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Merge pull request #435 from oborel/release-2021-03-08
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RO Release March 2021
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matentzn committed Mar 8, 2021
2 parents 3164dc1 + 2d4b430 commit aa1c398
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247 changes: 138 additions & 109 deletions ro-base.json
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29 changes: 22 additions & 7 deletions ro-base.obo
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
format-version: 1.2
data-version: ro/releases/2020-12-18/ro-base.owl
data-version: ro/releases/2021-03-08/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 @@ -625,6 +625,7 @@ is_a: RO:0003302 ! causes or contributes to condition
id: RO:0001025
name: located in
def: "a relation between two independent continuants, the target and the location, in which the target is entirely within the location" []
subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term
property_value: http://purl.org/dc/elements/1.1/source http://www.obofoundry.org/ro/#OBO_REL:located_in xsd:string
property_value: IAO:0000111 "located in" xsd:string
property_value: IAO:0000112 "my brain is located in my head" xsd:string
Expand Down Expand Up @@ -1626,7 +1627,6 @@ id: RO:0002211
name: regulates
def: "process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2." []
subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension
subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term
subset: http://purl.obolibrary.org/obo/valid_for_go_ontology
subset: http://purl.obolibrary.org/obo/valid_for_gocam
property_value: IAO:0000114 IAO:0000125
Expand All @@ -1653,7 +1653,6 @@ id: RO:0002212
name: negatively regulates
def: "Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2." []
subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension
subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term
subset: http://purl.obolibrary.org/obo/valid_for_go_ontology
subset: http://purl.obolibrary.org/obo/valid_for_gocam
property_value: IAO:0000117 "Chris Mungall" xsd:string
Expand All @@ -1670,7 +1669,6 @@ id: RO:0002213
name: positively regulates
def: "Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2." []
subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension
subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term
subset: http://purl.obolibrary.org/obo/valid_for_go_ontology
subset: http://purl.obolibrary.org/obo/valid_for_gocam
property_value: IAO:0000117 "Chris Mungall" xsd:string
Expand Down Expand Up @@ -2271,7 +2269,6 @@ property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "regulates localization of" xsd:string
is_a: RO:0002337 ! related via localization to
is_a: RO:0040036 ! has anatomical participant
transitive_over: BFO:0000051 ! has part

[Typedef]
id: RO:0002314
Expand Down Expand Up @@ -2331,6 +2328,7 @@ property_value: IAO:0000232 "Do not use this relation directly. It is ended as a
id: RO:0002325
name: colocalizes with
def: "a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]." []
subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term
property_value: http://purl.org/dc/terms/creator "Gene Ontology Consortium" xsd:string
property_value: IAO:0000112 "Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826)" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
Expand All @@ -2343,6 +2341,7 @@ is_a: RO:0002323 ! mereotopologically related to
[Typedef]
id: RO:0002326
name: contributes to
subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term
property_value: IAO:0000112 "ATP citrate lyase (ACL) in Arabidopsis: it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity." xsd:string
property_value: IAO:0000112 "eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to \"ribosome binding\". And all three are part_of an eIF2 complex" xsd:string
property_value: IAO:0000112 "Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity." xsd:string
Expand Down Expand Up @@ -2496,7 +2495,6 @@ def: "Holds between p and c when p is a transportation or localization process a
subset: http://purl.obolibrary.org/obo/valid_for_go_ontology
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: RO:0002020 ! transports
transitive_over: BFO:0000051 ! has part

[Typedef]
id: RO:0002341
Expand Down Expand Up @@ -2536,7 +2534,6 @@ def: "Holds between p and c when p is a transportation or localization process a
subset: http://purl.obolibrary.org/obo/valid_for_go_ontology
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: RO:0002020 ! transports
transitive_over: BFO:0000051 ! has part

[Typedef]
id: RO:0002348
Expand Down Expand Up @@ -4564,6 +4561,7 @@ is_a: RO:0002635 ! has endoparasite
id: RO:0002640
name: intracellular endoparasite of
def: "A sub-relation of endoparasite-of in which the parasite inhabits host cells." []
property_value: IAO:0000119 Communal:roosting
property_value: IAO:0000119 "Types"
is_a: RO:0002634 ! endoparasite of
inverse_of: RO:0002641 ! has intracellular endoparasite
Expand All @@ -4575,6 +4573,13 @@ def: "inverse of intracellular endoparasite of" []
subset: RO:0002259
is_a: RO:0002635 ! has endoparasite

[Typedef]
id: RO:0002801
name: co-roosts with
def: "Two or more individuals sharing the same roost site (cave, mine, tree or tree hollow, animal burrow, leaf tent, rock crack, space in man-made structure, etc.). Individuals that are sharing a communal roost may be said to be co-roosting. The roost may be either a day roost where the individuals rest during daytime hours, or a night roost where individuals roost to feed, groom, or rest in between flights and/or foraging bouts. Communal roosting as thus defined is an umbrella term within which different specialized types -- which are not mutually exclusive -- may be recognized based on taxonomy and the temporal and spatial relationships of the individuals that are co-roosting." []
is_symmetric: true
is_a: RO:0008506 ! ecologically co-occurs with

[Typedef]
id: RO:0003000
name: produces
Expand Down Expand Up @@ -5408,6 +5413,16 @@ is_a: RO:0040036 ! has anatomical participant
created_by: pg
creation_date: 2020-08-27T08:13:59Z

[Typedef]
id: RO:0012008
name: results in fusion of
subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension
subset: http://purl.obolibrary.org/obo/valid_for_go_ontology
subset: http://purl.obolibrary.org/obo/valid_for_gocam
is_a: RO:0002592 ! results in organization of
created_by: pg
creation_date: 2021-02-26T07:28:29Z

[Typedef]
id: RO:0013001
name: has synaptic IO in
Expand Down
46 changes: 30 additions & 16 deletions ro-base.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,7 @@
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/2020-12-18/ro-base.owl"/>
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/ro/releases/2021-03-08/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 @@ -1642,6 +1642,7 @@ range: spatial region or site (immaterial continuant)
<obo:IAO_0000118 xml:lang="en">located_in</obo:IAO_0000118>
<obo:RO_0001900 rdf:resource="http://purl.obolibrary.org/obo/RO_0001901"/>
<dc:source>http://www.obofoundry.org/ro/#OBO_REL:located_in</dc:source>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_go_gp2term"/>
<rdfs:label xml:lang="en">located in</rdfs:label>
</owl:ObjectProperty>
<owl:Axiom>
Expand Down Expand Up @@ -3406,7 +3407,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.</obo:I
<obo:IAO_0000589>regulates (processual)</obo:IAO_0000589>
<obo:IAO_0000600 rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">false</obo:IAO_0000600>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_go_annotation_extension"/>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_go_gp2term"/>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_go_ontology"/>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_gocam"/>
<rdfs:label xml:lang="en">regulates</rdfs:label>
Expand All @@ -3430,7 +3430,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.</obo:I
<obo:IAO_0000589>negatively regulates (process to process)</obo:IAO_0000589>
<obo:RO_0004050 rdf:resource="http://purl.obolibrary.org/obo/RO_0002211"/>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_go_annotation_extension"/>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_go_gp2term"/>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_go_ontology"/>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_gocam"/>
<rdfs:label xml:lang="en">negatively regulates</rdfs:label>
Expand Down Expand Up @@ -3459,7 +3458,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.</obo:I
<obo:IAO_0000589>positively regulates (process to process)</obo:IAO_0000589>
<obo:RO_0004049 rdf:resource="http://purl.obolibrary.org/obo/RO_0002211"/>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_go_annotation_extension"/>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_go_gp2term"/>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_go_ontology"/>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_gocam"/>
<rdfs:label xml:lang="en">positively regulates</rdfs:label>
Expand Down Expand Up @@ -4451,10 +4449,6 @@ where
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002313">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002337"/>
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0040036"/>
<owl:propertyChainAxiom rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002313"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000051"/>
</owl:propertyChainAxiom>
<obo:IAO_0000115>Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c.</obo:IAO_0000115>
<obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
<obo:IAO_0000118>regulates localization of</obo:IAO_0000118>
Expand Down Expand Up @@ -4590,6 +4584,7 @@ where
<obo:IAO_0000119>http://www.geneontology.org/GO.annotation.conventions.shtml#colocalizes_with</obo:IAO_0000119>
<obo:IAO_0000232>In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO]</obo:IAO_0000232>
<terms:creator>Gene Ontology Consortium</terms:creator>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_go_gp2term"/>
<rdfs:label xml:lang="en">colocalizes with</rdfs:label>
</owl:ObjectProperty>

Expand Down Expand Up @@ -4617,6 +4612,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati
<obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
<obo:IAO_0000119>http://www.geneontology.org/GO.annotation.conventions.shtml#contributes_to</obo:IAO_0000119>
<obo:IAO_0000232>In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. </obo:IAO_0000232>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_go_gp2term"/>
<rdfs:label xml:lang="en">contributes to</rdfs:label>
</owl:ObjectProperty>

Expand Down Expand Up @@ -4844,10 +4840,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati

<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002340">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002020"/>
<owl:propertyChainAxiom rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002340"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000051"/>
</owl:propertyChainAxiom>
<obo:IAO_0000115>Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s.</obo:IAO_0000115>
<obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_go_ontology"/>
Expand Down Expand Up @@ -4907,10 +4899,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati

<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002345">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002020"/>
<owl:propertyChainAxiom rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002345"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000051"/>
</owl:propertyChainAxiom>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the end location of c is part of the region that surrounds s.</obo:IAO_0000115>
<obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_go_ontology"/>
Expand Down Expand Up @@ -8165,6 +8153,7 @@ the a supports either the existence of b, or the truth value of b.</obo:IAO_0000
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002634"/>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002641"/>
<obo:IAO_0000115>A sub-relation of endoparasite-of in which the parasite inhabits host cells.</obo:IAO_0000115>
<obo:IAO_0000119 rdf:resource="https://en.wikipedia.org/wiki/Communal_roosting"/>
<obo:IAO_0000119 rdf:resource="https://en.wikipedia.org/wiki/Parasitism#Types"/>
<rdfs:label>intracellular endoparasite of</rdfs:label>
</owl:ObjectProperty>
Expand All @@ -8182,6 +8171,17 @@ the a supports either the existence of b, or the truth value of b.</obo:IAO_0000



<!-- http://purl.obolibrary.org/obo/RO_0002801 -->

<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002801">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0008506"/>
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#SymmetricProperty"/>
<obo:IAO_0000115 xml:lang="en">Two or more individuals sharing the same roost site (cave, mine, tree or tree hollow, animal burrow, leaf tent, rock crack, space in man-made structure, etc.). Individuals that are sharing a communal roost may be said to be co-roosting. The roost may be either a day roost where the individuals rest during daytime hours, or a night roost where individuals roost to feed, groom, or rest in between flights and/or foraging bouts. Communal roosting as thus defined is an umbrella term within which different specialized types -- which are not mutually exclusive -- may be recognized based on taxonomy and the temporal and spatial relationships of the individuals that are co-roosting.</obo:IAO_0000115>
<rdfs:label xml:lang="en">co-roosts with</rdfs:label>
</owl:ObjectProperty>



<!-- http://purl.obolibrary.org/obo/RO_0003000 -->

<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0003000">
Expand Down Expand Up @@ -9507,6 +9507,20 @@ For example, protein A (transcription factor) indirectly increases by expression



<!-- http://purl.obolibrary.org/obo/RO_0012008 -->

<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0012008">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002592"/>
<oboInOwl:created_by rdf:datatype="http://www.w3.org/2001/XMLSchema#string">pg</oboInOwl:created_by>
<oboInOwl:creation_date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2021-02-26T07:28:29Z</oboInOwl:creation_date>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_go_annotation_extension"/>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_go_ontology"/>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_gocam"/>
<rdfs:label xml:lang="en">results in fusion of</rdfs:label>
</owl:ObjectProperty>



<!-- http://purl.obolibrary.org/obo/RO_0013001 -->

<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0013001">
Expand Down
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