2022-08-16 release

[shawntanzk]

No description provided.

[anitacaron]

I checked that never_in_taxon properties are back!

[matentzn]

Impressive release:

• remove renal-minimal files from version control with git rm. Make sure they are in .gitignore.
• Check uberon.owl for dangling classes, there seem to be hundreds of removed terms in our imports

[matentzn]

lots of disjointnesses remove, intended?

[shawntanzk]

@bvarner-ebi & @nicolevasilevsky - I assume this is the work you guys did with the renal system stuff? could you check this please

[ghost]

@shawntanzk, sorry, these do not look familiar.

[shawntanzk]

sorry @balhoff - ignore that, was looking at the wrong thing >.<

[shawntanzk]

strange that the renal-minimal files got through, there is already this in .gitignore:

subsets/*.json
subsets/*.obo
subsets/*.owl
subsets/*.tsv

[shawntanzk]

Check uberon.owl for dangling classes, there seem to be hundreds of removed terms in our imports

hmmm this isn't good, there is indeed a whole bunch of ncbitaxon dangling - which I assume match the ncbi imports that were being removed in this release - any ideas why?

[anitacaron]

I saw in uberon.obo that some of the NCBITaxon class definitions were deleted but still have the relationship present_in_taxon.

[matentzn]

Anita my guess is: never in taxon are somehow not read by seed extraction process. Don't know why it ever worked..

[anitacaron]

But all classes in the image are used with only_in_taxon and present_in_taxon.

[matentzn]

Can someone verify that http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl contains all of these IDs now dangling?

[anitacaron]

It doesn't contain any of these terms.

[matentzn]

Can you make a PR here: https://github.com/obophenotype/ncbitaxon/blob/master/subsets/taxon-subset-ids.txt to get them in and assign me?

We will drive fast to get this resolved

[matentzn]

While we are working on this - are all the other dangling classes expected?

[shawntanzk]

While we are working on this - are all the other dangling classes expected?

1 GO term (http://purl.obolibrary.org/obo/GO_0097254) that should not be dangling

4 CARO terms:

http://purl.obolibrary.org/obo/RnorDv_0000010 -> not sure what this is

[matentzn]

Caro seems to be a proper import of uberon, but not included in the edit file. @shawntanzk can you try to add the caro import to the edit file and see if this breaks the uberon release?

[matentzn]

Whats the usage of teh GO dangler?

[shawntanzk]

Whats the usage of teh GO dangler?

[shawntanzk]

@shawntanzk can you try to add the caro import to the edit file and see if this breaks the uberon release?

on edit file seems to work fine - have not built the release file - happy to fix the danglers and make uberon if you arent already doing it?

[matentzn]

No I am not working on it

[matentzn]

Ok try refrshig imports https://github.com/obophenotype/ncbitaxon/releases/tag/v2022-08-17

[shawntanzk]

Ok try refrshig imports https://github.com/obophenotype/ncbitaxon/releases/tag/v2022-08-17

on it

[shawntanzk]

Ok try refrshig imports https://github.com/obophenotype/ncbitaxon/releases/tag/v2022-08-17

Tried refreshing all imports, no change
Tried updating mirror for ncbitaxon then refreshing ncbitaxon_import.owl, no change
Tried adding the missing terms to ncbitaxon_import.txt and refreshing ncbitaxon_import.owl, no change :(

[shawntanzk]

Just saw the NCBITaxon tagged as pre-release instead of latest - could this be the problem?

[shawntanzk]

Looks like the issue was brought in with the reinstatement of CARO as an import - maybe why it was removed before?

[matentzn]

Excellent this exact query should be a GitHub action, which if it fails, posts the unsat as a comment to the PR. Wouldnt this be awesome?

And lucking at this query, while being tired and annoyed, can't help you feel amazed by the awesomeness of the tech for this particular use case. No other stack can do that. Finding an inconsistency like that.

[matentzn]

Not sure man this unsat looks pretty legit to me. Removing caro would just hide an inconsistency!

[github-actions]

Here's a diff of how these changes impact the classified ontology (on -simple file):

Ontology comparison

Left

• Ontology IRI: http://purl.obolibrary.org/obo/uberon/uberon-simple.owl
• Version IRI: http://purl.obolibrary.org/obo/uberon/releases/2022-08-17/uberon-simple.owl
• Loaded from: file:/work/src/ontology/../../master/src/ontology/uberon-simple.owl

Right

• Ontology IRI: http://purl.obolibrary.org/obo/uberon/uberon-simple.owl
• Version IRI: http://purl.obolibrary.org/obo/uberon/releases/2022-08-17/uberon-simple.owl
• Loaded from: file:/work/src/ontology/uberon-simple.owl

Ontology imports

Ontology annotations

IAO_0000589 http://purl.obolibrary.org/obo/IAO_0000589

Added

• AnnotationProperty: IAO_0000589

RO_0002575 http://purl.obolibrary.org/obo/RO_0002575

Added

• AnnotationProperty: RO_0002575

adjacent_to http://purl.obolibrary.org/obo/RO_0002220

Added

• adjacent_to example of usage "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies."

• adjacent_to IAO_0000117 "Chris Mungall"

• adjacent_to IAO_0000114 IAO_0000125

• adjacent_to example of usage "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."

• adjacent_to in_subset valid_for_go_annotation_extension

• adjacent_to has_obo_namespace "external"

• adjacent_to in_subset valid_for_gocam

• adjacent_to in_subset valid_for_go_ontology

• adjacent_to RO_0001900 RO_0001901

• adjacent_to editor note "This relation acts as a join point with BSPO"

• adjacent_to example of usage "The epidermis layer of a vertebrate is adjacent to the dermis."

• adjacent_to example of usage "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."

  • see also issuecomment-218584934

attached to part of http://purl.obolibrary.org/obo/RO_0002177

Added

• attached to part of IAO_0000589 "attached to part of (anatomical structure to anatomical structure)"

attaches_to http://purl.obolibrary.org/obo/RO_0002371

Added

• attaches_to IAO_0000117 "Chris Mungall"

• attaches_to in_subset ro-eco

• attaches_to IAO_0000589 "attached to (anatomical structure to anatomical structure)"

bounding layer of http://purl.obolibrary.org/obo/RO_0002007

Added

• bounding layer of in_subset ro-eco

• bounding layer of has_obo_namespace "external"

• bounding layer of IAO_0000117 "David Osumi-Sutherland"

• bounding layer of 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."

branching part of http://purl.obolibrary.org/obo/RO_0002380

Added

• branching part of example of usage "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S"

• branching part of see also 2212

• branching part of see also "FMA:85994"

• branching part of IAO_0000117 "Chris Mungall"

• branching part of in_subset ro-eco

capable of part of http://purl.obolibrary.org/obo/RO_0002216

Added

• capable of part of see also http://purl.obolibrary.org/obo/ro/docs/reflexivity/

• capable of part of has_obo_namespace "external"

citesAsAuthority http://purl.org/spar/cito/citesAsAuthority

Added

• AnnotationProperty: citesAsAuthority

composed primarily of http://purl.obolibrary.org/obo/RO_0002473

Added

• composed primarily of in_subset ro-eco

• composed primarily of example of usage "'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'"

• composed primarily of IAO_0000119 22293552

• composed primarily of IAO_0000117 "Chris Mungall"

• composed primarily of RO_0001900 RO_0001901

confers advantage in http://purl.obolibrary.org/obo/RO_0002322

Added

• confers advantage in IAO_0000118 "adapted for"

• confers advantage in IAO_0000117 "Chris Mungall"

• confers advantage in editor note "An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial."

• confers advantage in in_subset ro-eco

connected to http://purl.obolibrary.org/obo/RO_0002170

Added

• connected to definition "Binary relationship: x connected_to y if and only if there exists some z such that z connects x and y in a ternary connected_to(x,y,z) relationship."

  • database_cross_reference "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern"

• connected to see also "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• connected to IAO_0000119 22293552

• connected to see also "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• connected to example of usage "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint connects these two bones)."

connects http://purl.obolibrary.org/obo/RO_0002176

Added

• connects see also "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• connects see also "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• connects example of usage "The M8 connects Glasgow and Edinburgh"

• connects IAO_0000119 22293552

• connects example of usage "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint connects these two bones)."

contains http://purl.obolibrary.org/obo/RO_0001019

Added

• contains IAO_0000111 "contains"@en

• contains RO_0001900 RO_0001901

• contains in_subset ro-eco

continuous with http://purl.obolibrary.org/obo/RO_0002150

Added

• continuous with RO_0001900 RO_0001901

• continuous with IAO_0000114 IAO_0000125

• continuous with IAO_0000117 "David Osumi-Sutherland"

• continuous with IAO_0000118 "connected to"

• continuous with curator notes "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)"

• continuous with see also "FMA:85972"

contributes to morphology of http://purl.obolibrary.org/obo/RO_0002433

Added

• contributes to morphology of IAO_0000117 "Chris Mungall"

developmentally replaces http://purl.obolibrary.org/obo/RO_0002285

Added

• developmentally replaces IAO_0000114 IAO_0000125

• developmentally replaces editor note "This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage"

• developmentally replaces IAO_0000118 "replaces"

• developmentally replaces IAO_0000117 "Chris Mungall"

developmentally_induced_by http://purl.obolibrary.org/obo/RO_0002256

Added

• developmentally_induced_by IAO_0000119 " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)"

• developmentally_induced_by IAO_0000118 "induced by"

• developmentally_induced_by IAO_0000119 "GO:0001759"

• developmentally_induced_by IAO_0000119 20064205

• developmentally_induced_by curator notes "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]"

• developmentally_induced_by IAO_0000117 "Chris Mungall"

• developmentally_induced_by IAO_0000117 "David Osumi-Sutherland"

• developmentally_induced_by IAO_0000114 IAO_0000125

• developmentally_induced_by IAO_0000117 "Melissa Haendel"

develops from part of http://purl.obolibrary.org/obo/RO_0002225

Added

• develops from part of IAO_0000114 IAO_0000125

• develops from part of IAO_0000117 "Chris Mungall"

develops in http://purl.obolibrary.org/obo/RO_0002226

Added

• develops in IAO_0000119 "Jonathan Bard, EHDAA2"

• develops in IAO_0000117 "Chris Mungall"

• develops in IAO_0000119 "EHDAA2"

• develops in IAO_0000114 IAO_0000125

directly develops from http://purl.obolibrary.org/obo/RO_0002207

Added

• directly develops from IAO_0000117 "Chris Mungall"

• directly develops from IAO_0000117 "David Osumi-Sutherland"

• directly develops from comment "TODO - add child relations from DOS"

• directly develops from IAO_0000119 "FBbt"

• directly develops from RO_0002575 develops from

• directly develops from IAO_0000114 IAO_0000125

• directly develops from IAO_0000117 "has developmental precursor"

drains http://purl.obolibrary.org/obo/RO_0002179

Added

• drains editor note "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure"

• drains IAO_0000119 20064205

ends http://purl.obolibrary.org/obo/RO_0002229

Added

• ends IAO_0000114 IAO_0000125

• ends in_subset ro-eco

• ends IAO_0000117 "Chris Mungall"

ends with http://purl.obolibrary.org/obo/RO_0002230

Added

• ends with has_obo_namespace "external"

• ends with in_subset ro-eco

• ends with IAO_0000118 "finished by"

• ends with IAO_0000114 IAO_0000125

• ends with IAO_0000117 "Chris Mungall"

existence ends during http://purl.obolibrary.org/obo/RO_0002492

Added

• existence ends during IAO_0000117 "Chris Mungall"

• existence ends during comment "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription."

existence ends during or before http://purl.obolibrary.org/obo/RO_0002497

Added

• existence ends during or before IAO_0000117 "Chris Mungall"

• existence ends during or before comment "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription."

existence ends with http://purl.obolibrary.org/obo/RO_0002493

Added

• existence ends with IAO_0000117 "Chris Mungall"

• existence ends with comment "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription."

existence starts and ends during http://purl.obolibrary.org/obo/RO_0002491

Added

• existence starts and ends during IAO_0000117 "Chris Mungall"

• existence starts and ends during comment "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription."

• existence starts and ends during has_exact_synonym "exists during"

existence starts during http://purl.obolibrary.org/obo/RO_0002488

Added

• existence starts during IAO_0000117 "Chris Mungall"

existence starts during or after http://purl.obolibrary.org/obo/RO_0002496

Added

• existence starts during or after comment "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription."

• existence starts during or after IAO_0000117 "Chris Mungall"

existence starts with http://purl.obolibrary.org/obo/RO_0002489

Added

• existence starts with IAO_0000117 "Chris Mungall"

has 2D boundary http://purl.obolibrary.org/obo/RO_0002002

Added

• has 2D boundary IAO_0000118 "has_2D_boundary"@en

• has 2D boundary example of usage "my body has 2D boundary the surface of my skin"@en

• has 2D boundary IAO_0000117 "David Osumi-Sutherland"

• has 2D boundary editor note "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape."@en

• has 2D boundary IAO_0000118 "has boundary"@en

• has 2D boundary label "has_boundary"@en

• has 2D boundary editor note "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts."@en

• has 2D boundary RO_0001900 RO_0001901

has branching part http://purl.obolibrary.org/obo/RO_0002569

Added

• has branching part IAO_0000117 "Chris Mungall"

• has branching part in_subset ro-eco

• has branching part in_subset RO_0002259

has component http://purl.obolibrary.org/obo/RO_0002180

Added

• has component has_obo_namespace "external"

has member http://purl.obolibrary.org/obo/RO_0002351

Added

• has member RO_0001900 RO_0001901

• has member IAO_0000119 "SIO"

has muscle antagonist http://purl.obolibrary.org/obo/RO_0002568

Added

• has muscle antagonist IAO_0000119 "Wikipedia:Antagonist_(muscle)"

• has muscle antagonist IAO_0000117 "Chris Mungall"

has muscle insertion http://purl.obolibrary.org/obo/RO_0002373

Added

• has muscle insertion see also insertion

• has muscle insertion IAO_0000119 "Wikipedia:Insertion_(anatomy)"@en

• has muscle insertion IAO_0000117 "Chris Mungall"

has muscle origin http://purl.obolibrary.org/obo/RO_0002372

Added

• has muscle origin IAO_0000117 "Chris Mungall"

• has muscle origin IAO_0000119 "Wikipedia:Insertion_(anatomy)"@en

• has muscle origin see also origin

has skeleton http://purl.obolibrary.org/obo/RO_0002551

Added

• has skeleton curator notes "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)."

• has skeleton IAO_0000117 "Chris Mungall"

• has skeleton IAO_0000118 "has supporting framework"

• has skeleton example of usage "Forelimb SubClassOf has_skeleton some 'Forelimb skeleton'"

has_part http://purl.obolibrary.org/obo/BFO_0000051

Added

• has_part editor note "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/"@en

immediate transformation of http://purl.obolibrary.org/obo/RO_0002495

Added

• immediate transformation of RO_0002575 transformation of

• immediate transformation of IAO_0000117 "Chris Mungall"

immediately preceded by http://purl.obolibrary.org/obo/RO_0002087

Added

• immediately preceded by definition "X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)."

• immediately preceded by external_definition "A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251]."

  • source "SIO:000251"

• immediately preceded by has_obo_namespace "external"

in taxon http://purl.obolibrary.org/obo/RO_0002162

Added

• in taxon comment "Connects a biological entity to its taxon of origin."

• in taxon IAO_0000119 20973947

• in taxon IAO_0000119 17921072

• in taxon IAO_0000114 IAO_0000125

• in taxon IAO_0000117 "Chris Mungall"@en

• in taxon in_subset ro-eco

• in taxon IAO_0000117 "Jennifer Deegan"

• in taxon see also Taxon-constraints

innervated_by http://purl.obolibrary.org/obo/RO_0002005

Added

• innervated_by see also dbprop_nerve

• innervated_by comment "http://code.google.com/p/obo-relations/issues/detail?id=6"

• innervated_by IAO_0000117 "David Osumi-Sutherland"

• innervated_by has_exact_synonym "nerve supply"

  • database_cross_reference "FMA:85999"

• innervated_by see also FMA_85999

• innervated_by citesAsAuthority "http://www.ncbi.nlm.nih.gov/pubmed/22402613"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

innervates http://purl.obolibrary.org/obo/RO_0002134

Added

• innervates IAO_0000114 IAO_0000125

• innervates has_obo_namespace "fly_anatomy.ontology"

• innervates definition "Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input. T innervates some R Expands_to: T has_fasciculating_neuron_projection that synapse_in some R."

  • database_cross_reference "FBC:DOS"

• innervates IAO_0000424 "RO_0002132 some (GO_0043005 that (RO_0002131 some (GO_0045202 that BFO_0000050 some ?Y)))"

• innervates IAO_0000117 "David Osumi-Sutherland"@en

• innervates IAO_0000424 "<http://purl.obolibrary.org/obo/RO_0002132> some (<http://purl.obolibrary.org/obo/GO_0043005> that (<http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?)))"

• innervates citesAsAuthority 22402613

• innervates RO_0001900 RO_0001901

• innervates comment "http://code.google.com/p/obo-relations/issues/detail?id=6"

located in http://purl.obolibrary.org/obo/RO_0001025

Added

• located in editor note "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"@en

• located in example of usage "my brain is located in my head"@en

• located in editor note "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/"@en

• located in RO_0001900 RO_0001901

• located in in_subset valid_for_go_gp2term

• located in IAO_0000118 "located_in"@en

• located in IAO_0000111 "located in"@en

• located in example of usage "this rat is located in this cage"@en

• located in derived from resource "http://www.obofoundry.org/ro/#OBO_REL:located_in"

location of http://purl.obolibrary.org/obo/RO_0001015

Added

• location of example of usage "this cage is the location of this rat"@en

• location of IAO_0000111 "is location of"@en

• location of example of usage "my head is the location of my brain"@en

• location of IAO_0000118 "location_of"@en

• location of editor note "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/"@en

• location of RO_0001900 RO_0001901

lumen of http://purl.obolibrary.org/obo/RO_0002571

Added

• lumen of in_subset ro-eco

• lumen of IAO_0000119 "GOC:cjm"

• lumen of IAO_0000117 "Chris Mungall"

luminal space of http://purl.obolibrary.org/obo/RO_0002572

Added

• luminal space of in_subset ro-eco

• luminal space of IAO_0000117 "Chris Mungall"

only_in_taxon http://purl.obolibrary.org/obo/RO_0002160

Added

• only_in_taxon IAO_0000117 "Chris Mungall"@en

• only_in_taxon IAO_0000119 20973947

• only_in_taxon editor note "The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g.

'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria"

• only_in_taxon example of usage "lactation SubClassOf 'only in taxon' some 'Mammalia'"

• only_in_taxon IAO_0000119 17921072

• only_in_taxon see also Taxon-constraints

• only_in_taxon IAO_0000114 IAO_0000125

output of http://purl.obolibrary.org/obo/RO_0002353

Added

• output of IAO_0000117 "Chris Mungall"

• output of in_subset RO_0002259

• output of has_obo_namespace "external"

• output of in_subset ro-eco

overlaps http://purl.obolibrary.org/obo/RO_0002131

Added

• overlaps IAO_0000424 "BFO_0000051 some (BFO_0000050 some ?Y)"

• overlaps has_obo_namespace "external"

part_of http://purl.obolibrary.org/obo/BFO_0000050

Added

• part_of editor note "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/"@en

participates in http://purl.obolibrary.org/obo/RO_0000056

Added

• participates in has_obo_namespace "external"

preceded_by http://purl.obolibrary.org/obo/BFO_0000062

Added

• preceded_by definition "X preceded_by Y iff: end(Y) before_or_simultaneous_with start(X)."

• preceded_by has_obo_namespace "external"

precedes http://purl.obolibrary.org/obo/BFO_0000063

Added

• precedes has_obo_namespace "external"

present in taxon http://purl.obolibrary.org/obo/RO_0002175

Added

• present in taxon comment "The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology."

produced_by http://purl.obolibrary.org/obo/RO_0003001

Added

• produced_by in_subset ro-eco

• produced_by IAO_0000117 "Melissa Haendel"

• produced_by has_obo_namespace "external"

• produced_by IAO_0000114 IAO_0000125

produces http://purl.obolibrary.org/obo/RO_0003000

Added

• produces IAO_0000114 IAO_0000125

• produces 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."

• produces has_obo_namespace "external"

• produces in_subset ro-eco

• produces IAO_0000117 "Melissa Haendel"

simultaneous with http://purl.obolibrary.org/obo/RO_0002082

Added

• simultaneous with IAO_0000117 "David Osumi-Sutherland"

• simultaneous with in_subset ro-eco

• simultaneous with comment "t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2)"@en

skeleton of http://purl.obolibrary.org/obo/RO_0002576

Added

• skeleton of IAO_0000117 "Chris Mungall"

• skeleton of in_subset RO_0002259

starts http://purl.obolibrary.org/obo/RO_0002223

Added

• starts IAO_0000117 "Chris Mungall"

• starts IAO_0000119 "Allen"

• starts in_subset ro-eco

• starts IAO_0000114 IAO_0000125

starts with http://purl.obolibrary.org/obo/RO_0002224

Added

• starts with has_obo_namespace "external"

• starts with IAO_0000114 IAO_0000125

• starts with example of usage "Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor"

• starts with IAO_0000118 "started by"

• starts with in_subset ro-eco

• starts with IAO_0000117 "Chris Mungall"

supplies http://purl.obolibrary.org/obo/RO_0002178

Added

• supplies editor note "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"

• supplies IAO_0000119 20064205

surrounded by http://purl.obolibrary.org/obo/RO_0002219

Added

• surrounded by RO_0001900 RO_0001901

• surrounded by IAO_0000117 "Chris Mungall"

• surrounded by IAO_0000114 IAO_0000125

surrounds http://purl.obolibrary.org/obo/RO_0002221

Added

• surrounds RO_0001900 RO_0001901

• surrounds in_subset RO_0002259

• surrounds IAO_0000114 IAO_0000125

• surrounds IAO_0000117 "Chris Mungall"

transformation of http://purl.obolibrary.org/obo/RO_0002494

Added

• transformation of IAO_0000117 "Chris Mungall"

tributary_of http://purl.obolibrary.org/obo/RO_0002376

Added

• tributary_of in_subset ro-eco

• tributary_of curator notes "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)"^^anyURI

• tributary_of see also "http://en.wikipedia.org/wiki/Tributary"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• tributary_of IAO_0000114 IAO_0000428

• tributary_of IAO_0000118 "tributary channel of"

• tributary_of IAO_0000117 "Chris Mungall"

• tributary_of IAO_0000118 "drains into"

• tributary_of see also drainsTo

• tributary_of example of usage "inferior epigastric vein tributary_of external iliac vein"

• tributary_of IAO_0000119 "http://en.wikipedia.org/wiki/Tributary"

• tributary_of IAO_0000118 "drains to"

• tributary_of example of usage "Deschutes River tributary_of Columbia River"

• tributary_of IAO_0000119 "http://www.medindia.net/glossary/venous_tributary.htm"

[github-actions]

Here's a diff of your edit file (unreasoned)

Ontology comparison

Left

• Ontology IRI: http://purl.obolibrary.org/obo/uberon/core.owl
• Version IRI: None
• Loaded from: file:/work/src/ontology/../../master/src/ontology/uberon-edit.obo

Right

• Ontology IRI: http://purl.obolibrary.org/obo/uberon/core.owl
• Version IRI: None
• Loaded from: file:/work/src/ontology/uberon-edit.obo

Ontology imports

Added

• caro_import.owl

Ontology annotations

[shawntanzk]

Unsat related to #2589
Fix - change innervate to 'extends_fibers_into'

[github-actions]

Here's a diff of how these changes impact the classified ontology (on -simple file):

Ontology comparison

Left

• Ontology IRI: http://purl.obolibrary.org/obo/uberon/uberon-simple.owl
• Version IRI: http://purl.obolibrary.org/obo/uberon/releases/2022-08-18/uberon-simple.owl
• Loaded from: file:/work/src/ontology/../../master/src/ontology/uberon-simple.owl

Right

• Ontology IRI: http://purl.obolibrary.org/obo/uberon/uberon-simple.owl
• Version IRI: http://purl.obolibrary.org/obo/uberon/releases/2022-08-18/uberon-simple.owl
• Loaded from: file:/work/src/ontology/uberon-simple.owl

Ontology imports

Ontology annotations

IAO_0000589 http://purl.obolibrary.org/obo/IAO_0000589

Added

• AnnotationProperty: IAO_0000589

RO_0002575 http://purl.obolibrary.org/obo/RO_0002575

Added

• AnnotationProperty: RO_0002575

adjacent_to http://purl.obolibrary.org/obo/RO_0002220

Added

• adjacent_to example of usage "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies."

• adjacent_to IAO_0000117 "Chris Mungall"

• adjacent_to IAO_0000114 IAO_0000125

• adjacent_to example of usage "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."

• adjacent_to in_subset valid_for_go_annotation_extension

• adjacent_to has_obo_namespace "external"

• adjacent_to in_subset valid_for_gocam

• adjacent_to in_subset valid_for_go_ontology

• adjacent_to RO_0001900 RO_0001901

• adjacent_to editor note "This relation acts as a join point with BSPO"

• adjacent_to example of usage "The epidermis layer of a vertebrate is adjacent to the dermis."

• adjacent_to example of usage "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."

  • see also issuecomment-218584934

attached to http://purl.obolibrary.org/obo/RO_0002371

Added

• attached to IAO_0000117 "Chris Mungall"

• attached to in_subset ro-eco

• attached to IAO_0000589 "attached to (anatomical structure to anatomical structure)"

attached to part of http://purl.obolibrary.org/obo/RO_0002177

Added

• attached to part of IAO_0000589 "attached to part of (anatomical structure to anatomical structure)"

bounding layer of http://purl.obolibrary.org/obo/RO_0002007

Added

• bounding layer of in_subset ro-eco

• bounding layer of has_obo_namespace "external"

• bounding layer of IAO_0000117 "David Osumi-Sutherland"

• bounding layer of 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."

branching part of http://purl.obolibrary.org/obo/RO_0002380

Added

• branching part of example of usage "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S"

• branching part of see also 2212

• branching part of see also "FMA:85994"

• branching part of IAO_0000117 "Chris Mungall"

• branching part of in_subset ro-eco

capable of part of http://purl.obolibrary.org/obo/RO_0002216

Added

• capable of part of see also http://purl.obolibrary.org/obo/ro/docs/reflexivity/

• capable of part of has_obo_namespace "external"

citesAsAuthority http://purl.org/spar/cito/citesAsAuthority

Added

• AnnotationProperty: citesAsAuthority

composed primarily of http://purl.obolibrary.org/obo/RO_0002473

Added

• composed primarily of in_subset ro-eco

• composed primarily of example of usage "'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'"

• composed primarily of IAO_0000119 22293552

• composed primarily of IAO_0000117 "Chris Mungall"

• composed primarily of RO_0001900 RO_0001901

confers advantage in http://purl.obolibrary.org/obo/RO_0002322

Added

• confers advantage in IAO_0000118 "adapted for"

• confers advantage in IAO_0000117 "Chris Mungall"

• confers advantage in editor note "An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial."

• confers advantage in in_subset ro-eco

connected to http://purl.obolibrary.org/obo/RO_0002170

Added

• connected to definition "Binary relationship: x connected_to y if and only if there exists some z such that z connects x and y in a ternary connected_to(x,y,z) relationship."

  • database_cross_reference "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern"

• connected to see also "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• connected to IAO_0000119 22293552

• connected to see also "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• connected to example of usage "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint connects these two bones)."

connects http://purl.obolibrary.org/obo/RO_0002176

Added

• connects see also "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• connects see also "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• connects example of usage "The M8 connects Glasgow and Edinburgh"

• connects IAO_0000119 22293552

• connects example of usage "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint connects these two bones)."

contains http://purl.obolibrary.org/obo/RO_0001019

Added

• contains IAO_0000111 "contains"@en

• contains RO_0001900 RO_0001901

• contains in_subset ro-eco

continuous_with http://purl.obolibrary.org/obo/RO_0002150

Added

• continuous_with RO_0001900 RO_0001901

• continuous_with IAO_0000114 IAO_0000125

• continuous_with IAO_0000117 "David Osumi-Sutherland"

• continuous_with IAO_0000118 "connected to"

• continuous_with curator notes "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)"

• continuous_with see also "FMA:85972"

contributes to morphology of http://purl.obolibrary.org/obo/RO_0002433

Added

• contributes to morphology of IAO_0000117 "Chris Mungall"

developmentally_induced_by http://purl.obolibrary.org/obo/RO_0002256

Added

• developmentally_induced_by IAO_0000119 " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)"

• developmentally_induced_by IAO_0000118 "induced by"

• developmentally_induced_by IAO_0000119 "GO:0001759"

• developmentally_induced_by IAO_0000119 20064205

• developmentally_induced_by curator notes "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]"

• developmentally_induced_by IAO_0000117 "Chris Mungall"

• developmentally_induced_by IAO_0000117 "David Osumi-Sutherland"

• developmentally_induced_by IAO_0000114 IAO_0000125

• developmentally_induced_by IAO_0000117 "Melissa Haendel"

developmentally_replaces http://purl.obolibrary.org/obo/RO_0002285

Added

• developmentally_replaces IAO_0000114 IAO_0000125

• developmentally_replaces editor note "This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage"

• developmentally_replaces IAO_0000118 "replaces"

• developmentally_replaces IAO_0000117 "Chris Mungall"

develops from part of http://purl.obolibrary.org/obo/RO_0002225

Added

• develops from part of IAO_0000114 IAO_0000125

• develops from part of IAO_0000117 "Chris Mungall"

develops in http://purl.obolibrary.org/obo/RO_0002226

Added

• develops in IAO_0000119 "Jonathan Bard, EHDAA2"

• develops in IAO_0000117 "Chris Mungall"

• develops in IAO_0000119 "EHDAA2"

• develops in IAO_0000114 IAO_0000125

directly develops from http://purl.obolibrary.org/obo/RO_0002207

Added

• directly develops from IAO_0000117 "Chris Mungall"

• directly develops from IAO_0000117 "David Osumi-Sutherland"

• directly develops from comment "TODO - add child relations from DOS"

• directly develops from IAO_0000119 "FBbt"

• directly develops from RO_0002575 develops from

• directly develops from IAO_0000114 IAO_0000125

• directly develops from IAO_0000117 "has developmental precursor"

drains http://purl.obolibrary.org/obo/RO_0002179

Added

• drains editor note "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure"

• drains IAO_0000119 20064205

ends http://purl.obolibrary.org/obo/RO_0002229

Added

• ends IAO_0000114 IAO_0000125

• ends in_subset ro-eco

• ends IAO_0000117 "Chris Mungall"

ends with http://purl.obolibrary.org/obo/RO_0002230

Added

• ends with has_obo_namespace "external"

• ends with in_subset ro-eco

• ends with IAO_0000118 "finished by"

• ends with IAO_0000114 IAO_0000125

• ends with IAO_0000117 "Chris Mungall"

existence ends during http://purl.obolibrary.org/obo/RO_0002492

Added

• existence ends during IAO_0000117 "Chris Mungall"

• existence ends during comment "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription."

existence ends during or before http://purl.obolibrary.org/obo/RO_0002497

Added

• existence ends during or before IAO_0000117 "Chris Mungall"

• existence ends during or before comment "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription."

existence ends with http://purl.obolibrary.org/obo/RO_0002493

Added

• existence ends with IAO_0000117 "Chris Mungall"

• existence ends with comment "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription."

existence starts and ends during http://purl.obolibrary.org/obo/RO_0002491

Added

• existence starts and ends during IAO_0000117 "Chris Mungall"

• existence starts and ends during comment "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription."

• existence starts and ends during has_exact_synonym "exists during"

existence starts during http://purl.obolibrary.org/obo/RO_0002488

Added

• existence starts during IAO_0000117 "Chris Mungall"

existence starts during or after http://purl.obolibrary.org/obo/RO_0002496

Added

• existence starts during or after comment "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription."

• existence starts during or after IAO_0000117 "Chris Mungall"

existence starts with http://purl.obolibrary.org/obo/RO_0002489

Added

• existence starts with IAO_0000117 "Chris Mungall"

has 2D boundary http://purl.obolibrary.org/obo/RO_0002002

Added

• has 2D boundary IAO_0000118 "has_2D_boundary"@en

• has 2D boundary example of usage "my body has 2D boundary the surface of my skin"@en

• has 2D boundary IAO_0000117 "David Osumi-Sutherland"

• has 2D boundary editor note "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape."@en

• has 2D boundary IAO_0000118 "has boundary"@en

• has 2D boundary label "has_boundary"@en

• has 2D boundary editor note "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts."@en

• has 2D boundary RO_0001900 RO_0001901

has branching part http://purl.obolibrary.org/obo/RO_0002569

Added

• has branching part IAO_0000117 "Chris Mungall"

• has branching part in_subset ro-eco

• has branching part in_subset RO_0002259

has component http://purl.obolibrary.org/obo/RO_0002180

Added

• has component has_obo_namespace "external"

has member http://purl.obolibrary.org/obo/RO_0002351

Added

• has member RO_0001900 RO_0001901

• has member IAO_0000119 "SIO"

has muscle antagonist http://purl.obolibrary.org/obo/RO_0002568

Added

• has muscle antagonist IAO_0000119 "Wikipedia:Antagonist_(muscle)"

• has muscle antagonist IAO_0000117 "Chris Mungall"

has muscle insertion http://purl.obolibrary.org/obo/RO_0002373

Added

• has muscle insertion see also insertion

• has muscle insertion IAO_0000119 "Wikipedia:Insertion_(anatomy)"@en

• has muscle insertion IAO_0000117 "Chris Mungall"

has muscle origin http://purl.obolibrary.org/obo/RO_0002372

Added

• has muscle origin IAO_0000117 "Chris Mungall"

• has muscle origin IAO_0000119 "Wikipedia:Insertion_(anatomy)"@en

• has muscle origin see also origin

has skeleton http://purl.obolibrary.org/obo/RO_0002551

Added

• has skeleton curator notes "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)."

• has skeleton IAO_0000117 "Chris Mungall"

• has skeleton IAO_0000118 "has supporting framework"

• has skeleton example of usage "Forelimb SubClassOf has_skeleton some 'Forelimb skeleton'"

has_part http://purl.obolibrary.org/obo/BFO_0000051

Added

• has_part editor note "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/"@en

immediate transformation of http://purl.obolibrary.org/obo/RO_0002495

Added

• immediate transformation of RO_0002575 transformation of

• immediate transformation of IAO_0000117 "Chris Mungall"

immediately preceded by http://purl.obolibrary.org/obo/RO_0002087

Added

• immediately preceded by definition "X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)."

• immediately preceded by external_definition "A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251]."

  • source "SIO:000251"

• immediately preceded by has_obo_namespace "external"

in taxon http://purl.obolibrary.org/obo/RO_0002162

Added

• in taxon comment "Connects a biological entity to its taxon of origin."

• in taxon IAO_0000119 20973947

• in taxon IAO_0000119 17921072

• in taxon IAO_0000114 IAO_0000125

• in taxon IAO_0000117 "Chris Mungall"@en

• in taxon in_subset ro-eco

• in taxon IAO_0000117 "Jennifer Deegan"

• in taxon see also Taxon-constraints

innervated_by http://purl.obolibrary.org/obo/RO_0002005

Added

• innervated_by see also dbprop_nerve

• innervated_by comment "http://code.google.com/p/obo-relations/issues/detail?id=6"

• innervated_by IAO_0000117 "David Osumi-Sutherland"

• innervated_by has_exact_synonym "nerve supply"

  • database_cross_reference "FMA:85999"

• innervated_by see also FMA_85999

• innervated_by citesAsAuthority "http://www.ncbi.nlm.nih.gov/pubmed/22402613"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

innervates http://purl.obolibrary.org/obo/RO_0002134

Added

• innervates IAO_0000114 IAO_0000125

• innervates has_obo_namespace "fly_anatomy.ontology"

• innervates definition "Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input. T innervates some R Expands_to: T has_fasciculating_neuron_projection that synapse_in some R."

  • database_cross_reference "FBC:DOS"

• innervates IAO_0000424 "RO_0002132 some (GO_0043005 that (RO_0002131 some (GO_0045202 that BFO_0000050 some ?Y)))"

• innervates IAO_0000117 "David Osumi-Sutherland"@en

• innervates IAO_0000424 "<http://purl.obolibrary.org/obo/RO_0002132> some (<http://purl.obolibrary.org/obo/GO_0043005> that (<http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?)))"

• innervates citesAsAuthority 22402613

• innervates RO_0001900 RO_0001901

• innervates comment "http://code.google.com/p/obo-relations/issues/detail?id=6"

located in http://purl.obolibrary.org/obo/RO_0001025

Added

• located in editor note "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"@en

• located in example of usage "my brain is located in my head"@en

• located in editor note "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/"@en

• located in RO_0001900 RO_0001901

• located in in_subset valid_for_go_gp2term

• located in IAO_0000118 "located_in"@en

• located in IAO_0000111 "located in"@en

• located in example of usage "this rat is located in this cage"@en

• located in derived from resource "http://www.obofoundry.org/ro/#OBO_REL:located_in"

location of http://purl.obolibrary.org/obo/RO_0001015

Added

• location of example of usage "this cage is the location of this rat"@en

• location of IAO_0000111 "is location of"@en

• location of example of usage "my head is the location of my brain"@en

• location of IAO_0000118 "location_of"@en

• location of editor note "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/"@en

• location of RO_0001900 RO_0001901

lumen of http://purl.obolibrary.org/obo/RO_0002571

Added

• lumen of in_subset ro-eco

• lumen of IAO_0000119 "GOC:cjm"

• lumen of IAO_0000117 "Chris Mungall"

luminal space of http://purl.obolibrary.org/obo/RO_0002572

Added

• luminal space of in_subset ro-eco

• luminal space of IAO_0000117 "Chris Mungall"

only_in_taxon http://purl.obolibrary.org/obo/RO_0002160

Added

• only_in_taxon IAO_0000117 "Chris Mungall"@en

• only_in_taxon IAO_0000119 20973947

• only_in_taxon editor note "The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g.

'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria"

• only_in_taxon example of usage "lactation SubClassOf 'only in taxon' some 'Mammalia'"

• only_in_taxon IAO_0000119 17921072

• only_in_taxon see also Taxon-constraints

• only_in_taxon IAO_0000114 IAO_0000125

otic ganglion http://purl.obolibrary.org/obo/UBERON_0003963

Removed

• otic ganglion SubClassOf innervates some parotid gland

Added

• otic ganglion SubClassOf extends_fibers_into some parotid gland

output of http://purl.obolibrary.org/obo/RO_0002353

Added

• output of IAO_0000117 "Chris Mungall"

• output of in_subset RO_0002259

• output of has_obo_namespace "external"

• output of in_subset ro-eco

overlaps http://purl.obolibrary.org/obo/RO_0002131

Added

• overlaps IAO_0000424 "BFO_0000051 some (BFO_0000050 some ?Y)"

• overlaps has_obo_namespace "external"

part_of http://purl.obolibrary.org/obo/BFO_0000050

Added

• part_of editor note "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/"@en

participates in http://purl.obolibrary.org/obo/RO_0000056

Added

• participates in has_obo_namespace "external"

preceded_by http://purl.obolibrary.org/obo/BFO_0000062

Added

• preceded_by definition "X preceded_by Y iff: end(Y) before_or_simultaneous_with start(X)."

• preceded_by has_obo_namespace "external"

precedes http://purl.obolibrary.org/obo/BFO_0000063

Added

• precedes has_obo_namespace "external"

present_in_taxon http://purl.obolibrary.org/obo/RO_0002175

Added

• present_in_taxon comment "The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology."

produced_by http://purl.obolibrary.org/obo/RO_0003001

Added

• produced_by in_subset ro-eco

• produced_by IAO_0000117 "Melissa Haendel"

• produced_by has_obo_namespace "external"

• produced_by IAO_0000114 IAO_0000125

produces http://purl.obolibrary.org/obo/RO_0003000

Added

• produces IAO_0000114 IAO_0000125

• produces 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."

• produces has_obo_namespace "external"

• produces in_subset ro-eco

• produces IAO_0000117 "Melissa Haendel"

simultaneous with http://purl.obolibrary.org/obo/RO_0002082

Added

• simultaneous with IAO_0000117 "David Osumi-Sutherland"

• simultaneous with in_subset ro-eco

• simultaneous with comment "t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2)"@en

skeleton of http://purl.obolibrary.org/obo/RO_0002576

Added

• skeleton of IAO_0000117 "Chris Mungall"

• skeleton of in_subset RO_0002259

starts http://purl.obolibrary.org/obo/RO_0002223

Added

• starts IAO_0000117 "Chris Mungall"

• starts IAO_0000119 "Allen"

• starts in_subset ro-eco

• starts IAO_0000114 IAO_0000125

starts with http://purl.obolibrary.org/obo/RO_0002224

Added

• starts with has_obo_namespace "external"

• starts with IAO_0000114 IAO_0000125

• starts with example of usage "Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor"

• starts with IAO_0000118 "started by"

• starts with in_subset ro-eco

• starts with IAO_0000117 "Chris Mungall"

supplies http://purl.obolibrary.org/obo/RO_0002178

Added

• supplies editor note "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"

• supplies IAO_0000119 20064205

surrounded by http://purl.obolibrary.org/obo/RO_0002219

Added

• surrounded by RO_0001900 RO_0001901

• surrounded by IAO_0000117 "Chris Mungall"

• surrounded by IAO_0000114 IAO_0000125

surrounds http://purl.obolibrary.org/obo/RO_0002221

Added

• surrounds RO_0001900 RO_0001901

• surrounds in_subset RO_0002259

• surrounds IAO_0000114 IAO_0000125

• surrounds IAO_0000117 "Chris Mungall"

transformation of http://purl.obolibrary.org/obo/RO_0002494

Added

• transformation of IAO_0000117 "Chris Mungall"

tributary_of http://purl.obolibrary.org/obo/RO_0002376

Added

• tributary_of in_subset ro-eco

• tributary_of curator notes "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)"^^anyURI

• tributary_of see also "http://en.wikipedia.org/wiki/Tributary"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• tributary_of IAO_0000114 IAO_0000428

• tributary_of IAO_0000118 "tributary channel of"

• tributary_of IAO_0000117 "Chris Mungall"

• tributary_of IAO_0000118 "drains into"

• tributary_of see also drainsTo

• tributary_of example of usage "inferior epigastric vein tributary_of external iliac vein"

• tributary_of IAO_0000119 "http://en.wikipedia.org/wiki/Tributary"

• tributary_of IAO_0000118 "drains to"

• tributary_of example of usage "Deschutes River tributary_of Columbia River"

• tributary_of IAO_0000119 "http://www.medindia.net/glossary/venous_tributary.htm"

[github-actions]

Here's a diff of your edit file (unreasoned)

Ontology comparison

Left

• Ontology IRI: http://purl.obolibrary.org/obo/uberon/core.owl
• Version IRI: None
• Loaded from: file:/work/src/ontology/../../master/src/ontology/uberon-edit.obo

Right

• Ontology IRI: http://purl.obolibrary.org/obo/uberon/core.owl
• Version IRI: None
• Loaded from: file:/work/src/ontology/uberon-edit.obo

Ontology imports

Added

• caro_import.owl

Ontology annotations

otic ganglion http://purl.obolibrary.org/obo/UBERON_0003963

Removed

• otic ganglion EquivalentTo cranial ganglion and (innervates some parotid gland) and (extends_fibers_into some glossopharyngeal nerve)

Added

• otic ganglion EquivalentTo cranial ganglion and (extends_fibers_into some glossopharyngeal nerve) and (extends_fibers_into some parotid gland)

[matentzn]

https://github.com/obophenotype/ncbitaxon/releases/tag/v2022-08-18

[shawntanzk]

More unsat funtimes :')

From:

% robot --catalog catalog-v001.xml explain -i tmp/uberon-edit-plus-tax-equivs.owl -M unsatisfiability --unsatisfiable random:10 --explanation unsat.md

AAO_0010670 SubClassOf Nothing

• AAO_0010670 EquivalentTo maxillary nerve and (part_of some Amphibia)
  • maxillary nerve SubClassOf branching part of some trigeminal nerve
    • trigeminal nerve EquivalentTo cranial nerve and (innervates some mouth) and (innervates some jaw muscle) and (innervates some skin of face) and (extends_fibers_into some trigeminal nucleus)
      • trigeminal nucleus EquivalentTo nucleus of brain and (part_of some trigeminal nuclear complex)
        • trigeminal nuclear complex SubClassOf overlaps some pontine tegmentum
          • pontine tegmentum SubClassOf has_part some locus ceruleus
            • locus ceruleus SubClassOf nucleus of brain
              • nucleus of brain EquivalentTo neural nucleus and (part_of some brain)
                • neural nucleus SubClassOf central nervous system cell part cluster
                  • central nervous system cell part cluster EquivalentTo multi cell part structure and (part_of some central nervous system)
                  • multi-cell-part structure EquivalentTo multi cell part structure
            • locus ceruleus SubClassOf noradrenergic cell groups
              • noradrenergic cell groups SubClassOf regional part of brain
                • regional part of brain EquivalentTo multi-tissue structure and (part_of some brain)
                  • multi-tissue structure SubClassOf multicellular anatomical structure
                  • multicellular anatomical structure EquivalentTo multicellular anatomical structure
• multi-cell-part structure DisjointWith multicellular anatomical structure

AAO_0010470 SubClassOf Nothing

• AAO_0010470 EquivalentTo trigeminal nerve and (part_of some Amphibia)
  • trigeminal nerve EquivalentTo cranial nerve and (innervates some mouth) and (innervates some jaw muscle) and (innervates some skin of face) and (extends_fibers_into some trigeminal nucleus)
    • trigeminal nucleus EquivalentTo nucleus of brain and (part_of some trigeminal nuclear complex)
      • trigeminal nuclear complex SubClassOf overlaps some pontine tegmentum
        • pontine tegmentum SubClassOf has_part some locus ceruleus
          • locus ceruleus SubClassOf nucleus of brain
            • nucleus of brain SubClassOf neural nucleus
              • neural nucleus SubClassOf central nervous system cell part cluster
                • central nervous system cell part cluster EquivalentTo multi cell part structure and (part_of some central nervous system)
                  • multi-cell-part structure EquivalentTo multi cell part structure
          • locus ceruleus SubClassOf noradrenergic cell groups
            • noradrenergic cell groups SubClassOf regional part of brain
              • regional part of brain EquivalentTo multi-tissue structure and (part_of some brain)
                • multi-tissue structure SubClassOf multicellular anatomical structure
                  • multicellular anatomical structure EquivalentTo multicellular anatomical structure
• multi-cell-part structure DisjointWith multicellular anatomical structure

AAO_0010730 SubClassOf Nothing

• AAO_0010730 EquivalentTo pterygoid muscle and (part_of some Amphibia)
  • pterygoid muscle SubClassOf masticatory muscle
    • masticatory muscle SubClassOf innervated_by some mandibular nerve
      • mandibular nerve SubClassOf branching part of some trigeminal nerve
        • trigeminal nerve EquivalentTo cranial nerve and (innervates some mouth) and (innervates some jaw muscle) and (innervates some skin of face) and (extends_fibers_into some trigeminal nucleus)
          • trigeminal nucleus EquivalentTo nucleus of brain and (part_of some trigeminal nuclear complex)
            • trigeminal nuclear complex SubClassOf overlaps some pontine tegmentum
              • pontine tegmentum SubClassOf has_part some locus ceruleus
                • locus ceruleus SubClassOf nucleus of brain
                  • nucleus of brain EquivalentTo neural nucleus and (part_of some brain)
                  • neural nucleus SubClassOf central nervous system cell part cluster
                  • central nervous system cell part cluster EquivalentTo multi cell part structure and (part_of some central nervous system)
                  • multi-cell-part structure EquivalentTo multi cell part structure
                • locus ceruleus SubClassOf noradrenergic cell groups
                  • noradrenergic cell groups SubClassOf regional part of brain
                  • regional part of brain EquivalentTo multi-tissue structure and (part_of some brain)
                  • multi-tissue structure SubClassOf multicellular anatomical structure
                  • multicellular anatomical structure EquivalentTo multicellular anatomical structure
• multi-cell-part structure DisjointWith multicellular anatomical structure

AAO_0010688 SubClassOf Nothing

• AAO_0010688 EquivalentTo mandibular nerve and (part_of some Amphibia)
  • mandibular nerve SubClassOf branching part of some trigeminal nerve
    • trigeminal nerve EquivalentTo cranial nerve and (innervates some mouth) and (innervates some jaw muscle) and (innervates some skin of face) and (extends_fibers_into some trigeminal nucleus)
      • trigeminal nucleus EquivalentTo nucleus of brain and (part_of some trigeminal nuclear complex)
        • trigeminal nuclear complex SubClassOf overlaps some pontine tegmentum
          • pontine tegmentum SubClassOf has_part some locus ceruleus
            • locus ceruleus SubClassOf nucleus of brain
              • nucleus of brain EquivalentTo neural nucleus and (part_of some brain)
                • neural nucleus SubClassOf central nervous system cell part cluster
                  • central nervous system cell part cluster EquivalentTo multi cell part structure and (part_of some central nervous system)
                  • multi-cell-part structure EquivalentTo multi cell part structure
            • locus ceruleus SubClassOf noradrenergic cell groups
              • noradrenergic cell groups SubClassOf regional part of brain
                • regional part of brain EquivalentTo multi-tissue structure and (part_of some brain)
                  • multi-tissue structure SubClassOf multicellular anatomical structure
                  • multicellular anatomical structure EquivalentTo multicellular anatomical structure
• multi-cell-part structure DisjointWith multicellular anatomical structure

AAO_0010648 SubClassOf Nothing

• AAO_0010648 EquivalentTo ophthalmic nerve and (part_of some Amphibia)
  • ophthalmic nerve SubClassOf branching part of some trigeminal nerve
    • trigeminal nerve EquivalentTo cranial nerve and (innervates some mouth) and (innervates some jaw muscle) and (innervates some skin of face) and (extends_fibers_into some trigeminal nucleus)
      • trigeminal nucleus EquivalentTo nucleus of brain and (part_of some trigeminal nuclear complex)
        • trigeminal nuclear complex SubClassOf overlaps some pontine tegmentum
          • pontine tegmentum SubClassOf has_part some locus ceruleus
            • locus ceruleus SubClassOf nucleus of brain
              • nucleus of brain EquivalentTo neural nucleus and (part_of some brain)
                • neural nucleus SubClassOf central nervous system cell part cluster
                  • central nervous system cell part cluster EquivalentTo multi cell part structure and (part_of some central nervous system)
                  • multi-cell-part structure EquivalentTo multi cell part structure
            • locus ceruleus SubClassOf noradrenergic cell groups
              • noradrenergic cell groups SubClassOf regional part of brain
                • regional part of brain EquivalentTo multi-tissue structure and (part_of some brain)
                  • multi-tissue structure SubClassOf multicellular anatomical structure
                  • multicellular anatomical structure EquivalentTo multicellular anatomical structure
• multi-cell-part structure DisjointWith multicellular anatomical structure

AAO_0010632 SubClassOf Nothing

• AAO_0010632 EquivalentTo inferior branch of oculomotor nerve and (part_of some Amphibia)
  • inferior branch of oculomotor nerve EquivalentTo nerve and (supplies some inferior rectus extraocular muscle) and (branching part of some oculomotor nerve)
    • supplies Domain artery
      • artery SubClassOf blood vessel
        • blood vessel SubClassOf channel for some blood
          • channel for Domain anatomical conduit
            • anatomical conduit SubClassOf multicellular anatomical structure
              • multicellular anatomical structure EquivalentTo multicellular anatomical structure
    • nerve SubClassOf neuron projection bundle
      • neuron projection bundle SubClassOf multi cell part structure
        • multi-cell-part structure EquivalentTo multi cell part structure
• multi-cell-part structure DisjointWith multicellular anatomical structure

AAO_0000194 SubClassOf Nothing

• AAO_0000194 EquivalentTo foramen rotundum and (part_of some Amphibia)
  • foramen rotundum EquivalentTo foramen of skull and (part_of some sphenoid bone) and (conduit for some maxillary nerve)
    • maxillary nerve SubClassOf branching part of some trigeminal nerve
      • trigeminal nerve EquivalentTo cranial nerve and (innervates some mouth) and (innervates some jaw muscle) and (innervates some skin of face) and (extends_fibers_into some trigeminal nucleus)
        • trigeminal nucleus EquivalentTo nucleus of brain and (part_of some trigeminal nuclear complex)
          • trigeminal nuclear complex SubClassOf overlaps some pontine tegmentum
            • pontine tegmentum SubClassOf has_part some locus ceruleus
              • locus ceruleus SubClassOf nucleus of brain
                • nucleus of brain EquivalentTo neural nucleus and (part_of some brain)
                  • neural nucleus SubClassOf central nervous system cell part cluster
                  • central nervous system cell part cluster EquivalentTo multi cell part structure and (part_of some central nervous system)
                  • multi-cell-part structure EquivalentTo multi cell part structure
              • locus ceruleus SubClassOf noradrenergic cell groups
                • noradrenergic cell groups SubClassOf regional part of brain
                  • regional part of brain EquivalentTo multi-tissue structure and (part_of some brain)
                  • multi-tissue structure SubClassOf multicellular anatomical structure
                  • multicellular anatomical structure EquivalentTo multicellular anatomical structure
• multi-cell-part structure DisjointWith multicellular anatomical structure

AAO_0000298 SubClassOf Nothing

• AAO_0000298 EquivalentTo mental foramen and (part_of some Amphibia)
  • mental foramen EquivalentTo foramen of skull and (conduit for some mental nerve)
    • mental nerve SubClassOf branching part of some inferior alveolar nerve
      • inferior alveolar nerve SubClassOf branching part of some lingual nerve
        • lingual nerve SubClassOf branching part of some mandibular nerve
          • mandibular nerve SubClassOf branching part of some trigeminal nerve
            • trigeminal nerve EquivalentTo cranial nerve and (innervates some mouth) and (innervates some jaw muscle) and (innervates some skin of face) and (extends_fibers_into some trigeminal nucleus)
              • trigeminal nucleus EquivalentTo nucleus of brain and (part_of some trigeminal nuclear complex)
                • trigeminal nuclear complex SubClassOf overlaps some pontine tegmentum
                  • pontine tegmentum SubClassOf has_part some locus ceruleus
                  • locus ceruleus SubClassOf nucleus of brain
                  • nucleus of brain EquivalentTo neural nucleus and (part_of some brain)
                  • neural nucleus SubClassOf central nervous system cell part cluster
                  • central nervous system cell part cluster EquivalentTo multi cell part structure and (part_of some central nervous system)
                  • multi-cell-part structure EquivalentTo multi cell part structure
                  • locus ceruleus SubClassOf noradrenergic cell groups
                  • noradrenergic cell groups SubClassOf regional part of brain
                  • regional part of brain SubClassOf regional part of nervous system
                  • regional part of nervous system SubClassOf multi-tissue structure
                  • multi-tissue structure SubClassOf multicellular anatomical structure
                  • multicellular anatomical structure EquivalentTo multicellular anatomical structure
• multi-cell-part structure DisjointWith multicellular anatomical structure

AAO_0010628 SubClassOf Nothing

• AAO_0010628 EquivalentTo superior branch of oculomotor nerve and (part_of some Amphibia)
  • superior branch of oculomotor nerve EquivalentTo nerve and (supplies some superior rectus extraocular muscle) and (branching part of some oculomotor nerve)
    • supplies Domain artery
      • artery SubClassOf blood vessel
        • blood vessel SubClassOf channel for some blood
          • channel for Domain anatomical conduit
            • anatomical conduit EquivalentTo multicellular anatomical structure and (has_part some anatomical conduit space) and (conduit for some anatomical structure)
              • multicellular anatomical structure EquivalentTo multicellular anatomical structure
    • nerve SubClassOf neuron projection bundle
      • neuron projection bundle SubClassOf multi cell part structure
        • multi-cell-part structure EquivalentTo multi cell part structure
• multi-cell-part structure DisjointWith multicellular anatomical structure

AAO_0010703 SubClassOf Nothing

• AAO_0010703 EquivalentTo mandibular nerve and (part_of some Amphibia)
  • mandibular nerve SubClassOf branching part of some trigeminal nerve
    • trigeminal nerve EquivalentTo cranial nerve and (innervates some mouth) and (innervates some jaw muscle) and (innervates some skin of face) and (extends_fibers_into some trigeminal nucleus)
      • trigeminal nucleus EquivalentTo nucleus of brain and (part_of some trigeminal nuclear complex)
        • trigeminal nuclear complex SubClassOf overlaps some pontine tegmentum
          • pontine tegmentum SubClassOf has_part some locus ceruleus
            • locus ceruleus SubClassOf nucleus of brain
              • nucleus of brain EquivalentTo neural nucleus and (part_of some brain)
                • neural nucleus SubClassOf central nervous system cell part cluster
                  • central nervous system cell part cluster EquivalentTo multi cell part structure and (part_of some central nervous system)
                  • multi-cell-part structure EquivalentTo multi cell part structure
            • locus ceruleus SubClassOf noradrenergic cell groups
              • noradrenergic cell groups SubClassOf regional part of brain
                • regional part of brain EquivalentTo multi-tissue structure and (part_of some brain)
                  • multi-tissue structure SubClassOf multicellular anatomical structure
                  • multicellular anatomical structure EquivalentTo multicellular anatomical structure
• multi-cell-part structure DisjointWith multicellular anatomical structure

Axiom Impact

Axioms used 10 times

• multi-cell-part structure EquivalentTo multi cell part structure [core.owl]
• multicellular anatomical structure EquivalentTo multicellular anatomical structure [core.owl]
• multi-cell-part structure DisjointWith multicellular anatomical structure [core.owl]

Axioms used 8 times

• trigeminal nerve EquivalentTo cranial nerve and (innervates some mouth) and (innervates some jaw muscle) and (innervates some skin of face) and (extends_fibers_into some trigeminal nucleus) [core.owl]
• trigeminal nucleus EquivalentTo nucleus of brain and (part_of some trigeminal nuclear complex) [core.owl]
• central nervous system cell part cluster EquivalentTo multi cell part structure and (part_of some central nervous system) [core.owl]
• neural nucleus SubClassOf central nervous system cell part cluster [core.owl]
• multi-tissue structure SubClassOf multicellular anatomical structure [core.owl]
• locus ceruleus SubClassOf nucleus of brain [core.owl]
• locus ceruleus SubClassOf noradrenergic cell groups [core.owl]
• pontine tegmentum SubClassOf has_part some locus ceruleus [core.owl]
• trigeminal nuclear complex SubClassOf overlaps some pontine tegmentum [core.owl]
• noradrenergic cell groups SubClassOf regional part of brain [core.owl]

Axioms used 7 times

• nucleus of brain EquivalentTo neural nucleus and (part_of some brain) [core.owl]
• regional part of brain EquivalentTo multi-tissue structure and (part_of some brain) [core.owl]

Axioms used 4 times

• mandibular nerve SubClassOf branching part of some trigeminal nerve [core.owl]

Axioms used 2 times

• neuron projection bundle SubClassOf multi cell part structure [core.owl]
• maxillary nerve SubClassOf branching part of some trigeminal nerve [core.owl]
• nerve SubClassOf neuron projection bundle [core.owl]
• artery SubClassOf blood vessel [core.owl]
• blood vessel SubClassOf channel for some blood [core.owl]
• supplies Domain artery [core.owl]
• channel for Domain anatomical conduit [core.owl]

Axioms used 1 times

• AAO_0000194 EquivalentTo foramen rotundum and (part_of some Amphibia) [core.owl]
• AAO_0000298 EquivalentTo mental foramen and (part_of some Amphibia) [core.owl]
• AAO_0010470 EquivalentTo trigeminal nerve and (part_of some Amphibia) [core.owl]
• AAO_0010628 EquivalentTo superior branch of oculomotor nerve and (part_of some Amphibia) [core.owl]
• AAO_0010632 EquivalentTo inferior branch of oculomotor nerve and (part_of some Amphibia) [core.owl]
• AAO_0010648 EquivalentTo ophthalmic nerve and (part_of some Amphibia) [core.owl]
• AAO_0010670 EquivalentTo maxillary nerve and (part_of some Amphibia) [core.owl]
• AAO_0010688 EquivalentTo mandibular nerve and (part_of some Amphibia) [core.owl]
• AAO_0010703 EquivalentTo mandibular nerve and (part_of some Amphibia) [core.owl]
• AAO_0010730 EquivalentTo pterygoid muscle and (part_of some Amphibia) [core.owl]
• anatomical conduit EquivalentTo multicellular anatomical structure and (has_part some anatomical conduit space) and (conduit for some anatomical structure) [core.owl]
• foramen rotundum EquivalentTo foramen of skull and (part_of some sphenoid bone) and (conduit for some maxillary nerve) [core.owl]
• mental foramen EquivalentTo foramen of skull and (conduit for some mental nerve) [core.owl]
• inferior branch of oculomotor nerve EquivalentTo nerve and (supplies some inferior rectus extraocular muscle) and (branching part of some oculomotor nerve) [core.owl]
• superior branch of oculomotor nerve EquivalentTo nerve and (supplies some superior rectus extraocular muscle) and (branching part of some oculomotor nerve) [core.owl]
• regional part of nervous system SubClassOf multi-tissue structure [core.owl]
• ophthalmic nerve SubClassOf branching part of some trigeminal nerve [core.owl]
• nucleus of brain SubClassOf neural nucleus [core.owl]
• regional part of brain SubClassOf regional part of nervous system [core.owl]
• masticatory muscle SubClassOf innervated_by some mandibular nerve [core.owl]
• lingual nerve SubClassOf branching part of some mandibular nerve [core.owl]
• anatomical conduit SubClassOf multicellular anatomical structure [core.owl]
• pterygoid muscle SubClassOf masticatory muscle [core.owl]
• inferior alveolar nerve SubClassOf branching part of some lingual nerve [core.owl]
• mental nerve SubClassOf branching part of some inferior alveolar nerve [core.owl]

Ontologies used:

• core.owl (http://purl.obolibrary.org/obo/uberon/core.owl)

[shawntanzk]

seems like it all leads back to multi-cell-part structure DisjointWith multicellular anatomical structure again

[matentzn]

Can you remove the disjointness axiom and see if that gets the release to run through?

[github-actions]

Here's a diff of how these changes impact the classified ontology (on -simple file):

Ontology comparison

Left

• Ontology IRI: http://purl.obolibrary.org/obo/uberon/uberon-simple.owl
• Version IRI: http://purl.obolibrary.org/obo/uberon/releases/2022-08-18/uberon-simple.owl
• Loaded from: file:/work/src/ontology/../../master/src/ontology/uberon-simple.owl

Right

• Ontology IRI: http://purl.obolibrary.org/obo/uberon/uberon-simple.owl
• Version IRI: http://purl.obolibrary.org/obo/uberon/releases/2022-08-18/uberon-simple.owl
• Loaded from: file:/work/src/ontology/uberon-simple.owl

Ontology imports

Ontology annotations

IAO_0000589 http://purl.obolibrary.org/obo/IAO_0000589

Added

• AnnotationProperty: IAO_0000589

RO_0002575 http://purl.obolibrary.org/obo/RO_0002575

Added

• AnnotationProperty: RO_0002575

adjacent_to http://purl.obolibrary.org/obo/RO_0002220

Added

• adjacent_to example of usage "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies."

• adjacent_to IAO_0000117 "Chris Mungall"

• adjacent_to IAO_0000114 IAO_0000125

• adjacent_to example of usage "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."

• adjacent_to in_subset valid_for_go_annotation_extension

• adjacent_to has_obo_namespace "external"

• adjacent_to in_subset valid_for_gocam

• adjacent_to in_subset valid_for_go_ontology

• adjacent_to RO_0001900 RO_0001901

• adjacent_to editor note "This relation acts as a join point with BSPO"

• adjacent_to example of usage "The epidermis layer of a vertebrate is adjacent to the dermis."

• adjacent_to example of usage "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."

  • see also issuecomment-218584934

attached to http://purl.obolibrary.org/obo/RO_0002371

Added

• attached to IAO_0000117 "Chris Mungall"

• attached to in_subset ro-eco

• attached to IAO_0000589 "attached to (anatomical structure to anatomical structure)"

attached to part of http://purl.obolibrary.org/obo/RO_0002177

Added

• attached to part of IAO_0000589 "attached to part of (anatomical structure to anatomical structure)"

bounding layer of http://purl.obolibrary.org/obo/RO_0002007

Added

• bounding layer of in_subset ro-eco

• bounding layer of has_obo_namespace "external"

• bounding layer of IAO_0000117 "David Osumi-Sutherland"

• bounding layer of 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."

branching part of http://purl.obolibrary.org/obo/RO_0002380

Added

• branching part of example of usage "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S"

• branching part of see also 2212

• branching part of see also "FMA:85994"

• branching part of IAO_0000117 "Chris Mungall"

• branching part of in_subset ro-eco

capable of part of http://purl.obolibrary.org/obo/RO_0002216

Added

• capable of part of see also http://purl.obolibrary.org/obo/ro/docs/reflexivity/

• capable of part of has_obo_namespace "external"

citesAsAuthority http://purl.org/spar/cito/citesAsAuthority

Added

• AnnotationProperty: citesAsAuthority

composed primarily of http://purl.obolibrary.org/obo/RO_0002473

Added

• composed primarily of in_subset ro-eco

• composed primarily of example of usage "'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'"

• composed primarily of IAO_0000119 22293552

• composed primarily of IAO_0000117 "Chris Mungall"

• composed primarily of RO_0001900 RO_0001901

confers advantage in http://purl.obolibrary.org/obo/RO_0002322

Added

• confers advantage in IAO_0000118 "adapted for"

• confers advantage in IAO_0000117 "Chris Mungall"

• confers advantage in editor note "An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial."

• confers advantage in in_subset ro-eco

connected to http://purl.obolibrary.org/obo/RO_0002170

Added

• connected to definition "Binary relationship: x connected_to y if and only if there exists some z such that z connects x and y in a ternary connected_to(x,y,z) relationship."

  • database_cross_reference "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern"

• connected to see also "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• connected to IAO_0000119 22293552

• connected to see also "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• connected to example of usage "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint connects these two bones)."

connects http://purl.obolibrary.org/obo/RO_0002176

Added

• connects see also "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• connects see also "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• connects example of usage "The M8 connects Glasgow and Edinburgh"

• connects IAO_0000119 22293552

• connects example of usage "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint connects these two bones)."

contains http://purl.obolibrary.org/obo/RO_0001019

Added

• contains IAO_0000111 "contains"@en

• contains RO_0001900 RO_0001901

• contains in_subset ro-eco

continuous_with http://purl.obolibrary.org/obo/RO_0002150

Added

• continuous_with RO_0001900 RO_0001901

• continuous_with IAO_0000114 IAO_0000125

• continuous_with IAO_0000117 "David Osumi-Sutherland"

• continuous_with IAO_0000118 "connected to"

• continuous_with curator notes "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)"

• continuous_with see also "FMA:85972"

contributes to morphology of http://purl.obolibrary.org/obo/RO_0002433

Added

• contributes to morphology of IAO_0000117 "Chris Mungall"

developmentally_induced_by http://purl.obolibrary.org/obo/RO_0002256

Added

• developmentally_induced_by IAO_0000119 " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)"

• developmentally_induced_by IAO_0000118 "induced by"

• developmentally_induced_by IAO_0000119 "GO:0001759"

• developmentally_induced_by IAO_0000119 20064205

• developmentally_induced_by curator notes "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]"

• developmentally_induced_by IAO_0000117 "Chris Mungall"

• developmentally_induced_by IAO_0000117 "David Osumi-Sutherland"

• developmentally_induced_by IAO_0000114 IAO_0000125

• developmentally_induced_by IAO_0000117 "Melissa Haendel"

developmentally_replaces http://purl.obolibrary.org/obo/RO_0002285

Added

• developmentally_replaces IAO_0000114 IAO_0000125

• developmentally_replaces editor note "This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage"

• developmentally_replaces IAO_0000118 "replaces"

• developmentally_replaces IAO_0000117 "Chris Mungall"

develops from part of http://purl.obolibrary.org/obo/RO_0002225

Added

• develops from part of IAO_0000114 IAO_0000125

• develops from part of IAO_0000117 "Chris Mungall"

develops in http://purl.obolibrary.org/obo/RO_0002226

Added

• develops in IAO_0000119 "Jonathan Bard, EHDAA2"

• develops in IAO_0000117 "Chris Mungall"

• develops in IAO_0000119 "EHDAA2"

• develops in IAO_0000114 IAO_0000125

directly develops from http://purl.obolibrary.org/obo/RO_0002207

Added

• directly develops from IAO_0000117 "Chris Mungall"

• directly develops from IAO_0000117 "David Osumi-Sutherland"

• directly develops from comment "TODO - add child relations from DOS"

• directly develops from IAO_0000119 "FBbt"

• directly develops from RO_0002575 develops from

• directly develops from IAO_0000114 IAO_0000125

• directly develops from IAO_0000117 "has developmental precursor"

drains http://purl.obolibrary.org/obo/RO_0002179

Added

• drains editor note "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure"

• drains IAO_0000119 20064205

ends http://purl.obolibrary.org/obo/RO_0002229

Added

• ends IAO_0000114 IAO_0000125

• ends in_subset ro-eco

• ends IAO_0000117 "Chris Mungall"

ends with http://purl.obolibrary.org/obo/RO_0002230

Added

• ends with has_obo_namespace "external"

• ends with in_subset ro-eco

• ends with IAO_0000118 "finished by"

• ends with IAO_0000114 IAO_0000125

• ends with IAO_0000117 "Chris Mungall"

existence ends during http://purl.obolibrary.org/obo/RO_0002492

Added

• existence ends during IAO_0000117 "Chris Mungall"

• existence ends during comment "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription."

existence ends during or before http://purl.obolibrary.org/obo/RO_0002497

Added

• existence ends during or before IAO_0000117 "Chris Mungall"

• existence ends during or before comment "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription."

existence ends with http://purl.obolibrary.org/obo/RO_0002493

Added

• existence ends with IAO_0000117 "Chris Mungall"

• existence ends with comment "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription."

existence starts and ends during http://purl.obolibrary.org/obo/RO_0002491

Added

• existence starts and ends during IAO_0000117 "Chris Mungall"

• existence starts and ends during comment "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription."

• existence starts and ends during has_exact_synonym "exists during"

existence starts during http://purl.obolibrary.org/obo/RO_0002488

Added

• existence starts during IAO_0000117 "Chris Mungall"

existence starts during or after http://purl.obolibrary.org/obo/RO_0002496

Added

• existence starts during or after comment "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription."

• existence starts during or after IAO_0000117 "Chris Mungall"

existence starts with http://purl.obolibrary.org/obo/RO_0002489

Added

• existence starts with IAO_0000117 "Chris Mungall"

has 2D boundary http://purl.obolibrary.org/obo/RO_0002002

Added

• has 2D boundary IAO_0000118 "has_2D_boundary"@en

• has 2D boundary example of usage "my body has 2D boundary the surface of my skin"@en

• has 2D boundary IAO_0000117 "David Osumi-Sutherland"

• has 2D boundary editor note "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape."@en

• has 2D boundary IAO_0000118 "has boundary"@en

• has 2D boundary label "has_boundary"@en

• has 2D boundary editor note "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts."@en

• has 2D boundary RO_0001900 RO_0001901

has branching part http://purl.obolibrary.org/obo/RO_0002569

Added

• has branching part IAO_0000117 "Chris Mungall"

• has branching part in_subset ro-eco

• has branching part in_subset RO_0002259

has component http://purl.obolibrary.org/obo/RO_0002180

Added

• has component has_obo_namespace "external"

has member http://purl.obolibrary.org/obo/RO_0002351

Added

• has member RO_0001900 RO_0001901

• has member IAO_0000119 "SIO"

has muscle antagonist http://purl.obolibrary.org/obo/RO_0002568

Added

• has muscle antagonist IAO_0000119 "Wikipedia:Antagonist_(muscle)"

• has muscle antagonist IAO_0000117 "Chris Mungall"

has muscle insertion http://purl.obolibrary.org/obo/RO_0002373

Added

• has muscle insertion see also insertion

• has muscle insertion IAO_0000119 "Wikipedia:Insertion_(anatomy)"@en

• has muscle insertion IAO_0000117 "Chris Mungall"

has muscle origin http://purl.obolibrary.org/obo/RO_0002372

Added

• has muscle origin IAO_0000117 "Chris Mungall"

• has muscle origin IAO_0000119 "Wikipedia:Insertion_(anatomy)"@en

• has muscle origin see also origin

has skeleton http://purl.obolibrary.org/obo/RO_0002551

Added

• has skeleton curator notes "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)."

• has skeleton IAO_0000117 "Chris Mungall"

• has skeleton IAO_0000118 "has supporting framework"

• has skeleton example of usage "Forelimb SubClassOf has_skeleton some 'Forelimb skeleton'"

has_part http://purl.obolibrary.org/obo/BFO_0000051

Added

• has_part editor note "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/"@en

immediate transformation of http://purl.obolibrary.org/obo/RO_0002495

Added

• immediate transformation of RO_0002575 transformation of

• immediate transformation of IAO_0000117 "Chris Mungall"

immediately preceded by http://purl.obolibrary.org/obo/RO_0002087

Added

• immediately preceded by definition "X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)."

• immediately preceded by external_definition "A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251]."

  • source "SIO:000251"

• immediately preceded by has_obo_namespace "external"

in taxon http://purl.obolibrary.org/obo/RO_0002162

Added

• in taxon comment "Connects a biological entity to its taxon of origin."

• in taxon IAO_0000119 20973947

• in taxon IAO_0000119 17921072

• in taxon IAO_0000114 IAO_0000125

• in taxon IAO_0000117 "Chris Mungall"@en

• in taxon in_subset ro-eco

• in taxon IAO_0000117 "Jennifer Deegan"

• in taxon see also Taxon-constraints

innervated_by http://purl.obolibrary.org/obo/RO_0002005

Added

• innervated_by see also dbprop_nerve

• innervated_by comment "http://code.google.com/p/obo-relations/issues/detail?id=6"

• innervated_by IAO_0000117 "David Osumi-Sutherland"

• innervated_by has_exact_synonym "nerve supply"

  • database_cross_reference "FMA:85999"

• innervated_by see also FMA_85999

• innervated_by citesAsAuthority "http://www.ncbi.nlm.nih.gov/pubmed/22402613"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

innervates http://purl.obolibrary.org/obo/RO_0002134

Added

• innervates IAO_0000114 IAO_0000125

• innervates has_obo_namespace "fly_anatomy.ontology"

• innervates definition "Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input. T innervates some R Expands_to: T has_fasciculating_neuron_projection that synapse_in some R."

  • database_cross_reference "FBC:DOS"

• innervates IAO_0000424 "RO_0002132 some (GO_0043005 that (RO_0002131 some (GO_0045202 that BFO_0000050 some ?Y)))"

• innervates IAO_0000117 "David Osumi-Sutherland"@en

• innervates IAO_0000424 "<http://purl.obolibrary.org/obo/RO_0002132> some (<http://purl.obolibrary.org/obo/GO_0043005> that (<http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?)))"

• innervates citesAsAuthority 22402613

• innervates RO_0001900 RO_0001901

• innervates comment "http://code.google.com/p/obo-relations/issues/detail?id=6"

located in http://purl.obolibrary.org/obo/RO_0001025

Added

• located in editor note "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"@en

• located in example of usage "my brain is located in my head"@en

• located in editor note "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/"@en

• located in RO_0001900 RO_0001901

• located in in_subset valid_for_go_gp2term

• located in IAO_0000118 "located_in"@en

• located in IAO_0000111 "located in"@en

• located in example of usage "this rat is located in this cage"@en

• located in derived from resource "http://www.obofoundry.org/ro/#OBO_REL:located_in"

location of http://purl.obolibrary.org/obo/RO_0001015

Added

• location of example of usage "this cage is the location of this rat"@en

• location of IAO_0000111 "is location of"@en

• location of example of usage "my head is the location of my brain"@en

• location of IAO_0000118 "location_of"@en

• location of editor note "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/"@en

• location of RO_0001900 RO_0001901

lumen of http://purl.obolibrary.org/obo/RO_0002571

Added

• lumen of in_subset ro-eco

• lumen of IAO_0000119 "GOC:cjm"

• lumen of IAO_0000117 "Chris Mungall"

luminal space of http://purl.obolibrary.org/obo/RO_0002572

Added

• luminal space of in_subset ro-eco

• luminal space of IAO_0000117 "Chris Mungall"

only in taxon http://purl.obolibrary.org/obo/RO_0002160

Added

• only in taxon IAO_0000117 "Chris Mungall"@en

• only in taxon IAO_0000119 20973947

• only in taxon editor note "The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g.

'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria"

• only in taxon example of usage "lactation SubClassOf 'only in taxon' some 'Mammalia'"

• only in taxon IAO_0000119 17921072

• only in taxon see also Taxon-constraints

• only in taxon IAO_0000114 IAO_0000125

otic ganglion http://purl.obolibrary.org/obo/UBERON_0003963

Removed

• otic ganglion SubClassOf innervates some parotid gland

Added

• otic ganglion SubClassOf extends_fibers_into some parotid gland

output of http://purl.obolibrary.org/obo/RO_0002353

Added

• output of IAO_0000117 "Chris Mungall"

• output of in_subset RO_0002259

• output of has_obo_namespace "external"

• output of in_subset ro-eco

overlaps http://purl.obolibrary.org/obo/RO_0002131

Added

• overlaps IAO_0000424 "BFO_0000051 some (BFO_0000050 some ?Y)"

• overlaps has_obo_namespace "external"

part_of http://purl.obolibrary.org/obo/BFO_0000050

Added

• part_of editor note "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/"@en

participates in http://purl.obolibrary.org/obo/RO_0000056

Added

• participates in has_obo_namespace "external"

preceded_by http://purl.obolibrary.org/obo/BFO_0000062

Added

• preceded_by definition "X preceded_by Y iff: end(Y) before_or_simultaneous_with start(X)."

• preceded_by has_obo_namespace "external"

precedes http://purl.obolibrary.org/obo/BFO_0000063

Added

• precedes has_obo_namespace "external"

present in taxon http://purl.obolibrary.org/obo/RO_0002175

Added

• present in taxon comment "The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology."

produced_by http://purl.obolibrary.org/obo/RO_0003001

Added

• produced_by in_subset ro-eco

• produced_by IAO_0000117 "Melissa Haendel"

• produced_by has_obo_namespace "external"

• produced_by IAO_0000114 IAO_0000125

produces http://purl.obolibrary.org/obo/RO_0003000

Added

• produces IAO_0000114 IAO_0000125

• produces 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."

• produces has_obo_namespace "external"

• produces in_subset ro-eco

• produces IAO_0000117 "Melissa Haendel"

simultaneous with http://purl.obolibrary.org/obo/RO_0002082

Added

• simultaneous with IAO_0000117 "David Osumi-Sutherland"

• simultaneous with in_subset ro-eco

• simultaneous with comment "t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2)"@en

skeleton of http://purl.obolibrary.org/obo/RO_0002576

Added

• skeleton of IAO_0000117 "Chris Mungall"

• skeleton of in_subset RO_0002259

starts http://purl.obolibrary.org/obo/RO_0002223

Added

• starts IAO_0000117 "Chris Mungall"

• starts IAO_0000119 "Allen"

• starts in_subset ro-eco

• starts IAO_0000114 IAO_0000125

starts with http://purl.obolibrary.org/obo/RO_0002224

Added

• starts with has_obo_namespace "external"

• starts with IAO_0000114 IAO_0000125

• starts with example of usage "Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor"

• starts with IAO_0000118 "started by"

• starts with in_subset ro-eco

• starts with IAO_0000117 "Chris Mungall"

supplies http://purl.obolibrary.org/obo/RO_0002178

Added

• supplies editor note "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"

• supplies IAO_0000119 20064205

surrounded by http://purl.obolibrary.org/obo/RO_0002219

Added

• surrounded by RO_0001900 RO_0001901

• surrounded by IAO_0000117 "Chris Mungall"

• surrounded by IAO_0000114 IAO_0000125

surrounds http://purl.obolibrary.org/obo/RO_0002221

Added

• surrounds RO_0001900 RO_0001901

• surrounds in_subset RO_0002259

• surrounds IAO_0000114 IAO_0000125

• surrounds IAO_0000117 "Chris Mungall"

transformation of http://purl.obolibrary.org/obo/RO_0002494

Added

• transformation of IAO_0000117 "Chris Mungall"

tributary_of http://purl.obolibrary.org/obo/RO_0002376

Added

• tributary_of in_subset ro-eco

• tributary_of curator notes "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)"^^anyURI

• tributary_of see also "http://en.wikipedia.org/wiki/Tributary"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• tributary_of IAO_0000114 IAO_0000428

• tributary_of IAO_0000118 "tributary channel of"

• tributary_of IAO_0000117 "Chris Mungall"

• tributary_of IAO_0000118 "drains into"

• tributary_of see also drainsTo

• tributary_of example of usage "inferior epigastric vein tributary_of external iliac vein"

• tributary_of IAO_0000119 "http://en.wikipedia.org/wiki/Tributary"

• tributary_of IAO_0000118 "drains to"

• tributary_of example of usage "Deschutes River tributary_of Columbia River"

• tributary_of IAO_0000119 "http://www.medindia.net/glossary/venous_tributary.htm"

[github-actions]

Here's a diff of your edit file (unreasoned)

Ontology comparison

Left

• Ontology IRI: http://purl.obolibrary.org/obo/uberon/core.owl
• Version IRI: None
• Loaded from: file:/work/src/ontology/../../master/src/ontology/uberon-edit.obo

Right

• Ontology IRI: http://purl.obolibrary.org/obo/uberon/core.owl
• Version IRI: None
• Loaded from: file:/work/src/ontology/uberon-edit.obo

Ontology imports

Added

• caro_import.owl

Ontology annotations

otic ganglion http://purl.obolibrary.org/obo/UBERON_0003963

Removed

• otic ganglion EquivalentTo cranial ganglion and (innervates some parotid gland) and (extends_fibers_into some glossopharyngeal nerve)

Added

• otic ganglion EquivalentTo cranial ganglion and (extends_fibers_into some glossopharyngeal nerve) and (extends_fibers_into some parotid gland)

[github-actions]

Here's a diff of how these changes impact the classified ontology (on -simple file):

Ontology comparison

Left

• Ontology IRI: http://purl.obolibrary.org/obo/uberon/uberon-simple.owl
• Version IRI: http://purl.obolibrary.org/obo/uberon/releases/2022-08-18/uberon-simple.owl
• Loaded from: file:/work/src/ontology/../../master/src/ontology/uberon-simple.owl

Right

• Ontology IRI: http://purl.obolibrary.org/obo/uberon/uberon-simple.owl
• Version IRI: http://purl.obolibrary.org/obo/uberon/releases/2022-08-18/uberon-simple.owl
• Loaded from: file:/work/src/ontology/uberon-simple.owl

Ontology imports

Ontology annotations

IAO_0000589 http://purl.obolibrary.org/obo/IAO_0000589

Added

• AnnotationProperty: IAO_0000589

RO_0002575 http://purl.obolibrary.org/obo/RO_0002575

Added

• AnnotationProperty: RO_0002575

adjacent_to http://purl.obolibrary.org/obo/RO_0002220

Added

• adjacent_to example of usage "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies."

• adjacent_to IAO_0000117 "Chris Mungall"

• adjacent_to IAO_0000114 IAO_0000125

• adjacent_to example of usage "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."

• adjacent_to in_subset valid_for_go_annotation_extension

• adjacent_to has_obo_namespace "external"

• adjacent_to in_subset valid_for_gocam

• adjacent_to in_subset valid_for_go_ontology

• adjacent_to RO_0001900 RO_0001901

• adjacent_to editor note "This relation acts as a join point with BSPO"

• adjacent_to example of usage "The epidermis layer of a vertebrate is adjacent to the dermis."

• adjacent_to example of usage "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."

  • see also issuecomment-218584934

attached to http://purl.obolibrary.org/obo/RO_0002371

Added

• attached to IAO_0000117 "Chris Mungall"

• attached to in_subset ro-eco

• attached to IAO_0000589 "attached to (anatomical structure to anatomical structure)"

attached to part of http://purl.obolibrary.org/obo/RO_0002177

Added

• attached to part of IAO_0000589 "attached to part of (anatomical structure to anatomical structure)"

bounding layer of http://purl.obolibrary.org/obo/RO_0002007

Added

• bounding layer of in_subset ro-eco

• bounding layer of has_obo_namespace "external"

• bounding layer of IAO_0000117 "David Osumi-Sutherland"

• bounding layer of 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."

branching_part_of http://purl.obolibrary.org/obo/RO_0002380

Added

• branching_part_of example of usage "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S"

• branching_part_of see also 2212

• branching_part_of see also "FMA:85994"

• branching_part_of IAO_0000117 "Chris Mungall"

• branching_part_of in_subset ro-eco

capable of part of http://purl.obolibrary.org/obo/RO_0002216

Added

• capable of part of see also http://purl.obolibrary.org/obo/ro/docs/reflexivity/

• capable of part of has_obo_namespace "external"

citesAsAuthority http://purl.org/spar/cito/citesAsAuthority

Added

• AnnotationProperty: citesAsAuthority

composed primarily of http://purl.obolibrary.org/obo/RO_0002473

Added

• composed primarily of in_subset ro-eco

• composed primarily of example of usage "'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'"

• composed primarily of IAO_0000119 22293552

• composed primarily of IAO_0000117 "Chris Mungall"

• composed primarily of RO_0001900 RO_0001901

confers advantage in http://purl.obolibrary.org/obo/RO_0002322

Added

• confers advantage in IAO_0000118 "adapted for"

• confers advantage in IAO_0000117 "Chris Mungall"

• confers advantage in editor note "An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial."

• confers advantage in in_subset ro-eco

connected to http://purl.obolibrary.org/obo/RO_0002170

Added

• connected to definition "Binary relationship: x connected_to y if and only if there exists some z such that z connects x and y in a ternary connected_to(x,y,z) relationship."

  • database_cross_reference "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern"

• connected to see also "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• connected to IAO_0000119 22293552

• connected to see also "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• connected to example of usage "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint connects these two bones)."

connects http://purl.obolibrary.org/obo/RO_0002176

Added

• connects see also "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• connects see also "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• connects example of usage "The M8 connects Glasgow and Edinburgh"

• connects IAO_0000119 22293552

• connects example of usage "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint connects these two bones)."

contains http://purl.obolibrary.org/obo/RO_0001019

Added

• contains IAO_0000111 "contains"@en

• contains RO_0001900 RO_0001901

• contains in_subset ro-eco

continuous_with http://purl.obolibrary.org/obo/RO_0002150

Added

• continuous_with RO_0001900 RO_0001901

• continuous_with IAO_0000114 IAO_0000125

• continuous_with IAO_0000117 "David Osumi-Sutherland"

• continuous_with IAO_0000118 "connected to"

• continuous_with curator notes "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)"

• continuous_with see also "FMA:85972"

contributes to morphology of http://purl.obolibrary.org/obo/RO_0002433

Added

• contributes to morphology of IAO_0000117 "Chris Mungall"

developmentally_induced_by http://purl.obolibrary.org/obo/RO_0002256

Added

• developmentally_induced_by IAO_0000119 " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)"

• developmentally_induced_by IAO_0000118 "induced by"

• developmentally_induced_by IAO_0000119 "GO:0001759"

• developmentally_induced_by IAO_0000119 20064205

• developmentally_induced_by curator notes "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]"

• developmentally_induced_by IAO_0000117 "Chris Mungall"

• developmentally_induced_by IAO_0000117 "David Osumi-Sutherland"

• developmentally_induced_by IAO_0000114 IAO_0000125

• developmentally_induced_by IAO_0000117 "Melissa Haendel"

developmentally_replaces http://purl.obolibrary.org/obo/RO_0002285

Added

• developmentally_replaces IAO_0000114 IAO_0000125

• developmentally_replaces editor note "This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage"

• developmentally_replaces IAO_0000118 "replaces"

• developmentally_replaces IAO_0000117 "Chris Mungall"

develops from part of http://purl.obolibrary.org/obo/RO_0002225

Added

• develops from part of IAO_0000114 IAO_0000125

• develops from part of IAO_0000117 "Chris Mungall"

develops in http://purl.obolibrary.org/obo/RO_0002226

Added

• develops in IAO_0000119 "Jonathan Bard, EHDAA2"

• develops in IAO_0000117 "Chris Mungall"

• develops in IAO_0000119 "EHDAA2"

• develops in IAO_0000114 IAO_0000125

directly develops from http://purl.obolibrary.org/obo/RO_0002207

Added

• directly develops from IAO_0000117 "Chris Mungall"

• directly develops from IAO_0000117 "David Osumi-Sutherland"

• directly develops from comment "TODO - add child relations from DOS"

• directly develops from IAO_0000119 "FBbt"

• directly develops from RO_0002575 develops from

• directly develops from IAO_0000114 IAO_0000125

• directly develops from IAO_0000117 "has developmental precursor"

drains http://purl.obolibrary.org/obo/RO_0002179

Added

• drains editor note "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure"

• drains IAO_0000119 20064205

ends http://purl.obolibrary.org/obo/RO_0002229

Added

• ends IAO_0000114 IAO_0000125

• ends in_subset ro-eco

• ends IAO_0000117 "Chris Mungall"

ends with http://purl.obolibrary.org/obo/RO_0002230

Added

• ends with has_obo_namespace "external"

• ends with in_subset ro-eco

• ends with IAO_0000118 "finished by"

• ends with IAO_0000114 IAO_0000125

• ends with IAO_0000117 "Chris Mungall"

existence ends during http://purl.obolibrary.org/obo/RO_0002492

Added

• existence ends during IAO_0000117 "Chris Mungall"

• existence ends during comment "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription."

existence ends during or before http://purl.obolibrary.org/obo/RO_0002497

Added

• existence ends during or before IAO_0000117 "Chris Mungall"

• existence ends during or before comment "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription."

existence ends with http://purl.obolibrary.org/obo/RO_0002493

Added

• existence ends with IAO_0000117 "Chris Mungall"

• existence ends with comment "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription."

existence starts and ends during http://purl.obolibrary.org/obo/RO_0002491

Added

• existence starts and ends during IAO_0000117 "Chris Mungall"

• existence starts and ends during comment "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription."

• existence starts and ends during has_exact_synonym "exists during"

existence starts during http://purl.obolibrary.org/obo/RO_0002488

Added

• existence starts during IAO_0000117 "Chris Mungall"

existence starts during or after http://purl.obolibrary.org/obo/RO_0002496

Added

• existence starts during or after comment "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription."

• existence starts during or after IAO_0000117 "Chris Mungall"

existence starts with http://purl.obolibrary.org/obo/RO_0002489

Added

• existence starts with IAO_0000117 "Chris Mungall"

has 2D boundary http://purl.obolibrary.org/obo/RO_0002002

Added

• has 2D boundary IAO_0000118 "has_2D_boundary"@en

• has 2D boundary example of usage "my body has 2D boundary the surface of my skin"@en

• has 2D boundary IAO_0000117 "David Osumi-Sutherland"

• has 2D boundary editor note "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape."@en

• has 2D boundary IAO_0000118 "has boundary"@en

• has 2D boundary label "has_boundary"@en

• has 2D boundary editor note "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts."@en

• has 2D boundary RO_0001900 RO_0001901

has branching part http://purl.obolibrary.org/obo/RO_0002569

Added

• has branching part IAO_0000117 "Chris Mungall"

• has branching part in_subset ro-eco

• has branching part in_subset RO_0002259

has component http://purl.obolibrary.org/obo/RO_0002180

Added

• has component has_obo_namespace "external"

has member http://purl.obolibrary.org/obo/RO_0002351

Added

• has member RO_0001900 RO_0001901

• has member IAO_0000119 "SIO"

has muscle antagonist http://purl.obolibrary.org/obo/RO_0002568

Added

• has muscle antagonist IAO_0000119 "Wikipedia:Antagonist_(muscle)"

• has muscle antagonist IAO_0000117 "Chris Mungall"

has muscle insertion http://purl.obolibrary.org/obo/RO_0002373

Added

• has muscle insertion see also insertion

• has muscle insertion IAO_0000119 "Wikipedia:Insertion_(anatomy)"@en

• has muscle insertion IAO_0000117 "Chris Mungall"

has muscle origin http://purl.obolibrary.org/obo/RO_0002372

Added

• has muscle origin IAO_0000117 "Chris Mungall"

• has muscle origin IAO_0000119 "Wikipedia:Insertion_(anatomy)"@en

• has muscle origin see also origin

has skeleton http://purl.obolibrary.org/obo/RO_0002551

Added

• has skeleton curator notes "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)."

• has skeleton IAO_0000117 "Chris Mungall"

• has skeleton IAO_0000118 "has supporting framework"

• has skeleton example of usage "Forelimb SubClassOf has_skeleton some 'Forelimb skeleton'"

has_part http://purl.obolibrary.org/obo/BFO_0000051

Added

• has_part editor note "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/"@en

immediate transformation of http://purl.obolibrary.org/obo/RO_0002495

Added

• immediate transformation of RO_0002575 transformation of

• immediate transformation of IAO_0000117 "Chris Mungall"

immediately preceded by http://purl.obolibrary.org/obo/RO_0002087

Added

• immediately preceded by definition "X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)."

• immediately preceded by external_definition "A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251]."

  • source "SIO:000251"

• immediately preceded by has_obo_namespace "external"

in taxon http://purl.obolibrary.org/obo/RO_0002162

Added

• in taxon comment "Connects a biological entity to its taxon of origin."

• in taxon IAO_0000119 20973947

• in taxon IAO_0000119 17921072

• in taxon IAO_0000114 IAO_0000125

• in taxon IAO_0000117 "Chris Mungall"@en

• in taxon in_subset ro-eco

• in taxon IAO_0000117 "Jennifer Deegan"

• in taxon see also Taxon-constraints

innervated_by http://purl.obolibrary.org/obo/RO_0002005

Added

• innervated_by see also dbprop_nerve

• innervated_by comment "http://code.google.com/p/obo-relations/issues/detail?id=6"

• innervated_by IAO_0000117 "David Osumi-Sutherland"

• innervated_by has_exact_synonym "nerve supply"

  • database_cross_reference "FMA:85999"

• innervated_by see also FMA_85999

• innervated_by citesAsAuthority "http://www.ncbi.nlm.nih.gov/pubmed/22402613"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

innervates http://purl.obolibrary.org/obo/RO_0002134

Added

• innervates IAO_0000114 IAO_0000125

• innervates has_obo_namespace "fly_anatomy.ontology"

• innervates definition "Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input. T innervates some R Expands_to: T has_fasciculating_neuron_projection that synapse_in some R."

  • database_cross_reference "FBC:DOS"

• innervates IAO_0000424 "RO_0002132 some (GO_0043005 that (RO_0002131 some (GO_0045202 that BFO_0000050 some ?Y)))"

• innervates IAO_0000117 "David Osumi-Sutherland"@en

• innervates IAO_0000424 "<http://purl.obolibrary.org/obo/RO_0002132> some (<http://purl.obolibrary.org/obo/GO_0043005> that (<http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?)))"

• innervates citesAsAuthority 22402613

• innervates RO_0001900 RO_0001901

• innervates comment "http://code.google.com/p/obo-relations/issues/detail?id=6"

located in http://purl.obolibrary.org/obo/RO_0001025

Added

• located in editor note "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"@en

• located in example of usage "my brain is located in my head"@en

• located in editor note "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/"@en

• located in RO_0001900 RO_0001901

• located in in_subset valid_for_go_gp2term

• located in IAO_0000118 "located_in"@en

• located in IAO_0000111 "located in"@en

• located in example of usage "this rat is located in this cage"@en

• located in derived from resource "http://www.obofoundry.org/ro/#OBO_REL:located_in"

location of http://purl.obolibrary.org/obo/RO_0001015

Added

• location of example of usage "this cage is the location of this rat"@en

• location of IAO_0000111 "is location of"@en

• location of example of usage "my head is the location of my brain"@en

• location of IAO_0000118 "location_of"@en

• location of editor note "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/"@en

• location of RO_0001900 RO_0001901

lumen of http://purl.obolibrary.org/obo/RO_0002571

Added

• lumen of in_subset ro-eco

• lumen of IAO_0000119 "GOC:cjm"

• lumen of IAO_0000117 "Chris Mungall"

luminal space of http://purl.obolibrary.org/obo/RO_0002572

Added

• luminal space of in_subset ro-eco

• luminal space of IAO_0000117 "Chris Mungall"

only in taxon http://purl.obolibrary.org/obo/RO_0002160

Added

• only in taxon IAO_0000117 "Chris Mungall"@en

• only in taxon IAO_0000119 20973947

• only in taxon editor note "The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g.

'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria"

• only in taxon example of usage "lactation SubClassOf 'only in taxon' some 'Mammalia'"

• only in taxon IAO_0000119 17921072

• only in taxon see also Taxon-constraints

• only in taxon IAO_0000114 IAO_0000125

otic ganglion http://purl.obolibrary.org/obo/UBERON_0003963

Removed

• otic ganglion SubClassOf innervates some parotid gland

Added

• otic ganglion SubClassOf extends_fibers_into some parotid gland

output of http://purl.obolibrary.org/obo/RO_0002353

Added

• output of IAO_0000117 "Chris Mungall"

• output of in_subset RO_0002259

• output of has_obo_namespace "external"

• output of in_subset ro-eco

overlaps http://purl.obolibrary.org/obo/RO_0002131

Added

• overlaps IAO_0000424 "BFO_0000051 some (BFO_0000050 some ?Y)"

• overlaps has_obo_namespace "external"

part_of http://purl.obolibrary.org/obo/BFO_0000050

Added

• part_of editor note "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/"@en

participates in http://purl.obolibrary.org/obo/RO_0000056

Added

• participates in has_obo_namespace "external"

preceded_by http://purl.obolibrary.org/obo/BFO_0000062

Added

• preceded_by definition "X preceded_by Y iff: end(Y) before_or_simultaneous_with start(X)."

• preceded_by has_obo_namespace "external"

precedes http://purl.obolibrary.org/obo/BFO_0000063

Added

• precedes has_obo_namespace "external"

present_in_taxon http://purl.obolibrary.org/obo/RO_0002175

Added

• present_in_taxon comment "The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology."

produced_by http://purl.obolibrary.org/obo/RO_0003001

Added

• produced_by in_subset ro-eco

• produced_by IAO_0000117 "Melissa Haendel"

• produced_by has_obo_namespace "external"

• produced_by IAO_0000114 IAO_0000125

produces http://purl.obolibrary.org/obo/RO_0003000

Added

• produces IAO_0000114 IAO_0000125

• produces 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."

• produces has_obo_namespace "external"

• produces in_subset ro-eco

• produces IAO_0000117 "Melissa Haendel"

simultaneous with http://purl.obolibrary.org/obo/RO_0002082

Added

• simultaneous with IAO_0000117 "David Osumi-Sutherland"

• simultaneous with in_subset ro-eco

• simultaneous with comment "t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2)"@en

skeleton of http://purl.obolibrary.org/obo/RO_0002576

Added

• skeleton of IAO_0000117 "Chris Mungall"

• skeleton of in_subset RO_0002259

starts http://purl.obolibrary.org/obo/RO_0002223

Added

• starts IAO_0000117 "Chris Mungall"

• starts IAO_0000119 "Allen"

• starts in_subset ro-eco

• starts IAO_0000114 IAO_0000125

starts with http://purl.obolibrary.org/obo/RO_0002224

Added

• starts with has_obo_namespace "external"

• starts with IAO_0000114 IAO_0000125

• starts with example of usage "Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor"

• starts with IAO_0000118 "started by"

• starts with in_subset ro-eco

• starts with IAO_0000117 "Chris Mungall"

supplies http://purl.obolibrary.org/obo/RO_0002178

Added

• supplies editor note "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"

• supplies IAO_0000119 20064205

surrounded by http://purl.obolibrary.org/obo/RO_0002219

Added

• surrounded by RO_0001900 RO_0001901

• surrounded by IAO_0000117 "Chris Mungall"

• surrounded by IAO_0000114 IAO_0000125

surrounds http://purl.obolibrary.org/obo/RO_0002221

Added

• surrounds RO_0001900 RO_0001901

• surrounds in_subset RO_0002259

• surrounds IAO_0000114 IAO_0000125

• surrounds IAO_0000117 "Chris Mungall"

transformation of http://purl.obolibrary.org/obo/RO_0002494

Added

• transformation of IAO_0000117 "Chris Mungall"

tributary_of http://purl.obolibrary.org/obo/RO_0002376

Added

• tributary_of in_subset ro-eco

• tributary_of curator notes "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)"^^anyURI

• tributary_of see also "http://en.wikipedia.org/wiki/Tributary"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• tributary_of IAO_0000114 IAO_0000428

• tributary_of IAO_0000118 "tributary channel of"

• tributary_of IAO_0000117 "Chris Mungall"

• tributary_of IAO_0000118 "drains into"

• tributary_of see also drainsTo

• tributary_of example of usage "inferior epigastric vein tributary_of external iliac vein"

• tributary_of IAO_0000119 "http://en.wikipedia.org/wiki/Tributary"

• tributary_of IAO_0000118 "drains to"

• tributary_of example of usage "Deschutes River tributary_of Columbia River"

• tributary_of IAO_0000119 "http://www.medindia.net/glossary/venous_tributary.htm"

[github-actions]

Here's a diff of your edit file (unreasoned)

Ontology comparison

Left

• Ontology IRI: http://purl.obolibrary.org/obo/uberon/core.owl
• Version IRI: None
• Loaded from: file:/work/src/ontology/../../master/src/ontology/uberon-edit.obo

Right

• Ontology IRI: http://purl.obolibrary.org/obo/uberon/core.owl
• Version IRI: None
• Loaded from: file:/work/src/ontology/uberon-edit.obo

Ontology imports

Added

• caro_import.owl

Ontology annotations

otic ganglion http://purl.obolibrary.org/obo/UBERON_0003963

Removed

• otic ganglion EquivalentTo cranial ganglion and (innervates some parotid gland) and (extends_fibers_into some glossopharyngeal nerve)

Added

• otic ganglion EquivalentTo cranial ganglion and (extends_fibers_into some glossopharyngeal nerve) and (extends_fibers_into some parotid gland)

[github-actions]

Here's a diff of how these changes impact the classified ontology (on -simple file):

Ontology comparison

Left

• Ontology IRI: http://purl.obolibrary.org/obo/uberon/uberon-simple.owl
• Version IRI: http://purl.obolibrary.org/obo/uberon/releases/2022-08-18/uberon-simple.owl
• Loaded from: file:/work/src/ontology/../../master/src/ontology/uberon-simple.owl

Right

• Ontology IRI: http://purl.obolibrary.org/obo/uberon/uberon-simple.owl
• Version IRI: http://purl.obolibrary.org/obo/uberon/releases/2022-08-18/uberon-simple.owl
• Loaded from: file:/work/src/ontology/uberon-simple.owl

Ontology imports

Ontology annotations

IAO_0000589 http://purl.obolibrary.org/obo/IAO_0000589

Added

• AnnotationProperty: IAO_0000589

RO_0002575 http://purl.obolibrary.org/obo/RO_0002575

Added

• AnnotationProperty: RO_0002575

adjacent_to http://purl.obolibrary.org/obo/RO_0002220

Added

• adjacent_to example of usage "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies."

• adjacent_to IAO_0000117 "Chris Mungall"

• adjacent_to IAO_0000114 IAO_0000125

• adjacent_to example of usage "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."

• adjacent_to in_subset valid_for_go_annotation_extension

• adjacent_to has_obo_namespace "external"

• adjacent_to in_subset valid_for_gocam

• adjacent_to in_subset valid_for_go_ontology

• adjacent_to RO_0001900 RO_0001901

• adjacent_to editor note "This relation acts as a join point with BSPO"

• adjacent_to example of usage "The epidermis layer of a vertebrate is adjacent to the dermis."

• adjacent_to example of usage "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."

  • see also issuecomment-218584934

attached to part of http://purl.obolibrary.org/obo/RO_0002177

Added

• attached to part of IAO_0000589 "attached to part of (anatomical structure to anatomical structure)"

attaches_to http://purl.obolibrary.org/obo/RO_0002371

Added

• attaches_to IAO_0000117 "Chris Mungall"

• attaches_to in_subset ro-eco

• attaches_to IAO_0000589 "attached to (anatomical structure to anatomical structure)"

bounding layer of http://purl.obolibrary.org/obo/RO_0002007

Added

• bounding layer of in_subset ro-eco

• bounding layer of has_obo_namespace "external"

• bounding layer of IAO_0000117 "David Osumi-Sutherland"

• bounding layer of 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."

branching_part_of http://purl.obolibrary.org/obo/RO_0002380

Added

• branching_part_of example of usage "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S"

• branching_part_of see also 2212

• branching_part_of see also "FMA:85994"

• branching_part_of IAO_0000117 "Chris Mungall"

• branching_part_of in_subset ro-eco

capable of part of http://purl.obolibrary.org/obo/RO_0002216

Added

• capable of part of see also http://purl.obolibrary.org/obo/ro/docs/reflexivity/

• capable of part of has_obo_namespace "external"

citesAsAuthority http://purl.org/spar/cito/citesAsAuthority

Added

• AnnotationProperty: citesAsAuthority

composed primarily of http://purl.obolibrary.org/obo/RO_0002473

Added

• composed primarily of in_subset ro-eco

• composed primarily of example of usage "'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'"

• composed primarily of IAO_0000119 22293552

• composed primarily of IAO_0000117 "Chris Mungall"

• composed primarily of RO_0001900 RO_0001901

confers advantage in http://purl.obolibrary.org/obo/RO_0002322

Added

• confers advantage in IAO_0000118 "adapted for"

• confers advantage in IAO_0000117 "Chris Mungall"

• confers advantage in editor note "An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial."

• confers advantage in in_subset ro-eco

connected to http://purl.obolibrary.org/obo/RO_0002170

Added

• connected to see also "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• connected to IAO_0000119 22293552

• connected to see also "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• connected to example of usage "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint connects these two bones)."

connects http://purl.obolibrary.org/obo/RO_0002176

Added

• connects see also "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• connects see also "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• connects example of usage "The M8 connects Glasgow and Edinburgh"

• connects IAO_0000119 22293552

• connects example of usage "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint connects these two bones)."

contains http://purl.obolibrary.org/obo/RO_0001019

Added

• contains IAO_0000111 "contains"@en

• contains RO_0001900 RO_0001901

• contains in_subset ro-eco

continuous_with http://purl.obolibrary.org/obo/RO_0002150

Added

• continuous_with RO_0001900 RO_0001901

• continuous_with IAO_0000114 IAO_0000125

• continuous_with IAO_0000117 "David Osumi-Sutherland"

• continuous_with IAO_0000118 "connected to"

• continuous_with curator notes "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)"

• continuous_with see also "FMA:85972"

contributes to morphology of http://purl.obolibrary.org/obo/RO_0002433

Added

• contributes to morphology of IAO_0000117 "Chris Mungall"

developmentally replaces http://purl.obolibrary.org/obo/RO_0002285

Added

• developmentally replaces IAO_0000114 IAO_0000125

• developmentally replaces editor note "This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage"

• developmentally replaces IAO_0000118 "replaces"

• developmentally replaces IAO_0000117 "Chris Mungall"

developmentally_induced_by http://purl.obolibrary.org/obo/RO_0002256

Added

• developmentally_induced_by IAO_0000119 " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)"

• developmentally_induced_by IAO_0000118 "induced by"

• developmentally_induced_by IAO_0000119 "GO:0001759"

• developmentally_induced_by IAO_0000119 20064205

• developmentally_induced_by curator notes "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]"

• developmentally_induced_by IAO_0000117 "Chris Mungall"

• developmentally_induced_by IAO_0000117 "David Osumi-Sutherland"

• developmentally_induced_by IAO_0000114 IAO_0000125

• developmentally_induced_by IAO_0000117 "Melissa Haendel"

develops from part of http://purl.obolibrary.org/obo/RO_0002225

Added

• develops from part of IAO_0000114 IAO_0000125

• develops from part of IAO_0000117 "Chris Mungall"

develops in http://purl.obolibrary.org/obo/RO_0002226

Added

• develops in IAO_0000119 "Jonathan Bard, EHDAA2"

• develops in IAO_0000117 "Chris Mungall"

• develops in IAO_0000119 "EHDAA2"

• develops in IAO_0000114 IAO_0000125

directly develops from http://purl.obolibrary.org/obo/RO_0002207

Added

• directly develops from IAO_0000117 "Chris Mungall"

• directly develops from IAO_0000117 "David Osumi-Sutherland"

• directly develops from comment "TODO - add child relations from DOS"

• directly develops from IAO_0000119 "FBbt"

• directly develops from RO_0002575 develops from

• directly develops from IAO_0000114 IAO_0000125

• directly develops from IAO_0000117 "has developmental precursor"

drains http://purl.obolibrary.org/obo/RO_0002179

Added

• drains editor note "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure"

• drains IAO_0000119 20064205

ends http://purl.obolibrary.org/obo/RO_0002229

Added

• ends IAO_0000114 IAO_0000125

• ends in_subset ro-eco

• ends IAO_0000117 "Chris Mungall"

ends with http://purl.obolibrary.org/obo/RO_0002230

Added

• ends with has_obo_namespace "external"

• ends with in_subset ro-eco

• ends with IAO_0000118 "finished by"

• ends with IAO_0000114 IAO_0000125

• ends with IAO_0000117 "Chris Mungall"

existence ends during http://purl.obolibrary.org/obo/RO_0002492

Added

• existence ends during IAO_0000117 "Chris Mungall"

• existence ends during comment "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription."

existence ends during or before http://purl.obolibrary.org/obo/RO_0002497

Added

• existence ends during or before IAO_0000117 "Chris Mungall"

• existence ends during or before comment "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription."

existence ends with http://purl.obolibrary.org/obo/RO_0002493

Added

• existence ends with IAO_0000117 "Chris Mungall"

• existence ends with comment "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription."

existence starts and ends during http://purl.obolibrary.org/obo/RO_0002491

Added

• existence starts and ends during IAO_0000117 "Chris Mungall"

• existence starts and ends during comment "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription."

• existence starts and ends during has_exact_synonym "exists during"

existence starts during http://purl.obolibrary.org/obo/RO_0002488

Added

• existence starts during IAO_0000117 "Chris Mungall"

existence starts during or after http://purl.obolibrary.org/obo/RO_0002496

Added

• existence starts during or after comment "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription."

• existence starts during or after IAO_0000117 "Chris Mungall"

existence starts with http://purl.obolibrary.org/obo/RO_0002489

Added

• existence starts with IAO_0000117 "Chris Mungall"

has 2D boundary http://purl.obolibrary.org/obo/RO_0002002

Added

• has 2D boundary IAO_0000118 "has_2D_boundary"@en

• has 2D boundary example of usage "my body has 2D boundary the surface of my skin"@en

• has 2D boundary IAO_0000117 "David Osumi-Sutherland"

• has 2D boundary editor note "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape."@en

• has 2D boundary IAO_0000118 "has boundary"@en

• has 2D boundary editor note "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts."@en

• has 2D boundary RO_0001900 RO_0001901

has branching part http://purl.obolibrary.org/obo/RO_0002569

Added

• has branching part IAO_0000117 "Chris Mungall"

• has branching part in_subset ro-eco

• has branching part in_subset RO_0002259

has component http://purl.obolibrary.org/obo/RO_0002180

Added

• has component has_obo_namespace "external"

has member http://purl.obolibrary.org/obo/RO_0002351

Added

• has member RO_0001900 RO_0001901

• has member IAO_0000119 "SIO"

has muscle antagonist http://purl.obolibrary.org/obo/RO_0002568

Added

• has muscle antagonist IAO_0000119 "Wikipedia:Antagonist_(muscle)"

• has muscle antagonist IAO_0000117 "Chris Mungall"

has muscle insertion http://purl.obolibrary.org/obo/RO_0002373

Added

• has muscle insertion see also insertion

• has muscle insertion IAO_0000119 "Wikipedia:Insertion_(anatomy)"@en

• has muscle insertion IAO_0000117 "Chris Mungall"

has muscle origin http://purl.obolibrary.org/obo/RO_0002372

Added

• has muscle origin IAO_0000117 "Chris Mungall"

• has muscle origin IAO_0000119 "Wikipedia:Insertion_(anatomy)"@en

• has muscle origin see also origin

has skeleton http://purl.obolibrary.org/obo/RO_0002551

Added

• has skeleton curator notes "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)."

• has skeleton IAO_0000117 "Chris Mungall"

• has skeleton IAO_0000118 "has supporting framework"

• has skeleton example of usage "Forelimb SubClassOf has_skeleton some 'Forelimb skeleton'"

has_part http://purl.obolibrary.org/obo/BFO_0000051

Added

• has_part editor note "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/"@en

immediate transformation of http://purl.obolibrary.org/obo/RO_0002495

Added

• immediate transformation of RO_0002575 transformation of

• immediate transformation of IAO_0000117 "Chris Mungall"

immediately preceded by http://purl.obolibrary.org/obo/RO_0002087

Added

• immediately preceded by has_obo_namespace "external"

in taxon http://purl.obolibrary.org/obo/RO_0002162

Added

• in taxon comment "Connects a biological entity to its taxon of origin."

• in taxon IAO_0000119 20973947

• in taxon IAO_0000119 17921072

• in taxon IAO_0000114 IAO_0000125

• in taxon IAO_0000117 "Chris Mungall"@en

• in taxon in_subset ro-eco

• in taxon IAO_0000117 "Jennifer Deegan"

• in taxon see also Taxon-constraints

innervated_by http://purl.obolibrary.org/obo/RO_0002005

Added

• innervated_by IAO_0000117 "David Osumi-Sutherland"

• innervated_by citesAsAuthority "http://www.ncbi.nlm.nih.gov/pubmed/22402613"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

innervates http://purl.obolibrary.org/obo/RO_0002134

Added

• innervates IAO_0000114 IAO_0000125

• innervates IAO_0000117 "David Osumi-Sutherland"@en

• innervates IAO_0000424 "<http://purl.obolibrary.org/obo/RO_0002132> some (<http://purl.obolibrary.org/obo/GO_0043005> that (<http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?)))"

• innervates citesAsAuthority 22402613

• innervates RO_0001900 RO_0001901

located in http://purl.obolibrary.org/obo/RO_0001025

Added

• located in editor note "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"@en

• located in example of usage "my brain is located in my head"@en

• located in editor note "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/"@en

• located in RO_0001900 RO_0001901

• located in in_subset valid_for_go_gp2term

• located in IAO_0000118 "located_in"@en

• located in IAO_0000111 "located in"@en

• located in example of usage "this rat is located in this cage"@en

• located in derived from resource "http://www.obofoundry.org/ro/#OBO_REL:located_in"

location of http://purl.obolibrary.org/obo/RO_0001015

Added

• location of example of usage "this cage is the location of this rat"@en

• location of IAO_0000111 "is location of"@en

• location of example of usage "my head is the location of my brain"@en

• location of IAO_0000118 "location_of"@en

• location of editor note "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/"@en

• location of RO_0001900 RO_0001901

lumen of http://purl.obolibrary.org/obo/RO_0002571

Added

• lumen of in_subset ro-eco

• lumen of IAO_0000119 "GOC:cjm"

• lumen of IAO_0000117 "Chris Mungall"

luminal space of http://purl.obolibrary.org/obo/RO_0002572

Added

• luminal space of in_subset ro-eco

• luminal space of IAO_0000117 "Chris Mungall"

only in taxon http://purl.obolibrary.org/obo/RO_0002160

Added

• only in taxon IAO_0000117 "Chris Mungall"@en

• only in taxon IAO_0000119 20973947

• only in taxon editor note "The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g.

'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria"

• only in taxon example of usage "lactation SubClassOf 'only in taxon' some 'Mammalia'"

• only in taxon IAO_0000119 17921072

• only in taxon see also Taxon-constraints

• only in taxon IAO_0000114 IAO_0000125

otic ganglion http://purl.obolibrary.org/obo/UBERON_0003963

Removed

• otic ganglion SubClassOf innervates some parotid gland

Added

• otic ganglion SubClassOf extends_fibers_into some parotid gland

output of http://purl.obolibrary.org/obo/RO_0002353

Added

• output of IAO_0000117 "Chris Mungall"

• output of in_subset RO_0002259

• output of has_obo_namespace "external"

• output of in_subset ro-eco

overlaps http://purl.obolibrary.org/obo/RO_0002131

Added

• overlaps has_obo_namespace "external"

part_of http://purl.obolibrary.org/obo/BFO_0000050

Added

• part_of editor note "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/"@en

participates in http://purl.obolibrary.org/obo/RO_0000056

Added

• participates in has_obo_namespace "external"

preceded_by http://purl.obolibrary.org/obo/BFO_0000062

Added

• preceded_by has_obo_namespace "external"

precedes http://purl.obolibrary.org/obo/BFO_0000063

Added

• precedes has_obo_namespace "external"

present_in_taxon http://purl.obolibrary.org/obo/RO_0002175

Added

• present_in_taxon comment "The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology."

produced_by http://purl.obolibrary.org/obo/RO_0003001

Added

• produced_by in_subset ro-eco

• produced_by IAO_0000117 "Melissa Haendel"

• produced_by has_obo_namespace "external"

• produced_by IAO_0000114 IAO_0000125

produces http://purl.obolibrary.org/obo/RO_0003000

Added

• produces IAO_0000114 IAO_0000125

• produces 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."

• produces has_obo_namespace "external"

• produces in_subset ro-eco

• produces IAO_0000117 "Melissa Haendel"

simultaneous with http://purl.obolibrary.org/obo/RO_0002082

Added

• simultaneous with IAO_0000117 "David Osumi-Sutherland"

• simultaneous with in_subset ro-eco

• simultaneous with comment "t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2)"@en

skeleton of http://purl.obolibrary.org/obo/RO_0002576

Added

• skeleton of IAO_0000117 "Chris Mungall"

• skeleton of in_subset RO_0002259

starts http://purl.obolibrary.org/obo/RO_0002223

Added

• starts IAO_0000117 "Chris Mungall"

• starts IAO_0000119 "Allen"

• starts in_subset ro-eco

• starts IAO_0000114 IAO_0000125

starts with http://purl.obolibrary.org/obo/RO_0002224

Added

• starts with has_obo_namespace "external"

• starts with IAO_0000114 IAO_0000125

• starts with example of usage "Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor"

• starts with IAO_0000118 "started by"

• starts with in_subset ro-eco

• starts with IAO_0000117 "Chris Mungall"

supplies http://purl.obolibrary.org/obo/RO_0002178

Added

• supplies editor note "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"

• supplies IAO_0000119 20064205

surrounded by http://purl.obolibrary.org/obo/RO_0002219

Added

• surrounded by RO_0001900 RO_0001901

• surrounded by IAO_0000117 "Chris Mungall"

• surrounded by IAO_0000114 IAO_0000125

surrounds http://purl.obolibrary.org/obo/RO_0002221

Added

• surrounds RO_0001900 RO_0001901

• surrounds in_subset RO_0002259

• surrounds IAO_0000114 IAO_0000125

• surrounds IAO_0000117 "Chris Mungall"

transformation of http://purl.obolibrary.org/obo/RO_0002494

Added

• transformation of IAO_0000117 "Chris Mungall"

tributary_of http://purl.obolibrary.org/obo/RO_0002376

Added

• tributary_of in_subset ro-eco

• tributary_of curator notes "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)"^^anyURI

• tributary_of see also "http://en.wikipedia.org/wiki/Tributary"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• tributary_of IAO_0000114 IAO_0000428

• tributary_of IAO_0000118 "tributary channel of"

• tributary_of IAO_0000117 "Chris Mungall"

• tributary_of IAO_0000118 "drains into"

• tributary_of see also drainsTo

• tributary_of example of usage "inferior epigastric vein tributary_of external iliac vein"

• tributary_of IAO_0000119 "http://en.wikipedia.org/wiki/Tributary"

• tributary_of IAO_0000118 "drains to"

• tributary_of example of usage "Deschutes River tributary_of Columbia River"

• tributary_of IAO_0000119 "http://www.medindia.net/glossary/venous_tributary.htm"

[github-actions]

Here's a diff of your edit file (unreasoned)

Ontology comparison

Left

• Ontology IRI: http://purl.obolibrary.org/obo/uberon/core.owl
• Version IRI: None
• Loaded from: file:/work/src/ontology/../../master/src/ontology/uberon-edit.obo

Right

• Ontology IRI: http://purl.obolibrary.org/obo/uberon/core.owl
• Version IRI: None
• Loaded from: file:/work/src/ontology/uberon-edit.obo

Ontology imports

Ontology annotations

otic ganglion http://purl.obolibrary.org/obo/UBERON_0003963

Removed

• otic ganglion EquivalentTo cranial ganglion and (innervates some parotid gland) and (extends_fibers_into some glossopharyngeal nerve)

Added

• otic ganglion EquivalentTo cranial ganglion and (extends_fibers_into some glossopharyngeal nerve) and (extends_fibers_into some parotid gland)

[shawntanzk]

also why is the robot diff actions going crazy >.< lol

[shawntanzk]

Currently trying to build uberon fails at

make[1]: *** [uberon.Makefile:652: reports/taxon-constraint-check.txt] Error 1
make[1]: Leaving directory '/work/src/ontology'
make: *** [uberon.Makefile:1306: uberon] Error 2

Looking into taxon-constraint-check.txt.tmp

UNSAT: EV:0100358 EV:0100358
UNSAT: HBA:9371 HBA:9371
UNSAT: FMA:312393 FMA:312393
UNSAT: EMAPA:16914 EMAPA:16914
UNSAT: MA:0000054 MA:0000054
UNSAT: EMAPA:16917 EMAPA:16917
NUMBER_OF_UNSATISFIABLE_CLASSES: 6

On investigation, all these dbxref have 2 terms that are mapped to them, which I'm guessing isn't allowed if we are making equiv classes out of them?

[shawntanzk]

closing for #2624