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Merge pull request #663 from oborel/2023-01-04-release
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2023-01-04 release
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@shawntanzk
shawntanzk authored Jan 5, 2023
2 parents 4783aea + 7daa083 commit a9f5e11
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449 changes: 262 additions & 187 deletions ro-base.json
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44 changes: 36 additions & 8 deletions ro-base.obo
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@@ -1,5 +1,5 @@
format-version: 1.2
data-version: ro/releases/2022-10-26/ro-base.owl
data-version: ro/releases/2023-01-04/ro-base.owl
subsetdef: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension ""
subsetdef: http://purl.obolibrary.org/obo/valid_for_go_gp2term ""
subsetdef: http://purl.obolibrary.org/obo/valid_for_go_ontology ""
Expand Down Expand Up @@ -2059,7 +2059,7 @@ is_a: RO:0002385 ! has potential to developmentally contribute to
[Typedef]
id: RO:0002256
name: developmentally induced by
def: "t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor anatomical structure type T to T', where T' develops_from T" []
def: "t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T" []
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string
Expand All @@ -2069,8 +2069,8 @@ property_value: IAO:0000119 " Developmental Biology, Gilbert, 8th edition, figur
property_value: IAO:0000119 GO:0001759 xsd:string
property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205
property_value: IAO:0000232 "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]" xsd:string
domain: CARO:0000003
range: CARO:0000003
domain: CARO:0000006
range: CARO:0000006
is_a: RO:0002258 ! developmentally preceded by
inverse_of: RO:0002257 ! developmentally induces

Expand Down Expand Up @@ -2193,13 +2193,13 @@ is_a: RO:0002292 ! expresses
[Typedef]
id: RO:0002295
name: results in developmental progression of
def: "p results in the developmental progression of s iff p is a developmental process and s is an anatomical structure and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss)." []
def: "p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss)." []
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000116 "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: seeAlso Ontology:extensions
domain: GO:0008150
range: CARO:0000003
range: CARO:0000000
is_a: RO:0002324 ! developmentally related to

[Typedef]
Expand Down Expand Up @@ -3068,10 +3068,11 @@ is_a: RO:0002411 ! causally upstream of

[Typedef]
id: RO:0002413
name: directly provides input for
name: provides input for
def: "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c." []
property_value: IAO:0000116 "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "directly provides input for" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: IAO:0000589 "directly provides input for (process to process)" xsd:string
holds_over_chain: RO:0002402 RO:0002400
Expand All @@ -3084,7 +3085,7 @@ name: transitively provides input for
def: "transitive form of directly_provides_input_for" []
property_value: IAO:0000114 IAO:0000428
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000232 "This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'directly provides input for' (which may later be relabeled simply to 'provides input for')" xsd:string
property_value: IAO:0000232 "This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'." xsd:string
property_value: IAO:0000589 "transitively provides input for (process to process)" xsd:string
domain: BFO:0000015 ! process
range: BFO:0000015 ! process
Expand Down Expand Up @@ -5843,6 +5844,33 @@ name: myristoylated by
def: "inverse of myristoylates" []
property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-4423-4370

[Typedef]
id: RO:0018027
name: is agonist of
def: "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor activates some activity of the receptor" []
property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0003-4423-4370
property_value: IAO:0000112 "mibolerone (CHEBI:34849) is agonist of androgen receptor (PR:P10275)" xsd:string
property_value: seeAlso https://www.wikidata.org/wiki/Property:P3772
is_a: RO:0002450 ! directly positively regulates activity of

[Typedef]
id: RO:0018028
name: is inverse agonist of
def: "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor inhibits some activity of the receptor to below basal level" []
property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0003-4423-4370
property_value: IAO:0000112 "pimavanserin (CHEBI:133017) is inverse agonist of HTR2A (PR:P28223)" xsd:string
property_value: seeAlso https://www.wikidata.org/wiki/Property:P9275
is_a: RO:0002449 ! directly negatively regulates activity of

[Typedef]
id: RO:0018029
name: is antagonist of
def: "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor reduces some activity of the receptor to basal level" []
property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0003-4423-4370
property_value: IAO:0000112 "tretinoin (CHEBI:15367) is antagonist of Nuclear receptor ROR-beta (PR:Q92753)" xsd:string
property_value: seeAlso https://www.wikidata.org/wiki/Property:P3773
is_a: RO:0002449 ! directly negatively regulates activity of

[Typedef]
id: RO:0019000
name: regulates characteristic
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56 changes: 48 additions & 8 deletions ro-base.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,7 @@
xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#"
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/ro/ro-base.owl">
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/ro/releases/2022-10-26/ro-base.owl"/>
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/ro/releases/2023-01-04/ro-base.owl"/>
<dc:description xml:lang="en">The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies.</dc:description>
<dc:title xml:lang="en">OBO Relations Ontology</dc:title>
<terms:license rdf:resource="https://creativecommons.org/publicdomain/zero/1.0/"/>
Expand Down Expand Up @@ -4230,10 +4230,10 @@ If you need an axiom that says &apos;has_participant min 2 object&apos;, you sho
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002256">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002258"/>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002257"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/CARO_0000003"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/CARO_0000003"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/CARO_0000006"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/CARO_0000006"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115>t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor anatomical structure type T to T&apos;, where T&apos; develops_from T</obo:IAO_0000115>
<obo:IAO_0000115>t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T&apos;, where T&apos; develops_from T</obo:IAO_0000115>
<obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
<obo:IAO_0000117>David Osumi-Sutherland</obo:IAO_0000117>
<obo:IAO_0000117>Melissa Haendel</obo:IAO_0000117>
Expand Down Expand Up @@ -4429,9 +4429,9 @@ If you need an axiom that says &apos;has_participant min 2 object&apos;, you sho
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002295">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002324"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/GO_0008150"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/CARO_0000003"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/CARO_0000000"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115>p results in the developmental progression of s iff p is a developmental process and s is an anatomical structure and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss).</obo:IAO_0000115>
<obo:IAO_0000115>p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss).</obo:IAO_0000115>
<obo:IAO_0000116>This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint.</obo:IAO_0000116>
<obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
<rdfs:label xml:lang="en">results in developmental progression of</rdfs:label>
Expand Down Expand Up @@ -5787,9 +5787,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different
<obo:IAO_0000115>p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c.</obo:IAO_0000115>
<obo:IAO_0000116>This is currently called &apos;directly provides input for&apos; to be consistent with our terminology where we use &apos;direct&apos; whenever two occurrents succeed one another directly. We may relabel this simply &apos;provides input for&apos;, as directness is implicit</obo:IAO_0000116>
<obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
<obo:IAO_0000118>directly provides input for</obo:IAO_0000118>
<obo:IAO_0000119 rdf:resource="http://purl.obolibrary.org/obo/ro/docs/causal-relations"/>
<obo:IAO_0000589>directly provides input for (process to process)</obo:IAO_0000589>
<rdfs:label xml:lang="en">directly provides input for</rdfs:label>
<rdfs:label xml:lang="en">provides input for</rdfs:label>
</owl:ObjectProperty>


Expand All @@ -5804,7 +5805,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000428"/>
<obo:IAO_0000115>transitive form of directly_provides_input_for</obo:IAO_0000115>
<obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
<obo:IAO_0000232>This is a grouping relation that should probably not be used in annotation. Consider instead the child relation &apos;directly provides input for&apos; (which may later be relabeled simply to &apos;provides input for&apos;)</obo:IAO_0000232>
<obo:IAO_0000232>This is a grouping relation that should probably not be used in annotation. Consider instead the child relation &apos;provides input for&apos;.</obo:IAO_0000232>
<obo:IAO_0000589>transitively provides input for (process to process)</obo:IAO_0000589>
<rdfs:label xml:lang="en">transitively provides input for</rdfs:label>
</owl:ObjectProperty>
Expand Down Expand Up @@ -10251,6 +10252,45 @@ For example, protein A (transcription factor) indirectly increases by expression



<!-- http://purl.obolibrary.org/obo/RO_0018027 -->

<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0018027">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002450"/>
<obo:IAO_0000112>mibolerone (CHEBI:34849) is agonist of androgen receptor (PR:P10275)</obo:IAO_0000112>
<obo:IAO_0000115>a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor activates some activity of the receptor</obo:IAO_0000115>
<dc:creator rdf:resource="https://orcid.org/0000-0003-4423-4370"/>
<rdfs:label>is agonist of</rdfs:label>
<rdfs:seeAlso rdf:resource="https://www.wikidata.org/wiki/Property:P3772"/>
</owl:ObjectProperty>



<!-- http://purl.obolibrary.org/obo/RO_0018028 -->

<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0018028">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002449"/>
<obo:IAO_0000112>pimavanserin (CHEBI:133017) is inverse agonist of HTR2A (PR:P28223)</obo:IAO_0000112>
<obo:IAO_0000115>a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor inhibits some activity of the receptor to below basal level</obo:IAO_0000115>
<dc:creator rdf:resource="https://orcid.org/0000-0003-4423-4370"/>
<rdfs:label>is inverse agonist of</rdfs:label>
<rdfs:seeAlso rdf:resource="https://www.wikidata.org/wiki/Property:P9275"/>
</owl:ObjectProperty>



<!-- http://purl.obolibrary.org/obo/RO_0018029 -->

<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0018029">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002449"/>
<obo:IAO_0000112>tretinoin (CHEBI:15367) is antagonist of Nuclear receptor ROR-beta (PR:Q92753)</obo:IAO_0000112>
<obo:IAO_0000115>a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor reduces some activity of the receptor to basal level</obo:IAO_0000115>
<dc:creator rdf:resource="https://orcid.org/0000-0003-4423-4370"/>
<rdfs:label>is antagonist of</rdfs:label>
<rdfs:seeAlso rdf:resource="https://www.wikidata.org/wiki/Property:P3773"/>
</owl:ObjectProperty>



<!-- http://purl.obolibrary.org/obo/RO_0019000 -->

<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0019000">
Expand Down
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