Typedef]
id: RO:0002448
name: activity directly regulates activity of
name: directly regulates activity of
def: "Holds between molecular entities A and B where A can physically interact with B and in doing so regulates a process that B is capable of.  For example, A and B may be gene products and binding of B by A regulates the kinase activity of B." []
def: "The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.\n\nA and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B." []
synonym: "molecularly controls" EXACT []
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000117 "Vasundra Touré" xsd:string
domain: BFO:0000040 ! material entity
range: BFO:0000040 ! material entity
is_a: RO:0002436 ! molecularly interacts with
is_a: RO:0002566 ! causally influences
is_a: RO:0011002 ! regulates activity of

[Typedef]
id: RO:0002449
name: activity directly negatively regulates activity of
name: directly negatively regulates activity of
def: "Holds between molecular entities A and B where A can physically interact with B and in doing so negatively regulates a process that B is capable of.  For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B." []
def: "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B." []
synonym: "molecularly decreases activity of" EXACT []
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000117 "Vasundra Touré" xsd:string
property_value: IAO:0000118 "directly inhibits" xsd:string
property_value: IAO:0000118 "inhibits" xsd:string
domain: BFO:0000040 ! material entity
range: BFO:0000040 ! material entity
is_a: RO:0002448 ! directly regulates activity of

[Typedef]
id: RO:0002450
name: activity directly positively regulates activity of
name: directly positively regulates activity of
def: "Holds between molecular entities A and B where A can physically interact with B and in doing so positively regulates a process that B is capable of.  For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B." []
def: "The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B." []
synonym: "molecularly increases activity of" EXACT []
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000117 "Vasundra Touré" xsd:string
property_value: IAO:0000118 "activates" xsd:string
property_value: IAO:0000118 "directly activates" xsd:string
domain: BFO:0000040 ! material entity
range: BFO:0000040 ! material entity
is_a: RO:0002448 ! directly regulates activity of

[Typedef]
id: RO:0002461
name: partner in
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000232 "Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target" xsd:string
is_a: RO:0000056 ! participates in

[Typedef]
id: RO:0002462
name: subject participant in
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000232 "Experimental: relation used for defining interaction relations; the meaning of s 'subject participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the subject is the predator. We can imagine a reciprocal prey-predatory process with subject and object reversed." xsd:string
is_a: RO:0002461 ! partner in

[Typedef]
id: RO:0002463
name: target participant in
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000232 "Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed." xsd:string
is_a: RO:0002461 ! partner in

[Typedef]
id: RO:0002464
name: helper property (not for use in curation)
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000232 "This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning." xsd:string

[Typedef]
id: RO:0002465
name: is symbiosis
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: RO:0002563 ! interaction relation helper property

[Typedef]
id: RO:0002466
name: is commensalism
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: RO:0002465 ! is symbiosis

[Typedef]
id: RO:0002467
name: is mutualism
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: RO:0002465 ! is symbiosis

[Typedef]
id: RO:0002468
name: is parasitism
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: RO:0002465 ! is symbiosis

[Typedef]
id: RO:0002472
name: is evidence for
def: "A relationship between a piece of evidence a and some entity b, where b is  an information content entity, material entity or process, and \nthe a supports either the existence of b, or the truth value of b." []
subset: ro-eco
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: RO:0002616 ! related via evidence or inference to
inverse_of: RO:0002558 ! has evidence

[Typedef]
id: RO:0002473
name: composed primarily of
def: "x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y." []
subset: ro-eco
property_value: IAO:0000112 "'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552
property_value: RO:0001900 RO:0001901
domain: BFO:0000040 ! material entity
range: BFO:0000040 ! material entity
is_a: BFO:0000051 ! has part

[Typedef]
id: RO:0002479
name: has part that occurs in
def: "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." []
subset: ro-eco
property_value: IAO:0000117 "Chris Mungall" xsd:string
domain: BFO:0000003 ! occurrent
range: BFO:0000004 ! independent continuant
holds_over_chain: BFO:0000051 BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"}

[Typedef]
id: RO:0002481
name: is kinase activity
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: RO:0002564 ! molecular interaction relation helper property

[Typedef]
id: RO:0002482
name: is ubiquitination
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: RO:0002564 ! molecular interaction relation helper property

[Typedef]
id: RO:0002485
name: receives input from
property_value: IAO:0000116 "See notes for inverse relation" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: RO:0002170 ! connected to
inverse_of: RO:0002486 ! sends output to

[Typedef]
id: RO:0002486
name: sends output to
property_value: IAO:0000116 "This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: RO:0002170 ! connected to

[Typedef]
id: RO:0002500
name: causal agent in process
def: "A relationship between a material entity and a process where the material entity has some causal role that influences the process" []
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
is_a: RO:0002595 ! causal relation between material entity and a process
inverse_of: RO:0002608 ! process has causal agent

[Typedef]
id: RO:0002501
name: causal relation between processes
def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q." []
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string
domain: BFO:0000003 ! occurrent
range: BFO:0000003 ! occurrent
is_a: RO:0002410 ! causally related to

[Typedef]
id: RO:0002502
name: depends on
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: seeAlso BFO:0000169

[Typedef]
id: RO:0002503
name: towards
def: "q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2" []
property_value: IAO:0000116 "This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C." xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205
is_a: RO:0002502 ! depends on

[Typedef]
id: RO:0002505
name: has intermediate
def: "p has intermediate c if and only if p has parts p1, p2 and p1 has output c, and p2 has input c" []
subset: ro-eco
property_value: IAO:0000112 "'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "has intermediate product" xsd:string
is_a: RO:0000057 ! has_participant

[Typedef]
id: RO:0002506
name: causal relation between entities
name: causal relation between material entities
property_value: IAO:0000116 "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string
domain: BFO:0000002 ! continuant
domain: BFO:0000040 ! material entity
range: BFO:0000002 ! continuant
range: BFO:0000040 ! material entity
is_a: RO:0002410 ! causally related to

[Typedef]
id: RO:0002507
name: determined by
def: "s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s." []
subset: ro-eco
property_value: http://purl.org/dc/elements/1.1/creator "Chris Mungall" xsd:string
property_value: http://purl.org/dc/elements/1.1/creator "Pier Buttigieg" xsd:string
property_value: IAO:0000112 "A coral reef environment is determined by a particular coral reef" xsd:string
property_value: IAO:0000116 "The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/24330602
property_value: IAO:0000589 "determined by (system to material entity)" xsd:string
domain: RO:0002577 ! system
range: BFO:0000040 ! material entity
is_a: BFO:0000050 ! part of
is_a: RO:0002509 ! determined by part of
is_a: RO:0002559 ! causally influenced by
inverse_of: RO:0002508 ! determines

[Typedef]
id: RO:0002508
name: determines
def: "inverse of determined by" []
subset: ro-eco
subset: RO:0002259
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000589 "determines (material entity to system)" xsd:string
is_a: RO:0002566 ! causally influences

[Typedef]
id: RO:0002509
name: determined by part of
def: "s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w." []
subset: ro-eco
property_value: IAO:0000117 "Chris Mungall" xsd:string
domain: RO:0002577 ! system
range: BFO:0000040 ! material entity
is_a: RO:0002131 ! overlaps
is_a: RO:0002506 ! causal relation between material entities

[Typedef]
id: RO:0002510
name: transcribed from
def: "x is transcribed from y if and only if x is synthesized from template y" []
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI

[Typedef]
id: RO:0002514
name: sequentially related to
def: "A relation that holds between two entities that have the property of being sequences or having sequences. " []
property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI
property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string
property_value: IAO:0000232 "The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene." xsd:string

[Typedef]
id: RO:0002515
name: sequentially adjacent to
def: "x is sequentially adjacent to y iff x and y do not overlap and if there are no base units intervening between x and y" []
property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract
property_value: IAO:0000112 "Every UTR is adjacent to a CDS of the same transcript" xsd:string
property_value: IAO:0000112 "Two consecutive DNA residues are sequentially adjacent" xsd:string
property_value: IAO:0000112 "Two exons on a processed transcript that were previously connected by an intron are adjacent" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI
is_a: RO:0002527 ! does not overlap sequence of

[Typedef]
id: RO:0002516
name: has start sequence
def: "x has start sequence y if the start of x is identical to the start of y, and x has y as a subsequence" []
property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract
property_value: IAO:0000112 "Every CDS has as a start sequence the start codon for that transcript" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "started by" xsd:string
property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI
is_transitive: true
is_a: RO:0002524 ! has subsequence
inverse_of: RO:0002517 ! is start sequence of

[Typedef]
id: RO:0002517
name: is start sequence of
def: "inverse of has start sequence" []
subset: RO:0002259
property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "starts" xsd:string
property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI
is_transitive: true
is_a: RO:0002525 ! is subsequence of

[Typedef]
id: RO:0002518
name: has end sequence
def: "x has end sequence y if the end of x is identical to the end of y, and x has y as a subsequence" []
property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract
property_value: IAO:0000112 "Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included)" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "ended by" xsd:string
property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI
is_transitive: true
is_a: RO:0002524 ! has subsequence
inverse_of: RO:0002519 ! is end sequence of

[Typedef]
id: RO:0002519
name: is end sequence of
def: "inverse of has end sequence" []
subset: RO:0002259
property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "ends" xsd:string
property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI
is_transitive: true
is_a: RO:0002525 ! is subsequence of

[Typedef]
id: RO:0002520
name: is consecutive sequence of
def: "x is a consecutive sequence of y iff x has subsequence y, and all the parts of x are made of zero or more repetitions of y or sequences as the same type as y." []
property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract
property_value: IAO:0000116 "In the SO paper, this was defined as an instance-type relation" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI
is_a: RO:0002524 ! has subsequence

[Typedef]
id: RO:0002521
name: is sequentially aligned with
def: "x is sequentially aligned with if a significant portion bases of x and y correspond in terms of their base type and their relative ordering" []
property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract
property_value: IAO:0000112 "Human Shh and Mouse Shh are sequentially aligned, by cirtue of the fact that they derive from the same ancestral sequence." xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_symmetric: true
is_a: RO:0002514 ! sequentially related to

[Typedef]
id: RO:0002522
name: bounds sequence of
def: "x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y" []
property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract
property_value: IAO:0000112 "The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons)" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_transitive: true
is_a: RO:0002514 ! sequentially related to
inverse_of: RO:0002523 ! is bound by sequence of

[Typedef]
id: RO:0002523
name: is bound by sequence of
def: "inverse of bounds sequence of" []
subset: RO:0002259
property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_transitive: true
is_a: RO:0002514 ! sequentially related to

[Typedef]
id: RO:0002524
name: has subsequence
def: "x has subsequence y iff all of the sequence parts of x are sequence parts of y" []
property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "contains" xsd:string
property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI
is_transitive: true
is_a: BFO:0000051 ! has part
is_a: RO:0002522 ! bounds sequence of
is_a: RO:0002526 ! overlaps sequence of
inverse_of: RO:0002525 ! is subsequence of

[Typedef]
id: RO:0002525
name: is subsequence of
def: "inverse of has subsequence" []
subset: RO:0002259
property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "contained by" xsd:string
is_transitive: true
is_a: BFO:0000050 ! part of
is_a: RO:0002523 ! is bound by sequence of
is_a: RO:0002526 ! overlaps sequence of

[Typedef]
id: RO:0002526
name: overlaps sequence of
def: "x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y." []
property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_symmetric: true
is_a: RO:0002131 ! overlaps
is_a: RO:0002514 ! sequentially related to

[Typedef]
id: RO:0002527
name: does not overlap sequence of
def: "x does not overlaps the sequence of x if and only if there is no z such that x has a subsequence z and z is a subsequence of y." []
property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "disconnected from" xsd:string
is_symmetric: true
is_a: RO:0002514 ! sequentially related to

[Typedef]
id: RO:0002528
name: is upstream of sequence of
def: "inverse of downstream of sequence of" []
property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_transitive: true
is_a: RO:0002527 ! does not overlap sequence of

[Typedef]
id: RO:0002529
name: is downstream of sequence of
def: "x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y." []
property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_transitive: true
is_a: RO:0002527 ! does not overlap sequence of
inverse_of: RO:0002529 ! is downstream of sequence of

[Typedef]
id: RO:0002530
name: is immediately downstream of sequence of
def: "x is immediately downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, and x is sequentially adjacent to y, or (2) x and y are sequence units, in which case the immediately downstream relation is primitive and defined by context: for DNA bases, y would be adjacent and 5' to y" []
property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract
property_value: IAO:0000112 "A 3'UTR is immediately downstream of the sequence of the CDS from the same monocistronic transcript" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: RO:0002575 RO:0002529
is_a: RO:0002515 ! sequentially adjacent to
is_a: RO:0002529 ! is downstream of sequence of

[Typedef]
id: RO:0002531
name: is immediately upstream of sequence of
def: "inverse of immediately downstream of" []
property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract
property_value: IAO:0000112 "A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: RO:0002515 ! sequentially adjacent to
is_a: RO:0002528 ! is upstream of sequence of

[Typedef]
id: RO:0002558
name: has evidence
def: "inverse of is evidence for" []
comment: x has evidence y iff , x is  an information content entity, material entity or process, and y supports either the existence of x, or the truth value of x.
subset: ro-eco
subset: RO:0002259
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/25052702
is_a: RO:0002616 ! related via evidence or inference to

[Typedef]
id: RO:0002559
name: causally influenced by
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: IAO:0000589 "causally influenced by (entity-centric)" xsd:string
property_value: IAO:0000589 "causally influenced by (material entity to material entity)" xsd:string
is_a: RO:0002506 ! causal relation between material entities
inverse_of: RO:0002566 ! causally influences

[Typedef]
id: RO:0002563
name: interaction relation helper property
property_value: http://xmlns.com/foaf/0.1/page https://github.com/oborel/obo-relations/wiki/InteractionRelations xsd:anyURI
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:N-Ary_Relation_Pattern_%28OWL_2%29
is_a: RO:0002464 ! helper property (not for use in curation)

[Typedef]
id: RO:0002564
name: molecular interaction relation helper property
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: RO:0002563 ! interaction relation helper property

[Typedef]
id: RO:0002566
name: causally influences
def: "Holds between materal entities a and b if the activity of a is causally upstream of the activity of b, or causally upstream of a an activity that modifies b" []
def: "The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size)." []
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000117 "Vasundra Touré" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: IAO:0000589 "causally influences (entity-centric)" xsd:string
property_value: IAO:0000589 "causally influences (material entity to material entity)" xsd:string
domain: BFO:0000002 ! continuant
range: BFO:0000002 ! continuant
is_a: RO:0002506 ! causal relation between material entities

[Typedef]
id: RO:0002569
name: has branching part
def: "inverse of branching part of" []
subset: ro-eco
subset: RO:0002259
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: RO:0002375 ! in branching relationship with

[Typedef]
id: RO:0002570
name: conduit for
def: "x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x." []
subset: ro-eco
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 UBERON:cjm xsd:string
property_value: IAO:0000232 "This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through." xsd:string
domain: BFO:0000040 ! material entity
range: BFO:0000040 ! material entity
is_a: RO:0002131 ! overlaps

[Typedef]
id: RO:0002571
name: lumen of
def: "x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull." []
subset: ro-eco
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 GOC:cjm xsd:string
range: BFO:0000040 ! material entity
is_a: BFO:0000050 ! part of

[Typedef]
id: RO:0002572
name: luminal space of
def: "s is luminal space of x iff s is lumen_of x and s is an immaterial entity" []
subset: ro-eco
property_value: IAO:0000117 "Chris Mungall" xsd:string
domain: BFO:0000141 ! immaterial entity
is_a: RO:0002571 ! lumen of

[Typedef]
id: RO:0002573
name: has modifier
def: "A relation that holds between an attribute or a qualifier and another attribute." []
subset: ro-eco
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205
property_value: IAO:0000232 "This relation is intended to be used in combination with PATO, to be able to refine PATO quality classes using modifiers such as 'abnormal' and 'normal'. It has yet to be formally aligned into an ontological framework; it's not clear what the ontological status of the \"modifiers\" are." xsd:string
domain: BFO:0000020 ! specifically dependent continuant
range: BFO:0000020 ! specifically dependent continuant

[Typedef]
id: RO:0002578
name: directly regulates
def: "Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2).  For example, if protein A has protein binding activity(P1) that targets protein B and this binding  regulates the kinase activity (P2) of protein B then P1 directly regulates P2." []
subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension
subset: http://purl.obolibrary.org/obo/valid_for_go_ontology
subset: http://purl.obolibrary.org/obo/valid_for_gocam
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: IAO:0000589 "directly regulates (processual)" xsd:string
property_value: RO:0002575 RO:0002211
is_a: RO:0002211 ! regulates
is_a: RO:0002412 ! immediately causally upstream of

[Typedef]
id: RO:0002584
name: has part structure that is capable of
def: "s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p" []
property_value: IAO:0000112 "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
holds_over_chain: BFO:0000051 RO:0002215
is_a: RO:0002328 ! functionally related to
is_a: RO:0002595 ! causal relation between material entity and a process

[Typedef]
id: RO:0002586
name: results in breakdown of
def: "p results in breakdown of c if and only if the execution of p leads to c no longer being present at the end of p" []
is_a: RO:0002233 ! has input

[Typedef]
id: RO:0002589
name: results in catabolism of
def: "p results in catabolism of c if and only if p is a catabolic process, and the execution of p results in c being broken into smaller parts with energy being released." []
is_a: RO:0002586 ! results in breakdown of

[Typedef]
id: RO:0002595
name: causal relation between material entity and a process
def: "A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity." []
property_value: IAO:0000116 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
domain: BFO:0000040 ! material entity
range: BFO:0000015 ! process
is_a: RO:0002410 ! causally related to

[Typedef]
id: RO:0002596
name: capable of regulating
def: "Holds between c and p if and only if c is capable of some activity a, and a regulates p." []
property_value: IAO:0000112 "pyrethroid -> growth" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
holds_over_chain: RO:0002215 RO:0002211
is_a: RO:0002500 ! causal agent in process

[Typedef]
id: RO:0002597
name: capable of negatively regulating
def: "Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p." []
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
holds_over_chain: RO:0002215 RO:0002212
is_a: RO:0002596 ! capable of regulating

[Typedef]
id: RO:0002598
name: capable of positively regulating
def: "Holds between c and p if and only if c is capable of some activity a, and a positively regulates p." []
property_value: IAO:0000112 "renin -> arteriolar smooth muscle contraction" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
holds_over_chain: RO:0002215 RO:0002213
is_a: RO:0002596 ! capable of regulating

[Typedef]
id: RO:0002599
name: capable of inhibiting or preventing pathological process
def: "Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a inhibits p." []
property_value: IAO:0000112 "pazopanib -> pathological angiogenesis" xsd:string
property_value: IAO:0000118 "treats" xsd:string {comment="Usage of the term 'treats' applies when we believe there to be a an inhibitory relationship"}
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: IAO:0000232 "The entity c may be a molecular entity with a drug role, or it could be some other entity used in a therapeutic context, such as a hyperbaric chamber." xsd:string
is_a: RO:0002597 ! capable of negatively regulating

[Typedef]
id: RO:0002600
name: capable of upregulating or causing pathological process
def: "Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a negatively regulates p." []
property_value: IAO:0000112 "benzene -> cancer [CHEBI]" xsd:string
property_value: IAO:0000118 "causes disease" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
is_a: RO:0002598 ! capable of positively regulating

[Typedef]
id: RO:0002606
name: is substance that treats
def: "c is a substance that treats d if c is a material entity (such as a small molecule or compound) and d is a pathological process, phenotype or disease, and c is capable of some activity that negative regulates or decreases the magnitude of d." []
property_value: IAO:0000118 "treats" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: seeAlso https://code.google.com/p/obo-relations/issues/detail?id=46
is_a: RO:0002599 ! capable of inhibiting or preventing pathological process

[Typedef]
id: RO:0002607
name: is marker for
def: "c is marker for d iff the presence or occurrence of d is correlated with the presence of occurrence of c, and the observation of c is used to infer the presence or occurrence of d. Note that this does not imply that c and d are in a direct causal relationship, as it may be the case that there is a third entity e that stands in a direct causal relationship with c and d." []
property_value: IAO:0000116 "May be ceded to OBI" xsd:string
is_a: RO:0002610 ! correlated with

[Typedef]
id: RO:0002608
name: process has causal agent
def: "Inverse of 'causal agent in process'" []
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
is_a: RO:0002410 ! causally related to

[Typedef]
id: RO:0002609
name: obsolete related via dependence to
def: "A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes." []
property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string
is_obsolete: true

[Typedef]
id: RO:0002610
name: correlated with
def: "A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes." []
property_value: IAO:0000232 "Groups both positive and negative correlation" xsd:string

[Typedef]
id: RO:0002614
name: is evidence with support from
def: "A relationship between a piece of evidence and an entity that plays a role in supporting that evidence." []
comment: In the Gene Ontology association model, this corresponds to the With/From field
property_value: IAO:0000112 "An instance of a sequence similarity evidence (ECO:0000044) that uses a homologous sequence UniProtKB:P12345 as support." xsd:string
is_a: RO:0002616 ! related via evidence or inference to

[Typedef]
id: RO:0002615
name: has model
def: "Inverse of is-model-of" []
inverse_of: RO:0003301 ! is model of

[Typedef]
id: RO:0002616
name: related via evidence or inference to
property_value: IAO:0000232 "Do not use this relation directly. It is a grouping relation." xsd:string

[Typedef]
id: RO:0002629
name: directly positively regulates
def: "Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2).  For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2." []
subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension
subset: http://purl.obolibrary.org/obo/valid_for_go_ontology
subset: http://purl.obolibrary.org/obo/valid_for_gocam
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: IAO:0000589 "directly positively regulates (process to process)" xsd:string
property_value: RO:0004049 RO:0002578
is_a: RO:0002213 ! positively regulates
is_a: RO:0002578 ! directly regulates

[Typedef]
id: RO:0002630
name: directly negatively regulates
def: "Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2).  For example, if protein A has protein binding activity(P1) that targets protein B and this binding  negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2." []
subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension
subset: http://purl.obolibrary.org/obo/valid_for_go_ontology
subset: http://purl.obolibrary.org/obo/valid_for_gocam
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: IAO:0000589 "directly negatively regulates (process to process)" xsd:string
property_value: RO:0004050 RO:0002578
is_a: RO:0002212 ! negatively regulates
is_a: RO:0002578 ! directly regulates

[Typedef]
id: RO:0003000
name: produces
def: "a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix." []
comment: Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue.
subset: ro-eco
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "Melissa Haendel" xsd:string
domain: BFO:0000040 ! material entity
range: BFO:0000040 ! material entity
inverse_of: RO:0003001 ! produced by

[Typedef]
id: RO:0003001
name: produced by
def: "a produced_by b iff some process that occurs_in b has_output a." []
subset: ro-eco
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "Melissa Haendel" xsd:string
domain: BFO:0000040 ! material entity
range: BFO:0000040 ! material entity

[Typedef]
id: RO:0003002
name: represses expression of
def: "Holds between protein a (a transcription factor) and DNA element b if and only if a diminishes the process of transcription of b." []
property_value: IAO:0000116 "Logical axioms to be added after the relevant branch of GO is MIREOTed in" xsd:string
is_a: RO:0002449 ! directly negatively regulates activity of

[Typedef]
id: RO:0003003
name: increases expression of
def: "Holds between protein a (a transcription factor) and DNA element b if and only if a activates the process of transcription of b." []
property_value: IAO:0000116 "Logical axioms to be added after the relevant branch of GO is MIREOTed in" xsd:string
is_a: RO:0002450 ! directly positively regulates activity of

[Typedef]
id: RO:0003301
name: is model of
def: "Relation between a research artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity." []
comment: The driving use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest.
property_value: IAO:0000116 "To Do: decide on scope of this relation - inclusive of computational models in domain, or only physical models?  Restricted to linking biological systems and phenomena?  Inclusive of only diseases in range, or broader?" xsd:string
property_value: IAO:0000117 "Matthew Brush" xsd:string
is_asymmetric: true

[Typedef]
id: RO:0003302
name: causes or contributes to condition
def: "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal or contributing role that influences the condition." []
comment: Genetic variations can span any level of granularity from a full genome or genotype to an individual gene  or sequence alteration.  These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology).  The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to.\n\nEnvironmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions.
property_value: IAO:0000112 "The genetic variant 'NM_007294.3(BRCA1):c.110C>A (p.Thr37Lys)' casues or contributes to the disease  'familial breast-ovarian cancer'.\n\nAn environment of exposure to arsenic causes or contributes to the phenotype of patchy skin hyperpigmentation, and the disease 'skin cancer'." xsd:string
property_value: IAO:0000116 "Note that relationships of phenotypes to organisms/strains that bear them, or diseases they are manifest in, should continue to use RO:0002200 ! 'has phenotype' and RO:0002201 ! 'phenotype of'." xsd:string
is_a: RO:0002410 ! causally related to

[Typedef]
id: RO:0003303
name: causes condition
def: "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal role for the condition." []
is_a: RO:0003302 ! causes or contributes to condition

[Typedef]
id: RO:0003304
name: contributes to condition
def: "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some contributing role that influences the condition." []
is_a: RO:0003302 ! causes or contributes to condition

[Typedef]
id: RO:0003305
name: contributes to severity of condition
def: "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the severity with which a condition manifests in an individual." []
property_value: IAO:0000118 "contributes to expressivity of condition" xsd:string
is_a: RO:0003304 ! contributes to condition

[Typedef]
id: RO:0003306
name: contributes to frequency of condition
def: "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the frequency of the condition in a population." []
property_value: IAO:0000118 "contributes to penetrance of condition" xsd:string
is_a: RO:0003304 ! contributes to condition

[Typedef]
id: RO:0003307
name: ameliorates condition
def: "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the presence of the entity reduces or eliminates some or all aspects of the condition." []
comment: Genetic variations can span any level of granularity from a full genome or genotype to an individual gene  or sequence alteration.  These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology).  The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. \n\nEnvironmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions.
property_value: IAO:0000118 "is preventative for condition" xsd:string
is_a: RO:0003305 ! contributes to severity of condition

[Typedef]
id: RO:0003308
name: correlated with condition
def: "A relationship between an entity and a condition (phenotype or disease) with which it exhibits a statistical dependence relationship." []
is_a: RO:0002610 ! correlated with

[Typedef]
id: RO:0003309
name: exacerbates condition
def: "A relationship between an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) and a condition (a phenotype or disease), where the presence of the entity worsens some or all aspects of the condition." []
is_a: RO:0003305 ! contributes to severity of condition

[Typedef]
id: RO:0003310
name: condition ameliorated by
def: "A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are reduced or eliminated by the presence of the entity." []
is_a: RO:0002410 ! causally related to

[Typedef]
id: RO:0003311
name: condition exacerbated by
def: "A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are worsened by the presence of the entity." []
is_a: RO:0002410 ! causally related to

[Typedef]
id: RO:0004000
name: condition has genetic basis in
property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a more specific relations" xsd:string
domain: BFO:0000017 ! realizable entity
is_a: RO:0002410 ! causally related to
inverse_of: RO:0004010 ! is genetic basis for condition
created_by: cjm
creation_date: 2017-11-05T02:38:20Z

[Typedef]
id: RO:0004001
name: has material basis in gain of function germline mutation in
property_value: seeAlso Orphanet:410295
property_value: seeAlso Orphanet:410296
is_a: RO:0004000 ! condition has genetic basis in
inverse_of: RO:0004011 ! is causal gain of function germline mutation of in
created_by: cjm
creation_date: 2017-11-05T02:45:20Z

[Typedef]
id: RO:0004002
name: has material basis in loss of function germline mutation in
is_a: RO:0004000 ! condition has genetic basis in
inverse_of: RO:0004012 ! is causal loss of function germline mutation of in
created_by: cjm
creation_date: 2017-11-05T02:45:37Z

[Typedef]
id: RO:0004003
name: has material basis in germline mutation in
property_value: seeAlso Orphanet:317343
is_a: RO:0004000 ! condition has genetic basis in
inverse_of: RO:0004013 ! is causal germline mutation in
created_by: cjm
creation_date: 2017-11-05T02:45:54Z

[Typedef]
id: RO:0004004
name: has material basis in somatic mutation in
property_value: seeAlso Orphanet:317344
is_a: RO:0004000 ! condition has genetic basis in
inverse_of: RO:0004014 ! is causal somatic mutation in
created_by: cjm
creation_date: 2017-11-05T02:46:07Z

[Typedef]
id: RO:0004005
name: has major susceptibility factor
is_a: RO:0004000 ! condition has genetic basis in
inverse_of: RO:0004015 ! is causal susceptibility factor for
created_by: cjm
creation_date: 2017-11-05T02:46:26Z

[Typedef]
id: RO:0004006
name: has partial material basis in germline mutation in
is_a: RO:0004000 ! condition has genetic basis in
inverse_of: RO:0004016 ! is causal germline mutation partially giving rise to
created_by: cjm
creation_date: 2017-11-05T02:46:57Z

[Typedef]
id: RO:0004007
name: has primary input or output
def: "p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c." []
is_a: RO:0000057 ! has_participant
created_by: cjm
creation_date: 2018-12-13T11:26:17Z

[Typedef]
id: RO:0004008
name: has primary output
def: "p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c." [GOC:cjm, GOC:dph, GOC:kva, GOC:pt] {comment="PMID:27812932"}
is_a: RO:0002234 ! has output
is_a: RO:0004007 ! has primary input or output
created_by: cjm
creation_date: 2018-12-13T11:26:32Z

[Typedef]
id: RO:0004009
name: has primary input
def: "p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c." [GOC:cjm, GOC:dph, GOC:kva, GOC:pt] {comment="PMID:27812932"}
is_a: RO:0002233 ! has input
is_a: RO:0004007 ! has primary input or output
created_by: cjm
creation_date: 2018-12-13T11:26:56Z

[Typedef]
id: RO:0004010
name: is genetic basis for condition
property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a more specific relations" xsd:string
range: BFO:0000017 ! realizable entity
is_a: RO:0004018 ! is basis for realizable
created_by: cjm
creation_date: 2017-11-05T02:53:08Z

[Typedef]
id: RO:0004011
name: is causal gain of function germline mutation of in
def: "Relates a gene to condition, such that a mutation in this gene in a germ cell provides a new function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]." []
property_value: seeAlso Orphanet:410296
is_a: RO:0004010 ! is genetic basis for condition
created_by: cjm
creation_date: 2017-11-05T02:55:51Z

[Typedef]
id: RO:0004012
name: is causal loss of function germline mutation of in
def: "Relates a gene to condition, such that a mutation in this gene in a germ cell impairs the function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]." []
property_value: seeAlso Orphanet:410295
is_a: RO:0004010 ! is genetic basis for condition
created_by: cjm
creation_date: 2017-11-05T02:56:06Z

[Typedef]
id: RO:0004013
name: is causal germline mutation in
def: "Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]." []
property_value: seeAlso Orphanet:317343
is_a: RO:0004010 ! is genetic basis for condition
created_by: cjm
creation_date: 2017-11-05T02:56:40Z

[Typedef]
id: RO:0004014
name: is causal somatic mutation in
def: "Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition but that cannot be passed on to offspring[modified from orphanet]." []
property_value: seeAlso Orphanet:317344
is_a: RO:0004010 ! is genetic basis for condition
created_by: cjm
creation_date: 2017-11-05T02:57:07Z

[Typedef]
id: RO:0004015
name: is causal susceptibility factor for
def: "Relates a gene to condition, such that a mutation in this gene predisposes to the development of a condition  and that is necessary but not sufficient to develop the condition[modified from orphanet]." []
property_value: seeAlso Orphanet:317345
is_a: RO:0004010 ! is genetic basis for condition
created_by: cjm
creation_date: 2017-11-05T02:57:43Z

[Typedef]
id: RO:0004016
name: is causal germline mutation partially giving rise to
def: "Relates a gene to condition, such that a mutation in this gene partially contributes to the presentation of this condition[modified from orphanet]." []
property_value: seeAlso Orphanet:317346
is_a: RO:0004010 ! is genetic basis for condition
created_by: cjm
creation_date: 2017-11-05T02:58:43Z

[Typedef]
id: RO:0004017
name: realizable has basis in
is_a: RO:0002410 ! causally related to
inverse_of: RO:0004018 ! is basis for realizable
created_by: cjm
creation_date: 2017-11-05T03:20:01Z

[Typedef]
id: RO:0004018
name: is basis for realizable
is_a: RO:0002410 ! causally related to
created_by: cjm
creation_date: 2017-11-05T03:20:29Z

[Typedef]
id: RO:0004019
name: disease has basis in
domain: OGMS:0000031 ! disease
is_a: RO:0004017 ! realizable has basis in
created_by: cjm
creation_date: 2017-11-05T03:26:47Z

[Typedef]
id: RO:0004021
name: disease has basis in disruption of
def: "A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process." []
property_value: IAO:0000589 "disease has basis in disruption of (disease to process)" xsd:string
range: BFO:0000015 ! process
is_a: RO:0004019 ! disease has basis in
created_by: cjm
creation_date: 2017-11-05T03:37:52Z

[Typedef]
id: RO:0004028
name: realized in response to stimulus
def: "A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M." []
domain: BFO:0000017 ! realizable entity
range: BFO:0000040 ! material entity
holds_over_chain: RO:0009501 RO:0002233
is_a: RO:0002410 ! causally related to
created_by: cjm
creation_date: 2017-12-26T19:45:49Z

[Typedef]
id: RO:0004029
name: disease has feature
def: "A relationship between a disease and some feature of that disease, where the feature is either a phenotype or an isolated disease." []
domain: OGMS:0000031 ! disease
created_by: cjm
creation_date: 2017-12-26T19:50:53Z

[Typedef]
id: RO:0004031
name: enables subfunction
def: "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P." []
holds_over_chain: RO:0002327 BFO:0000051
is_a: RO:0002328 ! functionally related to
created_by: cjm
creation_date: 2018-01-25T23:20:13Z

[Typedef]
id: RO:0004032
name: acts upstream of or within, positive effect
subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term
property_value: RO:0004049 RO:0002264
property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect
holds_over_chain: RO:0002327 RO:0004047
is_a: RO:0002264 ! acts upstream of or within
created_by: cjm
creation_date: 2018-01-26T23:49:30Z

[Typedef]
id: RO:0004033
name: acts upstream of or within, negative effect
subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term
property_value: RO:0004050 RO:0002264
holds_over_chain: RO:0002327 RO:0004046
is_a: RO:0002264 ! acts upstream of or within
created_by: cjm
creation_date: 2018-01-26T23:49:51Z

[Typedef]
id: RO:0004034
name: acts upstream of, positive effect
def: "c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive" []
subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term
property_value: RO:0004049 RO:0002263
property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect
holds_over_chain: RO:0002327 RO:0002304
is_a: RO:0002263 ! acts upstream of
is_a: RO:0004032 ! acts upstream of or within, positive effect
created_by: cjm
creation_date: 2018-01-26T23:53:14Z

[Typedef]
id: RO:0004035
name: acts upstream of, negative effect
def: "c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative" []
subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term
property_value: RO:0004050 RO:0002263
property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect
holds_over_chain: RO:0002327 RO:0002305
is_a: RO:0002263 ! acts upstream of
is_a: RO:0004033 ! acts upstream of or within, negative effect
created_by: cjm
creation_date: 2018-01-26T23:53:22Z

[Typedef]
id: RO:0004046
name: causally upstream of or within, negative effect
property_value: RO:0004050 RO:0002418
is_a: RO:0002418 ! causally upstream of or within
created_by: cjm
creation_date: 2018-03-13T23:55:05Z

[Typedef]
id: RO:0004047
name: causally upstream of or within, positive effect
property_value: RO:0004049 RO:0002418
is_a: RO:0002418 ! causally upstream of or within
created_by: cjm
creation_date: 2018-03-13T23:55:19Z

[Typedef]
id: RO:0004096
name: DEPRECATED inheres in
comment: DEPRECATED This relation is similar to but different in important respects to the characteristic-of relation. See comments on that relation for more information.
inverse_of: RO:0004097 ! DEPRECATED bearer of
is_obsolete: true

[Typedef]
id: RO:0004097
name: DEPRECATED bearer of
is_obsolete: true

[Typedef]
id: RO:0009001
name: has substance added
def: "\"has substance added\" is a relation existing between a (physical) entity and a substance in which the entity has had the substance added to it at some point in time." []
property_value: IAO:0000112 "muffin 'has substance added' some 'baking soda'" xsd:string
property_value: IAO:0000114 IAO:0000428
property_value: IAO:0000116 "The relation X 'has substance added' some Y doesn't imply that X still has Y in any detectable fashion subsequent to the addition. Water in dehydrated food or ice cubes are examples, as is food that undergoes chemical transformation. This definition should encompass recipe ingredients." xsd:string
property_value: IAO:0000117 "Damion Dooley" xsd:string
domain: BFO:0000040 ! material entity
range: BFO:0000040 ! material entity

[Typedef]
id: RO:0009002
name: has substance removed
def: "\"has substance removed\" is a relation existing between two physical entities in which the first entity has had the second entity (a substance) removed from it at some point in time." []
property_value: IAO:0000112 "'egg white' 'has substance removed' some 'egg yolk'" xsd:string
property_value: IAO:0000114 IAO:0000428
property_value: IAO:0000117 "Damion Dooley" xsd:string
domain: BFO:0000040 ! material entity
range: BFO:0000040 ! material entity

[Typedef]
id: RO:0009003
name: immersed in
def: "\"immersed in\" is a relation between a (physical) entity and a fluid substance in which the entity is wholely or substantially surrounded by the substance." []
property_value: IAO:0000112 "sardines 'immersed in' some 'oil and mustard'" xsd:string
property_value: IAO:0000114 IAO:0000428
property_value: IAO:0000117 "Damion Dooley" xsd:string
domain: BFO:0000040 ! material entity
range: BFO:0000040 ! material entity

[Typedef]
id: RO:0009005
name: has primary substance added
def: "'has primary substance added' indicates that an entity has had the given substance added to it in a proportion greater than any other added substance." []
property_value: IAO:0000112 "bread 'has primary substance added' some 'flour'" xsd:string
property_value: IAO:0000114 IAO:0000428
property_value: IAO:0000117 "Damion Dooley" xsd:string
is_a: RO:0009001 ! has substance added

[Typedef]
id: RO:0009501
name: realized in response to
def: "r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r." []
synonym: "triggered by process" EXACT [RO:cjm]
property_value: http://purl.org/dc/elements/1.1/contributor "Austin Meier" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Chris Mungall" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "David Osumi-Sutherland" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Marie Angelique Laporte" xsd:string
property_value: http://purl.org/dc/terms/contributor "Austin Meier" xsd:string
property_value: http://purl.org/dc/terms/contributor "Chris Mungall" xsd:string
property_value: http://purl.org/dc/terms/contributor "David Osumi-Sutherland" xsd:string
property_value: http://purl.org/dc/terms/contributor "Marie Angelique Laporte" xsd:string
property_value: IAO:0000112 "A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions." xsd:string
property_value: IAO:0000112 "An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)" xsd:string
property_value: IAO:0000112 "Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph." xsd:string
property_value: seeAlso https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit xsd:anyURI
domain: BFO:0000017 ! realizable entity
range: BFO:0000015 ! process
holds_over_chain: BFO:0000054 RO:0002404
is_a: RO:0002410 ! causally related to

[Typedef]
id: RO:0010001
name: generically depends on
def: "A generically dependent continuant *b* generically depends on an independent continuant *c* at time *t* means: there inheres in *c* a specifically deendent continuant which concretizes *b* at *t*." []
synonym: "g-depends on" EXACT []
property_value: IAO:0000112 "Genetic information generically depend on molecules of DNA." xsd:string
property_value: IAO:0000112 "The novel *War and Peace* generically depends on this copy of the novel." xsd:string
property_value: IAO:0000112 "The pattern shared by chess boards generically depends on any chess board." xsd:string
property_value: IAO:0000112 "The score of a symphony g-depends on a copy of the score." xsd:string
property_value: IAO:0000112 "This pdf file generically depends on this server." xsd:string
property_value: IAO:0000119 "[072-ISO]" xsd:string
domain: BFO:0000031 ! generically dependent continuant
range: BFO:0000004 ! independent continuant
holds_over_chain: RO:0000052 RO:0000058
inverse_of: RO:0010002 ! is carrier of

[Typedef]
id: RO:0010002
name: is carrier of
def: "*b* is carrier of *c* at time *t* if and only if *c* *g-depends on* *b* at *t*" []
property_value: IAO:0000112 "Molecules of DNA are carriers of genetic information." xsd:string
property_value: IAO:0000112 "This copy of *War and Peace* is carrier of the novel written by Tolstoy." xsd:string
property_value: IAO:0000112 "This hard drive is carrier of these data items." xsd:string
property_value: IAO:0000119 "[072-ISO]" xsd:string
domain: BFO:0000004 ! independent continuant
range: BFO:0000031 ! generically dependent continuant
holds_over_chain: RO:0000059 RO:0000053

[Typedef]
id: RO:0011002
name: regulates activity of
def: "The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B." []
property_value: IAO:0000117 "Vasundra Touré" xsd:string
domain: BFO:0000040 ! material entity
range: BFO:0000040 ! material entity
is_a: RO:0002566 ! causally influences

[Typedef]
id: RO:HOM0000000
name: in similarity relationship with
def: "Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison." [BGEE:curator, http://purl.obolibrary.org/obo/HOM_0000000]
synonym: "correspondence" RELATED [http://dx.doi.org/10.1007/BF02814479]
synonym: "resemblance" RELATED []
synonym: "sameness" EXACT []
synonym: "similar to" EXACT []
xref: ECO:0000041
xref: SO:similar_to
property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch
property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127
property_value: seeAlso HOM:0000000
is_symmetric: true

[Typedef]
id: RO:HOM0000001
name: in homology relationship with
def: "Similarity that results from common evolutionary origin." [http://dx.doi.org/10.1002/bies.950180611, http://dx.doi.org/10.1002/jmor.1051730307, http://dx.doi.org/10.1007/BF02814480, http://purl.obolibrary.org/obo/HOM_0000001]
comment: This broad definition encompasses all the working definitions proposed so far in the literature.
synonym: "homologous to" EXACT []
property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch
property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127
property_value: seeAlso HOM:0000001
is_symmetric: true
is_a: RO:HOM0000000 ! in similarity relationship with
disjoint_from: RO:HOM0000002 ! in homoplasy relationship with

[Typedef]
id: RO:HOM0000002
name: in homoplasy relationship with
def: "Similarity that results from independent evolution." [http://dx.doi.org/10.1016/j.jhevol.2006.11.010, http://purl.obolibrary.org/obo/HOM_0000002]
synonym: "analogy" RELATED []
synonym: "homoplasous to" EXACT []
property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch
property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127
property_value: seeAlso HOM:0000002
is_symmetric: true
is_a: RO:HOM0000000 ! in similarity relationship with

[Typedef]
id: RO:HOM0000003
name: in homocracy relationship with
def: "Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes." [http://dx.doi.org/10.1007/BF02814484, http://dx.doi.org/10.1007/s00427-003-0301-4, http://dx.doi.org/10.1186/1742-9994-2-15, http://purl.obolibrary.org/obo/HOM_0000003]
comment: Homology and homocracy are not mutually exclusive. The homology relationships of patterning genes may be unresolved and thus may include orthologues and paralogues.
synonym: "homocracous to" EXACT []
xref: ECO:0000075
property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch
property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127
property_value: seeAlso HOM:0000003
is_symmetric: true
is_a: RO:HOM0000000 ! in similarity relationship with

[Typedef]
id: RO:HOM0000004
name: in convergence relationship with
def: "Homoplasy that involves different underlying mechanisms or structures." [http://dx.doi.org/10.1016/j.jhevol.2006.11.010, http://purl.obolibrary.org/obo/HOM_0000004]
comment: Convergence usually implies a notion of adaptation.
synonym: "analogy" RELATED []
property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch
property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127
property_value: seeAlso HOM:0000004
is_symmetric: true
is_a: RO:HOM0000002 ! in homoplasy relationship with

[Typedef]
id: RO:HOM0000005
name: in parallelism relationship with
def: "Homoplasy that involves homologous underlying mechanisms or structures." [http://dx.doi.org/10.1016/j.jhevol.2006.11.010, http://purl.obolibrary.org/obo/HOM_0000005]
comment: Can be applied for features present in closely related organisms but not present continuously in all the members of the lineage.
synonym: "parallel evolution" EXACT []
property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch
property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127
property_value: seeAlso HOM:0000005
is_symmetric: true
is_a: RO:HOM0000002 ! in homoplasy relationship with

[Typedef]
id: RO:HOM0000006
name: in structural homology relationship with
def: "Homology that is defined by similarity with regard to selected structural parameters." [http://dx.doi.org/10.1016/j.jhevol.2006.11.014, http://dx.doi.org/10.1146/annurev.es.20.110189.000411, http://purl.obolibrary.org/obo/HOM_0000006, ISBN:0123195837]
synonym: "idealistic homology" RELATED []
synonym: "structural homologous to" EXACT []
xref: ECO:0000071
xref: MI:2163
property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch
property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127
property_value: seeAlso HOM:0000006
is_symmetric: true
is_a: RO:HOM0000001 ! in homology relationship with

[Typedef]
id: RO:HOM0000007
name: in historical homology relationship with
def: "Homology that is defined by common descent." [http://dx.doi.org/10.1016/S0169-5347(97)01125-7, http://purl.obolibrary.org/obo/HOM_0000007, ISBN:0123195837]
synonym: "cladistic homology" EXACT []
synonym: "historical homologous to" EXACT []
synonym: "homology" BROAD []
synonym: "phylogenetic homology" EXACT []
synonym: "taxic homology" EXACT []
synonym: "true homology" RELATED []
xref: ECO:0000080
xref: RO_proposed_relation:homologous_to
xref: SO:0000330
xref: SO:0000853
xref: SO:0000857
xref: SO:homologous_to
xref: TAO:homologous_to
property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch
property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127
property_value: seeAlso HOM:0000007
is_symmetric: true
is_a: RO:HOM0000001 ! in homology relationship with

[Typedef]
id: RO:HOM0000008
name: in biological homology relationship with
def: "Homology that is defined by sharing of a set of developmental constraints, caused by locally acting self-regulatory mechanisms of differentiation, between individualized parts of the phenotype." [http://dx.doi.org/10.1016/S0169-5347(97)01125-7, http://dx.doi.org/10.1146/annurev.es.20.110189.000411, http://purl.obolibrary.org/obo/HOM_0000008]
comment: Applicable only to morphology. A certain degree of ambiguity is accepted between biological homology and parallelism.
synonym: "biological homologous to" EXACT []
synonym: "transformational homology" RELATED []
xref: ECO:0000067
property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch
property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127
property_value: seeAlso HOM:0000008
is_symmetric: true
is_a: RO:HOM0000001 ! in homology relationship with

[Typedef]
id: RO:HOM0000009
name: in reversal relationship with
def: "Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage." [http://dx.doi.org/10.1016/j.jhevol.2006.11.010, http://purl.obolibrary.org/obo/HOM_0000009]
synonym: "atavism" EXACT []
synonym: "reversion" RELATED []
synonym: "rudiment" EXACT []
property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch
property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127
property_value: seeAlso HOM:0000009
is_symmetric: true
is_a: RO:HOM0000002 ! in homoplasy relationship with

[Typedef]
id: RO:HOM0000010
name: in syntenic homology relationship with
def: "Structural homology that is detected by similarity in content and organization between chromosomes." [http://purl.obolibrary.org/obo/HOM_0000010, MeSH:Synteny]
synonym: "syntenic homologous to" EXACT []
synonym: "synteny" RELATED []
xref: MeSH:Synteny
xref: SO:0000860
xref: SO:0005858
property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch
property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127
property_value: seeAlso HOM:0000010
is_symmetric: true
is_a: RO:HOM0000006 ! in structural homology relationship with

[Typedef]
id: RO:HOM0000011
name: in paralogy relationship with
def: "Historical homology that involves genes that diverged after a duplication event." [http://dx.doi.org/10.1016/S0168-9525(00)02005-9, http://dx.doi.org/10.1146/annurev.genet.39.073003.114725, http://purl.obolibrary.org/obo/HOM_0000011, http://www.ncbi.nlm.nih.gov/pubmed/5449325]
synonym: "paralogous to" EXACT []
xref: SO:0000854
xref: SO:0000859
xref: SO:paralogous_to
property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch
property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127
property_value: seeAlso HOM:0000011
is_symmetric: true
is_a: RO:HOM0000007 ! in historical homology relationship with
disjoint_from: RO:HOM0000017 ! in orthology relationship with

[Typedef]
id: RO:HOM0000012
name: in syntenic paralogy relationship with
def: "Paralogy that involves sets of syntenic blocks." [DOI:10.1002/1097-010X(20001215)288\:4<345\:\:AID-JEZ7>3.0.CO;2-Y, http://dx.doi.org/10.1186/1471-213X-7-100, http://purl.obolibrary.org/obo/HOM_0000012]
synonym: "duplicon" RELATED []
synonym: "paralogon" RELATED []
synonym: "syntenic paralogous to" EXACT []
property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch
property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127
property_value: seeAlso HOM:0000012
is_symmetric: true
is_a: RO:HOM0000010 ! in syntenic homology relationship with
is_a: RO:HOM0000011 ! in paralogy relationship with

[Typedef]
id: RO:HOM0000013
name: in syntenic orthology relationship with
def: "Syntenic homology that involves chromosomes of different species." [http://dx.doi.org/10.1101/gr.6380007, http://purl.obolibrary.org/obo/HOM_0000013]
synonym: "syntenic orthologous to" EXACT []
property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch
property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127
property_value: seeAlso HOM:0000013
is_symmetric: true
is_a: RO:HOM0000010 ! in syntenic homology relationship with

[Typedef]
id: RO:HOM0000014
name: in partial homology relationship with
def: "Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous." [http://purl.obolibrary.org/obo/HOM_0000014, ISBN:0123195837, ISBN:978-0471984931]
synonym: "fractional homology" EXACT []
synonym: "mixed homology" RELATED []
synonym: "modular homology" RELATED []
synonym: "partial correspondence" RELATED []
synonym: "partial homologous to" EXACT []
synonym: "percent homology" RELATED []
synonym: "segmental homology" EXACT []
property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch
property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127
property_value: seeAlso HOM:0000014
is_symmetric: true
is_a: RO:HOM0000006 ! in structural homology relationship with

[Typedef]
id: RO:HOM0000015
name: in protein structural homology relationship with
def: "Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence." [http://dx.doi.org/10.1016/0022-2836(76)90195-9, http://purl.obolibrary.org/obo/HOM_0000015]
synonym: "protein structural homologous to" EXACT []
xref: MeSH:Structural_Homology\,_Protein
property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch
property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127
property_value: seeAlso HOM:0000015
is_symmetric: true
is_a: RO:HOM0000006 ! in structural homology relationship with

[Typedef]
id: RO:HOM0000016
name: in non functional homology relationship with
def: "Structural homology that involves a pseudogenic feature and its functional ancestor." [http://purl.obolibrary.org/obo/HOM_0000016, SO:non_functional_homolog_of]
synonym: "non functional homologous to" EXACT []
synonym: "pseudogene" BROAD []
xref: SO:non_functional_homolog_of
property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch
property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127
property_value: seeAlso HOM:0000016
is_symmetric: true
is_a: RO:HOM0000006 ! in structural homology relationship with
disjoint_from: RO:HOM0000062 ! in equivalogy relationship with

[Typedef]
id: RO:HOM0000017
name: in orthology relationship with
def: "Historical homology that involves genes that diverged after a speciation event." [http://dx.doi.org/10.1007/BF02814484, http://dx.doi.org/10.1016/S0168-9525(00)02005-9, http://dx.doi.org/10.1146/annurev.genet.39.073003.114725, http://purl.obolibrary.org/obo/HOM_0000017, http://www.ncbi.nlm.nih.gov/pubmed/5449325]
comment: The term is sometimes also used for anatomical structures.
synonym: "orthologous to" EXACT []
xref: ECO:00000060
xref: SO:0000855
xref: SO:0000858
xref: SO:orthologous_to
property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch
property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127
property_value: seeAlso HOM:0000017
is_symmetric: true
is_a: RO:HOM0000007 ! in historical homology relationship with

[Typedef]
id: RO:HOM0000018
name: in xenology relationship with
def: "Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor." [http://dx.doi.org/10.1016/S0168-9525(00)02005-9, http://dx.doi.org/10.1146/annurev.genet.39.073003.114725, http://purl.obolibrary.org/obo/HOM_0000018]
comment: The term is sometimes also used for anatomical structures (e.g. in case of a symbiosis).
synonym: "xenologous to" EXACT []
property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch
property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127
property_value: seeAlso HOM:0000018
is_symmetric: true
is_a: RO:HOM0000007 ! in historical homology relationship with

[Typedef]
id: RO:HOM0000019
name: in 1 to 1 homology relationship with
def: "Historical homology that involves two members sharing no other homologs in the lineages considered." [BGEE:curator, http://purl.obolibrary.org/obo/HOM_0000019]
synonym: "1 to 1 homologous to" EXACT []
synonym: "1:1 homology" EXACT []
synonym: "one-to-one homology" EXACT []
property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch
property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127
property_value: seeAlso HOM:0000019
is_symmetric: true
is_a: RO:HOM0000007 ! in historical homology relationship with

[Typedef]
id: RO:HOM0000020
name: in 1 to 1 orthology relationship with
def: "Orthology that involves two genes that did not experience any duplication after the speciation event that created them." [http://dx.doi.org/10.1007/BF02814484, http://purl.obolibrary.org/obo/HOM_0000020, http://www.ensembl.org/info/docs/compara/homology_method.html]
synonym: "1 to 1 orthologous to" EXACT []
synonym: "1:1 orthology" EXACT []
synonym: "one-to-one orthology" EXACT []
property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch
property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127
property_value: seeAlso HOM:0000020
is_symmetric: true
is_a: RO:HOM0000017 ! in orthology relationship with
is_a: RO:HOM0000019 ! in 1 to 1 homology relationship with

[Typedef]
id: RO:HOM0000022
name: in ohnology relationship with
def: "Paralogy that results from a whole genome duplication event." [http://dx.doi.org/10.1038/75560, http://purl.obolibrary.org/obo/HOM_0000022]
synonym: "homoeology" RELATED []
synonym: "ohnologous to" EXACT []
property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch
property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127
property_value: seeAlso HOM:0000022
is_symmetric: true
is_a: RO:HOM0000011 ! in paralogy relationship with

[Typedef]
id: RO:HOM0000023
name: in in-paralogy relationship with
def: "Paralogy that results from a lineage-specific duplication subsequent to a given speciation event." [http://dx.doi.org/10.1146/annurev.genet.39.073003.114725, http://purl.obolibrary.org/obo/HOM_0000023]
synonym: "in-paralogous to" EXACT []
synonym: "inparalogy" EXACT []
synonym: "symparalogy" EXACT []
property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch
property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127
property_value: seeAlso HOM:0000023
is_symmetric: true
is_a: RO:HOM0000011 ! in paralogy relationship with
disjoint_from: RO:HOM0000024 ! in out-paralogy relationship with

[Typedef]
id: RO:HOM0000024
name: in out-paralogy relationship with
def: "Paralogy that results from a duplication preceding a given speciation event." [http://dx.doi.org/10.1146/annurev.genet.39.073003.114725, http://purl.obolibrary.org/obo/HOM_0000024]
synonym: "alloparalogy" EXACT []
synonym: "out-paralogous to" EXACT []
synonym: "outparalogy" EXACT []
property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch
property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127
property_value: seeAlso HOM:0000024
is_symmetric: true
is_a: RO:HOM0000011 ! in paralogy relationship with

[Typedef]
id: RO:HOM0000025
name: in pro-orthology relationship with
def: "1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A." [http://dx.doi.org/10.1006/scdb.1999.0338, http://dx.doi.org/10.1038/nrg2099, http://purl.obolibrary.org/obo/HOM_0000025]
synonym: "pro-orthologous to" EXACT []
property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch
property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127
property_value: seeAlso HOM:0000025
is_symmetric: true
is_a: RO:HOM0000034 ! in 1 to many orthology relationship with

[Typedef]
id: RO:HOM0000026
name: in semi-orthology relationship with
def: "1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B." [http://dx.doi.org/10.1006/scdb.1999.0338, http://dx.doi.org/10.1038/nrg2099, http://purl.obolibrary.org/obo/HOM_0000026]
comment: The converse of pro-orthologous.
synonym: "semi-orthologous to" EXACT []
property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch
property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127
property_value: seeAlso HOM:0000026
is_symmetric: true
is_a: RO:HOM0000034 ! in 1 to many orthology relationship with

[Typedef]
id: RO:HOM0000027
name: in serial homology relationship with
def: "Iterative homology that involves structures arranged along the main body axis." [http://dx.doi.org/10.1146/annurev.es.20.110189.000411, http://purl.obolibrary.org/obo/HOM_0000027]
synonym: "homonomy" RELATED []
synonym: "serial homologous to" EXACT []
property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch
property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127
property_value: seeAlso HOM:0000027
is_symmetric: true
is_a: RO:HOM0000066 ! in iterative homology relationship with

[Typedef]
id: RO:HOM0000028
name: in heterochronous homology relationship with
def: "Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures." [http://purl.obolibrary.org/obo/HOM_0000028, ISBN:978-0674639416]
synonym: "heterochronous homologous to" EXACT []
synonym: "heterochrony" EXACT []
property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch
property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127
property_value: seeAlso HOM:0000028
is_symmetric: true
is_a: RO:HOM0000008 ! in biological homology relationship with

[Typedef]
id: RO:HOM0000029
name: in paedomorphorsis relationship with
def: "Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles." [http://en.wikipedia.org/wiki/Pedomorphosis, http://purl.obolibrary.org/obo/HOM_0000029, ISBN:978-0674639416]
synonym: "juvenification" EXACT []
synonym: "pedomorphosis" EXACT []
property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch
property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127
property_value: seeAlso HOM:0000029
is_symmetric: true
is_a: RO:HOM0000028 ! in heterochronous homology relationship with
disjoint_from: RO:HOM0000030 ! in peramorphosis relationship with

[Typedef]
id: RO:HOM0000030
name: in peramorphosis relationship with
def: "Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits." [http://en.wikipedia.org/wiki/Peramorphosis, http://purl.obolibrary.org/obo/HOM_0000030]
property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch
property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127
property_value: seeAlso HOM:0000030
is_symmetric: true
is_a: RO:HOM0000028 ! in heterochronous homology relationship with

[Typedef]
id: RO:HOM0000031
name: in progenesis relationship with
def: "Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage." [http://en.wikipedia.org/wiki/Progenesis, http://purl.obolibrary.org/obo/HOM_0000031, ISBN:978-0674639416]
property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch
property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127
property_value: seeAlso HOM:0000031
is_symmetric: true
is_a: RO:HOM0000029 ! in paedomorphorsis relationship with

[Typedef]
id: RO:HOM0000032
name: in neoteny relationship with
def: "Paedomorphosis that is produced by a retardation of somatic development." [http://en.wikipedia.org/wiki/Neoteny, http://purl.obolibrary.org/obo/HOM_0000032, ISBN:978-0674639416]
synonym: "juvenilization" EXACT []
synonym: "neotenous to" EXACT []
property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch
property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127
property_value: seeAlso HOM:0000032
is_symmetric: true
is_a: RO:HOM0000029 ! in paedomorphorsis relationship with

[Typedef]
id: RO:HOM0000033
name: in mimicry relationship with
def: "Convergence that results from co-evolution usually involving an evolutionary arms race." [http://en.wikipedia.org/wiki/Mimicry, http://purl.obolibrary.org/obo/HOM_0000033]
synonym: "mimicrous to" EXACT []
property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch
property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127
property_value: seeAlso HOM:0000033
is_symmetric: true
is_a: RO:HOM0000004 ! in convergence relationship with

[Typedef]
id: RO:HOM0000034
name: in 1 to many orthology relationship with
def: "Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other." [http://dx.doi.org/10.1038/415741a, http://purl.obolibrary.org/obo/HOM_0000034, http://www.ensembl.org/info/docs/compara/homology_method.html]
synonym: "1 to many orthologous to" EXACT []
synonym: "1:many orthology" EXACT []
synonym: "co-orthology" RELATED []
synonym: "many to 1 orthology" RELATED []
synonym: "one-to-many orthology" EXACT []
property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch
property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127
property_value: seeAlso HOM:0000034
is_symmetric: true
is_a: RO:HOM0000017 ! in orthology relationship with
is_a: RO:HOM0000037 ! in 1 to many homology relationship with

[Typedef]
id: RO:HOM0000036
name: in many to many homology relationship with
def: "Historical homology that involves two members of a larger set of homologs." [http://dx.doi.org/10.1093/molbev/msp002, http://purl.obolibrary.org/obo/HOM_0000036]
synonym: "many to many homologous to" EXACT []
synonym: "many-to-many homology" EXACT []
synonym: "many:many homology " EXACT []
property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch
property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127
property_value: seeAlso HOM:0000036
is_symmetric: true
is_a: RO:HOM0000007 ! in historical homology relationship with

[Typedef]
id: RO:HOM0000037
name: in 1 to many homology relationship with
def: "Historical homology that involves a structure that has no other homologs in the species in which it is defined, and several homologous structures in another species." [BGEE:curator, http://purl.obolibrary.org/obo/HOM_0000037]
synonym: "1 to many homologous to" EXACT []
synonym: "1:many homology" RELATED []
synonym: "one-to-many homology" EXACT []
property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch
property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127
property_value: seeAlso HOM:0000037
is_symmetric: true
is_a: RO:HOM0000007 ! in historical homology relationship with

[Typedef]
id: RO:HOM0000042
name: in apomorphy relationship with
def: "Historical homology that is based on recent shared ancestry, characterizing a monophyletic group." [http://purl.obolibrary.org/obo/HOM_0000042, ISBN:978-0252068140]
synonym: "apomorphous to" EXACT []
synonym: "synapomorphy" RELATED []
property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch
property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127
property_value: seeAlso HOM:0000042
is_symmetric: true
is_a: RO:HOM0000007 ! in historical homology relationship with
disjoint_from: RO:HOM0000043 ! in plesiomorphy relationship with

[Typedef]
id: RO:HOM0000043
name: in plesiomorphy relationship with
def: "Historical homology that is based on distant shared ancestry." [http://purl.obolibrary.org/obo/HOM_0000043, ISBN:978-0252068140]
comment: This term is usually contrasted to apomorphy.
synonym: "plesiomorphous to" EXACT []
synonym: "symplesiomorphy" RELATED []
property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch
property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127
property_value: seeAlso HOM:0000043
is_symmetric: true
is_a: RO:HOM0000007 ! in historical homology relationship with

[Typedef]
id: RO:HOM0000044
name: in deep homology relationship with
def: "Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution." [http://dx.doi.org/10.1007/BF02814485, http://dx.doi.org/10.1038/nature07891, http://purl.obolibrary.org/obo/HOM_0000044]
comment: Used for structures in distantly related taxa.
synonym: "deep genetic homology" EXACT []
synonym: "deep homologous to" EXACT []
synonym: "generative homology" RELATED []
synonym: "homoiology" RELATED []
property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch
property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127
property_value: seeAlso HOM:0000044
is_symmetric: true
is_a: RO:HOM0000003 ! in homocracy relationship with
is_a: RO:HOM0000005 ! in parallelism relationship with

[Typedef]
id: RO:HOM0000045
name: in hemiplasy relationship with
def: "Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree." [http://dx.doi.org/10.1073/pnas.0807433105, http://purl.obolibrary.org/obo/HOM_0000045]
synonym: "hemiplasous to" EXACT []
property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch
property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127
property_value: seeAlso HOM:0000045
is_symmetric: true
is_a: RO:HOM0000007 ! in historical homology relationship with

[Typedef]
id: RO:HOM0000046
name: in gametology relationship with
def: "Historical homology that involves not recombining and subsequently differentiated sex chromosomes." [http://purl.obolibrary.org/obo/HOM_0000046, http://www.ncbi.nlm.nih.gov/pubmed/11110898]
synonym: "gametologous to" EXACT []
property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch
property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127
property_value: seeAlso HOM:0000046
is_symmetric: true
is_a: RO:HOM0000047 ! in chromosomal homology relationship with

[Typedef]
id: RO:HOM0000047
name: in chromosomal homology relationship with
def: "Historical homology that involves the chromosomes able to pair (synapse) during meiosis." [http://purl.obolibrary.org/obo/HOM_0000047, ISBN:0195307615]
synonym: "chromosomal homologous to" EXACT []
xref: MeSH:Chromosome_Pairing
property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch
property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127
property_value: seeAlso HOM:0000047
is_symmetric: true
is_a: RO:HOM0000007 ! in historical homology relationship with

[Typedef]
id: RO:HOM0000048
name: in many to many orthology relationship with
def: "Orthology that involves two genes that experienced duplications more recent than the species split that created them." [http://dx.doi.org/10.1038/415741a, http://purl.obolibrary.org/obo/HOM_0000048, http://www.ensembl.org/info/docs/compara/homology_method.html]
synonym: "co-orthology" RELATED []
synonym: "many to many orthologous to" EXACT []
synonym: "many-to-many orthology" EXACT []
synonym: "many:many orthology" EXACT []
synonym: "trans-homology" RELATED []
synonym: "trans-orthology" EXACT []
property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch
property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127
property_value: seeAlso HOM:0000048
is_symmetric: true
is_a: RO:HOM0000017 ! in orthology relationship with
is_a: RO:HOM0000036 ! in many to many homology relationship with

[Typedef]
id: RO:HOM0000049
name: in within-species paralogy relationship with
def: "Paralogy that involves genes from the same species." [http://purl.obolibrary.org/obo/HOM_0000049, http://www.ensembl.org/info/docs/compara/homology_method.html]
synonym: "within-species paralogous to" EXACT []
property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch
property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127
property_value: seeAlso HOM:0000049
is_symmetric: true
is_a: RO:HOM0000011 ! in paralogy relationship with
disjoint_from: RO:HOM0000050 ! in between-species paralogy relationship with

[Typedef]
id: RO:HOM0000050
name: in between-species paralogy relationship with
def: "Paralogy that involves genes from different species." [http://purl.obolibrary.org/obo/HOM_0000050, http://www.ensembl.org/info/docs/compara/homology_method.html]
comment: The genes have diverged before a speciation event.
synonym: "between-species paralogous to" EXACT []
property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch
property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127
property_value: seeAlso HOM:0000050
is_symmetric: true
is_a: RO:HOM0000011 ! in paralogy relationship with

[Typedef]
id: RO:HOM0000051
name: in postdisplacement relationship with
def: "Paedomorphosis that is produced by delayed growth of immature structures into the adult form." [http://en.wikipedia.org/wiki/Pedomorphosis, http://purl.obolibrary.org/obo/HOM_0000051]
synonym: "post-displacement" EXACT []
property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch
property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127
property_value: seeAlso HOM:0000051
is_symmetric: true
is_a: RO:HOM0000029 ! in paedomorphorsis relationship with

[Typedef]
id: RO:HOM0000052
name: in hypermorphosis relationship with
def: "Peramorphosis that is produced by a delay in the offset of development." [http://en.wikipedia.org/wiki/Peramorphosis, http://purl.obolibrary.org/obo/HOM_0000052, ISBN:978-0674639416]
property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch
property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127
property_value: seeAlso HOM:0000052
is_symmetric: true
is_a: RO:HOM0000030 ! in peramorphosis relationship with

[Typedef]
id: RO:HOM0000053
name: in synology relationship with
def: "Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species." [http://dx.doi.org/10.1007/BF00173425, http://dx.doi.org/10.1016/S0168-9525(00)02005-9, http://purl.obolibrary.org/obo/HOM_0000053]
synonym: "synologous to" EXACT []
property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch
property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127
property_value: seeAlso HOM:0000053
is_symmetric: true
is_a: RO:HOM0000018 ! in xenology relationship with

[Typedef]
id: RO:HOM0000054
name: in isoorthology relationship with
def: "Orthology that involves functional equivalent genes with retention of the ancestral function." [http://dx.doi.org/10.1016/S0168-9525(00)02005-9, http://purl.obolibrary.org/obo/HOM_0000054]
synonym: "isoorthologous to" EXACT []
xref: ECO:0000080
property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch
property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127
property_value: seeAlso HOM:0000054
is_symmetric: true
is_a: RO:HOM0000017 ! in orthology relationship with
is_a: RO:HOM0000062 ! in equivalogy relationship with

[Typedef]
id: RO:HOM0000055
name: in tandem paralogy relationship with
def: "Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment." [http://dx.doi.org/10.1016/S0168-9525(00)02005-9, http://purl.obolibrary.org/obo/HOM_0000055, ISBN:978-0878932665]
synonym: "iterative paralogy" RELATED []
synonym: "serial paralogy" RELATED []
synonym: "tandem paralogous to" EXACT []
property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch
property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127
property_value: seeAlso HOM:0000055
is_symmetric: true
is_a: RO:HOM0000011 ! in paralogy relationship with

[Typedef]
id: RO:HOM0000057
name: in latent homology relationship with
def: "Parallelism that involves morphologically very similar structures, occurring only within some members of a taxon and absent in the common ancestor (which possessed the developmental basis to develop this character)." [http://dx.doi.org/10.1007/BF02814485, http://dx.doi.org/10.1016/j.jhevol.2006.11.010, http://dx.doi.org/10.1186/1742-9994-2-15, http://purl.obolibrary.org/obo/HOM_0000057, ISBN:0199141118]
comment: Used for structures in closely related taxa.
synonym: "apomorphic tendency" EXACT []
synonym: "cryptic homology" EXACT []
synonym: "homoiology" RELATED []
synonym: "homoplastic tendency" RELATED []
synonym: "latent homologous to" EXACT []
synonym: "re-awakening" RELATED []
synonym: "underlying synapomorphy" EXACT []
property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch
property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127
property_value: seeAlso HOM:0000057
is_symmetric: true
is_a: RO:HOM0000005 ! in parallelism relationship with
is_a: RO:HOM0000058 ! in syngeny relationship with

[Typedef]
id: RO:HOM0000058
name: in syngeny relationship with
def: "Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual." [DOI:10.1002/1521-1878(200009)22\:9<846\:\:AID-BIES10>3.0.CO;2-R, http://dx.doi.org/10.1186/1742-9994-2-15, http://purl.obolibrary.org/obo/HOM_0000058]
comment: Cannot be used when orthologous patterning gene are organizing obviously non-homologous structures in different organisms due for example to pleiotropic functions of these genes.
synonym: "generative homology" EXACT []
synonym: "syngenous to" EXACT []
property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch
property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127
property_value: seeAlso HOM:0000058
is_symmetric: true
is_a: RO:HOM0000003 ! in homocracy relationship with

[Typedef]
id: RO:HOM0000060
name: in apparent orthology relationship with
def: "Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss." [http://dx.doi.org/10.1146/annurev.genet.39.073003.114725, http://purl.obolibrary.org/obo/HOM_0000060, http://www.ensembl.org/info/docs/compara/homology_method.html]
comment: The genes are actually paralogs but appear to be orthologous due to differential, lineage-specific gene loss.
synonym: "1:1 paralogy" EXACT []
synonym: "apparent 1:1 orthology" EXACT []
synonym: "apparent orthologous to" EXACT []
synonym: "pseudoorthology" EXACT []
property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch
property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127
property_value: seeAlso HOM:0000060
is_symmetric: true
is_a: RO:HOM0000019 ! in 1 to 1 homology relationship with
is_a: RO:HOM0000050 ! in between-species paralogy relationship with

[Typedef]
id: RO:HOM0000061
name: in pseudoparalogy relationship with
def: "Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer." [http://dx.doi.org/10.1146/annurev.genet.39.073003.114725, http://purl.obolibrary.org/obo/HOM_0000061]
comment: These genes may come out as paralogs in a single-genome analysis.
synonym: "pseudoparalogous to" EXACT []
property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch
property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127
property_value: seeAlso HOM:0000061
is_symmetric: true
is_a: RO:HOM0000018 ! in xenology relationship with

[Typedef]
id: RO:HOM0000062
name: in equivalogy relationship with
def: "Historical homology that involves functional equivalent genes with retention of the ancestral function." [http://dx.doi.org/10.1093/nar/gkl1043, http://purl.obolibrary.org/obo/HOM_0000062]
comment: This may include examples of orthology, paralogy and xenology.
synonym: "equivalogous to" EXACT []
property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch
property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127
property_value: seeAlso HOM:0000062
is_symmetric: true
is_a: RO:HOM0000007 ! in historical homology relationship with
is_a: RO:HOM0000065 ! in functional equivalence relationship with

[Typedef]
id: RO:HOM0000063
name: in interology relationship with
def: "Historical homology that involves orthologous pairs of interacting molecules in different organisms." [http://dx.doi.org/10.1101/gr.1774904, http://dx.doi.org/10.1126/science.287.5450.116, http://purl.obolibrary.org/obo/HOM_0000063]
synonym: "interologous to" EXACT []
property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch
property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127
property_value: seeAlso HOM:0000063
is_symmetric: true
is_a: RO:HOM0000007 ! in historical homology relationship with

[Typedef]
id: RO:HOM0000065
name: in functional equivalence relationship with
def: "Similarity that is characterized by interchangeability in function." [http://dx.doi.org/10.1007/BF02814484, http://dx.doi.org/10.1038/415741a, http://purl.obolibrary.org/obo/HOM_0000065]
synonym: "functional similarity" RELATED []
property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch
property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127
property_value: seeAlso HOM:0000065
is_symmetric: true
is_a: RO:HOM0000000 ! in similarity relationship with

[Typedef]
id: RO:HOM0000066
name: in iterative homology relationship with
def: "Biological homology that involves parts of the same organism." [http://dx.doi.org/10.1146/annurev.es.20.110189.000411, http://purl.obolibrary.org/obo/HOM_0000066]
synonym: "iterative homologous to" EXACT []
property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch
property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127
property_value: seeAlso HOM:0000066
is_symmetric: true
is_a: RO:HOM0000008 ! in biological homology relationship with

[Typedef]
id: RO:HOM0000068
name: in paraxenology relationship with
def: "Xenology that is characterized by multiple horizontal transfer events, resulting in the presence of two or more copies of the foreign gene in the host genome." [http://purl.obolibrary.org/obo/HOM_0000068, http://www.ncbi.nlm.nih.gov/pubmed/3065587]
synonym: "duplicate xenology" EXACT []
synonym: "multiple xenology" EXACT []
synonym: "paraxenologous to" EXACT []
property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch
property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127
property_value: seeAlso HOM:0000068
is_symmetric: true
is_a: RO:HOM0000018 ! in xenology relationship with

[Typedef]
id: RO:HOM0000069
name: in plerology relationship with
def: "Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution." [http://purl.obolibrary.org/obo/HOM_0000069, http://www.ncbi.nlm.nih.gov/pubmed/3065587]
comment: This phenomenon is usually due to gene conversion process.
synonym: "plerologous to" EXACT []
property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch
property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127
property_value: seeAlso HOM:0000069
is_symmetric: true
is_a: RO:HOM0000011 ! in paralogy relationship with

[Typedef]
id: RO:HOM0000071
name: in homotopy relationship with
def: "Structural homology that involves structures with the same or similar relative positions." [http://dx.doi.org/10.1007/BF02814484, http://dx.doi.org/10.1007/BF02814485, http://purl.obolibrary.org/obo/HOM_0000071, ISBN:0123195837]
comment: Theissen (2005) mentions that some authors may consider homotopy to be distinct from homology, but this is not the standard use.
synonym: "homotopous to" EXACT []
property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch
property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127
property_value: seeAlso HOM:0000071
is_symmetric: true
is_a: RO:HOM0000006 ! in structural homology relationship with
disjoint_from: RO:HOM0000072 ! in homeosis relationship with

[Typedef]
id: RO:HOM0000072
name: in homeosis relationship with
def: "Biological homology that involves an ectopic structure and the normally positioned structure." [http://dx.doi.org/10.1007/BF02814485, http://dx.doi.org/10.1016/j.cell.2008.06.030, http://purl.obolibrary.org/obo/HOM_0000072]
synonym: "heterotopy" RELATED []
property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch
property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127
property_value: seeAlso HOM:0000072
is_symmetric: true
is_a: RO:HOM0000008 ! in biological homology relationship with

[Typedef]
id: RO:HOM0000073
name: in homoeology relationship with
def: "Synology that results from allopolyploidy." [http://dx.doi.org/10.1073/pnas.0505156102, http://purl.obolibrary.org/obo/HOM_0000073]
comment: On a long term, it is hard to distinguish allopolyploidy from whole genome duplication.
synonym: "homoeologous to" EXACT []
property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch
property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127
property_value: seeAlso HOM:0000073
is_symmetric: true
is_a: RO:HOM0000022 ! in ohnology relationship with
is_a: RO:HOM0000053 ! in synology relationship with

[Typedef]
id: RO:HOM0000074
name: in paramorphism relationship with
def: "Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure." [http://dx.doi.org/10.1007/s10441-007-9023-8, http://dx.doi.org/10.1046/j.1525-142x.2000.00054.x, http://purl.obolibrary.org/obo/HOM_0000074]
synonym: "axis paramorphism" RELATED []
property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch
property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127
property_value: seeAlso HOM:0000074
is_symmetric: true
is_a: RO:HOM0000003 ! in homocracy relationship with
is_a: RO:HOM0000066 ! in iterative homology relationship with

[Typedef]
id: RO:HOM0000075
name: in regulogy relationship with
def: "Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms." [http://dx.doi.org/10.1101/gr.1774904, http://purl.obolibrary.org/obo/HOM_0000075]
synonym: "regulogous to" EXACT []
property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch
property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127
property_value: seeAlso HOM:0000075
is_symmetric: true
is_a: RO:HOM0000007 ! in historical homology relationship with