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cmungall committed May 11, 2018
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25 changes: 14 additions & 11 deletions ro.json
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Expand Up @@ -1245,7 +1245,7 @@
"id" : "http://purl.obolibrary.org/obo/RO_0002263",
"meta" : {
"definition" : {
"val" : "c involved in regulation of p if c enables f and f causally upstream of p",
"val" : "c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes.",
"xrefs" : [ ]
},
"basicPropertyValues" : [ {
Expand Down Expand Up @@ -4555,9 +4555,6 @@
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
"val" : "Chris Mungall"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000114",
"val" : "http://purl.obolibrary.org/obo/IAO_0000125"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
"val" : "agent in"
Expand Down Expand Up @@ -4960,9 +4957,6 @@
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000119",
"val" : "http://www.ncbi.nlm.nih.gov/pubmed/21208450"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000114",
"val" : "http://purl.obolibrary.org/obo/IAO_0000125"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000424",
"val" : "RO_0000053 some (RO_0000054 only ?Y)"
Expand Down Expand Up @@ -5066,9 +5060,6 @@
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
"val" : "Chris Mungall"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000114",
"val" : "http://purl.obolibrary.org/obo/IAO_0000125"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000424",
"val" : "RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y))"
Expand Down Expand Up @@ -6798,6 +6789,10 @@
}, {
"id" : "http://purl.obolibrary.org/obo/RO_0002430",
"meta" : {
"definition" : {
"val" : "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p",
"xrefs" : [ ]
},
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
"val" : "Chris Mungall"
Expand Down Expand Up @@ -7021,6 +7016,10 @@
}, {
"id" : "http://purl.obolibrary.org/obo/RO_0002429",
"meta" : {
"definition" : {
"val" : "c involved in regulation of p if c is involved in some p' and p' positively regulates some p",
"xrefs" : [ ]
},
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/RO_0004049",
"val" : "http://purl.obolibrary.org/obo/RO_0002428"
Expand Down Expand Up @@ -13509,6 +13508,10 @@
"sub" : "http://purl.obolibrary.org/obo/RO_0000056",
"pred" : "inverseOf",
"obj" : "http://purl.obolibrary.org/obo/RO_0000057"
}, {
"sub" : "http://purl.obolibrary.org/obo/RO_0002331",
"pred" : "subPropertyOf",
"obj" : "http://purl.obolibrary.org/obo/RO_0002217"
}, {
"sub" : "http://purl.obolibrary.org/obo/RO_0002630",
"pred" : "subPropertyOf",
Expand Down Expand Up @@ -15822,7 +15825,7 @@
"pred" : "http://purl.org/dc/elements/1.1/title",
"val" : "OBO Relations Ontology"
} ],
"version" : "http://purl.obolibrary.org/obo/ro/releases/2018-03-27/ro.owl"
"version" : "http://purl.obolibrary.org/obo/ro/releases/2018-05-11/ro.owl"
},
"equivalentNodesSets" : [ ],
"logicalDefinitionAxioms" : [ ],
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12 changes: 6 additions & 6 deletions ro.obo
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22 changes: 11 additions & 11 deletions ro.owl
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Expand Up @@ -17,7 +17,7 @@
xmlns:dc="http://purl.org/dc/elements/1.1/"
xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#">
<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/ro.owl">
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/ro/releases/2018-03-27/ro.owl"/>
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/ro/releases/2018-05-11/ro.owl"/>
<owl:imports rdf:resource="http://purl.obolibrary.org/obo/ro/annotations.owl"/>
<owl:imports rdf:resource="http://purl.obolibrary.org/obo/ro/pato_import.owl"/>
<owl:imports rdf:resource="http://purl.obolibrary.org/obo/ro/temporal-intervals.owl"/>
Expand Down Expand Up @@ -2696,7 +2696,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.</obo:I
</owl:propertyChainAxiom>
<obo:IAO_0000112>mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)</obo:IAO_0000112>
<obo:IAO_0000112>osteoclast SubClassOf &apos;capable of&apos; some &apos;bone resorption&apos;</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115>A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. </obo:IAO_0000115>
<obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
<obo:IAO_0000118>has function realized in</obo:IAO_0000118>
Expand All @@ -2719,7 +2718,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.</obo:I
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002215"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000050"/>
</owl:propertyChainAxiom>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115>c stands in this relationship to p if and only if there exists some p&apos; such that c is capable_of p&apos;, and p&apos; is part_of p.</obo:IAO_0000115>
<obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
<obo:IAO_0000118>has function in</obo:IAO_0000118>
Expand All @@ -2743,7 +2741,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.</obo:I
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002217">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000056"/>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002218"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115>x actively participates in y if and only if x participates in y and x realizes some active role</obo:IAO_0000115>
<obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
<obo:IAO_0000118>agent in</obo:IAO_0000118>
Expand Down Expand Up @@ -3291,7 +3288,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.</obo:I
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002411"/>
</owl:propertyChainAxiom>
<obo:IAO_0000112>A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision.</obo:IAO_0000112>
<obo:IAO_0000115>c involved in regulation of p if c enables f and f causally upstream of p</obo:IAO_0000115>
<obo:IAO_0000115>c acts upstream of p if and only if c enables some f that is involved in p&apos; and p&apos; occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p&apos; are processes.</obo:IAO_0000115>
<rdfs:label>acts upstream of</rdfs:label>
<rdfs:seeAlso rdf:resource="http://wiki.geneontology.org/index.php/Acts_upstream_of"/>
</owl:ObjectProperty>
Expand Down Expand Up @@ -3836,6 +3833,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati
<!-- http://purl.obolibrary.org/obo/RO_0002331 -->

<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002331">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002217"/>
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002431"/>
<owl:propertyChainAxiom rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002327"/>
Expand Down Expand Up @@ -4808,6 +4806,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002331"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002213"/>
</owl:propertyChainAxiom>
<obo:IAO_0000115>c involved in regulation of p if c is involved in some p&apos; and p&apos; positively regulates some p</obo:IAO_0000115>
<obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
<obo:RO_0004049 rdf:resource="http://purl.obolibrary.org/obo/RO_0002428"/>
<rdfs:label>involved in positive regulation of</rdfs:label>
Expand All @@ -4827,6 +4826,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002331"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002212"/>
</owl:propertyChainAxiom>
<obo:IAO_0000115>c involved in regulation of p if c is involved in some p&apos; and p&apos; negatively regulates some p</obo:IAO_0000115>
<obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
<obo:RO_0004050 rdf:resource="http://purl.obolibrary.org/obo/RO_0002428"/>
<rdfs:label>involved in negative regulation of</rdfs:label>
Expand Down Expand Up @@ -9042,9 +9042,9 @@ e.g. if GP X enables ATPase coupled transporter activity&apos; and &apos;ATPase
<rdf:first>
<rdf:Description>
<rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#IndividualPropertyAtom"/>
<swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0002019"/>
<swrl:argument1 rdf:resource="urn:swrl#x"/>
<swrl:argument2 rdf:resource="urn:swrl#y"/>
<swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0002327"/>
<swrl:argument1 rdf:resource="urn:swrl#y"/>
<swrl:argument2 rdf:resource="urn:swrl#z"/>
</rdf:Description>
</rdf:first>
<rdf:rest>
Expand All @@ -9053,9 +9053,9 @@ e.g. if GP X enables ATPase coupled transporter activity&apos; and &apos;ATPase
<rdf:first>
<rdf:Description>
<rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#IndividualPropertyAtom"/>
<swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0002327"/>
<swrl:argument1 rdf:resource="urn:swrl#y"/>
<swrl:argument2 rdf:resource="urn:swrl#z"/>
<swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0002019"/>
<swrl:argument1 rdf:resource="urn:swrl#x"/>
<swrl:argument2 rdf:resource="urn:swrl#y"/>
</rdf:Description>
</rdf:first>
<rdf:rest rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>
Expand Down
2 changes: 1 addition & 1 deletion src/ontology/Makefile
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Expand Up @@ -46,7 +46,7 @@ validate-using-oort: ro-edit.owl
# DIFFS
# ========================================
ro-lastbuild.owl: ro-edit.owl
wget $(OBO)/ro.owl -O $@
wget --no-check-certificate $(OBO)/ro.owl -O $@

ro-diff.md: ro.owl ro-lastbuild.owl
owljs-diff -o $@ ro-lastbuild.owl $<
Expand Down
8 changes: 4 additions & 4 deletions subsets/ro-causal.obo
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Expand Up @@ -30,7 +30,6 @@ id: actively_participates_in
name: actively participates in
def: "x actively participates in y if and only if x participates in y and x realizes some active role" []
xref: RO:0002217
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "agent in" xsd:string
is_a: participates_in
Expand Down Expand Up @@ -69,7 +68,7 @@ is_a: molecularly_interacts_with ! molecularly interacts with
[Typedef]
id: acts_upstream_of
name: acts upstream of
def: "c involved in regulation of p if c enables f and f causally upstream of p" []
def: "c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes." []
xref: RO:0002263
property_value: IAO:0000112 "A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision." xsd:string
property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of
Expand Down Expand Up @@ -288,7 +287,6 @@ subset: ro-eco
xref: RO:0002215
property_value: IAO:0000112 "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" xsd:string
property_value: IAO:0000112 "osteoclast SubClassOf 'capable of' some 'bone resorption'" xsd:string
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "has function realized in" xsd:string
property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20123131
Expand Down Expand Up @@ -323,7 +321,6 @@ id: capable_of_part_of
name: capable of part of
def: "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." []
xref: RO:0002216
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "has function in" xsd:string
is_a: causal_agent_in_process ! causal agent in process
Expand Down Expand Up @@ -2390,11 +2387,13 @@ property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "actively involved in" xsd:string
property_value: IAO:0000118 "enables part of" xsd:string
property_value: seeAlso Involved:in
is_a: actively_participates_in ! actively participates in
is_a: involved_in_or_involved_in_regulation_of ! involved in or involved in regulation of

[Typedef]
id: involved_in_negative_regulation_of
name: involved in negative regulation of
def: "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" []
xref: RO:0002430
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: RO:0004050 RO:0002428
Expand All @@ -2414,6 +2413,7 @@ is_a: functionally_related_to ! functionally related to
[Typedef]
id: involved_in_positive_regulation_of
name: involved in positive regulation of
def: "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" []
xref: RO:0002429
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: RO:0004049 RO:0002428
Expand Down
8 changes: 4 additions & 4 deletions subsets/ro-causal.owl
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Expand Up @@ -1511,7 +1511,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.</obo:I
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
<obo:IAO_0000112>mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)</obo:IAO_0000112>
<obo:IAO_0000112>osteoclast SubClassOf &apos;capable of&apos; some &apos;bone resorption&apos;</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115>A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. </obo:IAO_0000115>
<obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
<obo:IAO_0000118>has function realized in</obo:IAO_0000118>
Expand All @@ -1532,7 +1531,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.</obo:I
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002216">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002328"/>
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002500"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115>c stands in this relationship to p if and only if there exists some p&apos; such that c is capable_of p&apos;, and p&apos; is part_of p.</obo:IAO_0000115>
<obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
<obo:IAO_0000118>has function in</obo:IAO_0000118>
Expand All @@ -1549,7 +1547,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.</obo:I
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002217">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000056"/>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002218"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115>x actively participates in y if and only if x participates in y and x realizes some active role</obo:IAO_0000115>
<obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
<obo:IAO_0000118>agent in</obo:IAO_0000118>
Expand Down Expand Up @@ -2081,7 +2078,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.</obo:I
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002263">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002264"/>
<obo:IAO_0000112>A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision.</obo:IAO_0000112>
<obo:IAO_0000115>c involved in regulation of p if c enables f and f causally upstream of p</obo:IAO_0000115>
<obo:IAO_0000115>c acts upstream of p if and only if c enables some f that is involved in p&apos; and p&apos; occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p&apos; are processes.</obo:IAO_0000115>
<oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RO:0002263</oboInOwl:hasDbXref>
<oboInOwl:shorthand rdf:datatype="http://www.w3.org/2001/XMLSchema#string">acts_upstream_of</oboInOwl:shorthand>
<rdfs:label>acts upstream of</rdfs:label>
Expand Down Expand Up @@ -2538,6 +2535,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati
<!-- http://purl.obolibrary.org/obo/RO_0002331 -->

<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002331">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002217"/>
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002431"/>
<obo:IAO_0000115>c involved_in p if and only if c enables some process p&apos;, and p&apos; is part of p</obo:IAO_0000115>
<obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
Expand Down Expand Up @@ -3450,6 +3448,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different

<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002429">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002428"/>
<obo:IAO_0000115>c involved in regulation of p if c is involved in some p&apos; and p&apos; positively regulates some p</obo:IAO_0000115>
<obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
<obo:RO_0004049 rdf:resource="http://purl.obolibrary.org/obo/RO_0002428"/>
<oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RO:0002429</oboInOwl:hasDbXref>
Expand All @@ -3463,6 +3462,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different

<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002430">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002428"/>
<obo:IAO_0000115>c involved in regulation of p if c is involved in some p&apos; and p&apos; negatively regulates some p</obo:IAO_0000115>
<obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
<obo:RO_0004050 rdf:resource="http://purl.obolibrary.org/obo/RO_0002428"/>
<oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RO:0002430</oboInOwl:hasDbXref>
Expand Down
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