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domain-range constrs
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@cmungall
cmungall committed Sep 26, 2018
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41 changes: 28 additions & 13 deletions src/ontology/ro-edit.owl
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Expand Up @@ -1889,7 +1889,7 @@ AnnotationAssertion(rdfs:comment obo:RO_0002162 "Connects a biological entity to
AnnotationAssertion(rdfs:label obo:RO_0002162 "in taxon"^^xsd:string)
AnnotationAssertion(rdfs:seeAlso obo:RO_0002162 <https://github.com/obophenotype/uberon/wiki/Taxon-constraints>)
SubObjectPropertyOf(obo:RO_0002162 obo:RO_0002320)
ObjectPropertyRange(obo:RO_0002162 obo:BFO_0000004)
ObjectPropertyRange(obo:RO_0002162 obo:CARO_0001010)

# Object Property: obo:RO_0002163 (spatially disjoint from)

Expand Down Expand Up @@ -1934,11 +1934,12 @@ ObjectPropertyRange(obo:RO_0002176 ObjectSomeValuesFrom(obo:BFO_0000050 obo:RO_0
# Object Property: obo:RO_0002177 (attached to part of)

AnnotationAssertion(obo:IAO_0000115 obo:RO_0002177 "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b.")
AnnotationAssertion(obo:IAO_0000589 obo:RO_0002177 "attached to part of (anatomical structure to anatomical structure)")
AnnotationAssertion(rdfs:label obo:RO_0002177 "attached to part of"@en)
SubObjectPropertyOf(obo:RO_0002177 obo:RO_0002323)
SubObjectPropertyOf(obo:RO_0002177 obo:RO_0002567)
ObjectPropertyDomain(obo:RO_0002177 obo:BFO_0000040)
ObjectPropertyRange(obo:RO_0002177 obo:BFO_0000040)
ObjectPropertyDomain(obo:RO_0002177 obo:CARO_0000003)
ObjectPropertyRange(obo:RO_0002177 obo:CARO_0000003)

# Object Property: obo:RO_0002178 (supplies)

Expand Down Expand Up @@ -2055,7 +2056,7 @@ AnnotationAssertion(rdfs:label obo:RO_0002206 "expressed in"@en)
SubObjectPropertyOf(obo:RO_0002206 obo:RO_0002330)
InverseObjectProperties(obo:RO_0002206 obo:RO_0002292)
ObjectPropertyDomain(obo:RO_0002206 obo:BFO_0000002)
ObjectPropertyRange(obo:RO_0002206 obo:BFO_0000004)
ObjectPropertyRange(obo:RO_0002206 obo:CARO_0000006)

# Object Property: obo:RO_0002207 (directly develops from)

Expand Down Expand Up @@ -2177,6 +2178,7 @@ AnnotationAssertion(obo:IAO_0000117 obo:RO_0002216 "Chris Mungall")
AnnotationAssertion(obo:IAO_0000118 obo:RO_0002216 "has function in")
AnnotationAssertion(obo:IAO_0000424 obo:RO_0002216 "RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y))")
AnnotationAssertion(rdfs:label obo:RO_0002216 "capable of part of"@en)
AnnotationAssertion(rdfs:seeAlso obo:RO_0002216 <https://github.com/oborel/obo-relations/wiki/ROGuide#defining-property-chains-involving-reflexivity>)
SubObjectPropertyOf(obo:RO_0002216 obo:RO_0002328)
SubObjectPropertyOf(obo:RO_0002216 obo:RO_0002500)

Expand Down Expand Up @@ -2682,7 +2684,7 @@ AnnotationAssertion(oboInOwl:inSubset obo:RO_0002303 subsets:ro-eco)
AnnotationAssertion(rdfs:comment obo:RO_0002303 "A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to exist and grow in y.")
AnnotationAssertion(rdfs:label obo:RO_0002303 "has habitat"@en)
SubObjectPropertyOf(obo:RO_0002303 obo:RO_0002321)
ObjectPropertyDomain(obo:RO_0002303 obo:CARO_0000006)
ObjectPropertyDomain(obo:RO_0002303 obo:CARO_0001010)
ObjectPropertyRange(obo:RO_0002303 obo:ENVO_01000254)

# Object Property: obo:RO_0002304 (causally upstream of, positive effect)
Expand Down Expand Up @@ -2737,6 +2739,7 @@ AnnotationAssertion(obo:IAO_0000117 obo:RO_0002314 "Chris Mungall")
AnnotationAssertion(obo:IAO_0000119 obo:RO_0002314 <http://www.ncbi.nlm.nih.gov/pubmed/20064205>)
AnnotationAssertion(obo:RO_0001900 obo:RO_0002314 obo:RO_0001901)
AnnotationAssertion(rdfs:label obo:RO_0002314 "inheres in part of"@en)
AnnotationAssertion(rdfs:seeAlso obo:RO_0002314 <https://github.com/oborel/obo-relations/wiki/ROGuide#defining-property-chains-involving-reflexivity>)
SubObjectPropertyOf(obo:RO_0002314 obo:RO_0002502)

# Object Property: obo:RO_0002315 (results in acquisition of features of)
Expand Down Expand Up @@ -2775,6 +2778,7 @@ AnnotationAssertion(obo:IAO_0000118 obo:RO_0002322 "adapted for")
AnnotationAssertion(oboInOwl:inSubset obo:RO_0002322 subsets:ro-eco)
AnnotationAssertion(rdfs:label obo:RO_0002322 "confers advantage in"@en)
SubObjectPropertyOf(obo:RO_0002322 obo:RO_0002321)
ObjectPropertyRange(obo:RO_0002322 obo:ENVO_01000254)

# Object Property: obo:RO_0002323 (mereotopologically related to)

Expand Down Expand Up @@ -2844,6 +2848,7 @@ InverseObjectProperties(obo:RO_0002327 obo:RO_0002333)

# Object Property: obo:RO_0002328 (functionally related to)

AnnotationAssertion(obo:IAO_0000115 obo:RO_0002328 "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.")
AnnotationAssertion(obo:IAO_0000117 obo:RO_0002328 "Chris Mungall")
AnnotationAssertion(obo:IAO_0000232 obo:RO_0002328 "This is a grouping relation that collects relations used for the purpose of connecting structure and function")
AnnotationAssertion(rdfs:label obo:RO_0002328 "functionally related to"@en)
Expand Down Expand Up @@ -3066,6 +3071,7 @@ SubObjectPropertyOf(obo:RO_0002360 obo:RO_0002131)

AnnotationAssertion(obo:IAO_0000115 obo:RO_0002371 "a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a")
AnnotationAssertion(obo:IAO_0000117 obo:RO_0002371 "Chris Mungall")
AnnotationAssertion(obo:IAO_0000589 obo:RO_0002371 "attached to (anatomical structure to anatomical structure)")
AnnotationAssertion(oboInOwl:inSubset obo:RO_0002371 subsets:ro-eco)
AnnotationAssertion(rdfs:label obo:RO_0002371 "attached to"@en)
SubObjectPropertyOf(obo:RO_0002371 obo:RO_0002170)
Expand All @@ -3081,6 +3087,7 @@ AnnotationAssertion(rdfs:label obo:RO_0002372 "has muscle origin"@en)
AnnotationAssertion(rdfs:seeAlso obo:RO_0002372 <http://dbpedia.org/property/origin>)
SubObjectPropertyOf(obo:RO_0002372 obo:RO_0002371)
SubObjectPropertyOf(obo:RO_0002372 obo:RO_0002567)
ObjectPropertyDomain(Annotation(rdfs:comment "We need to import uberon muscle to create a stricter domain constraint") obo:RO_0002372 obo:CARO_0000003)

# Object Property: obo:RO_0002373 (has muscle insertion)

Expand All @@ -3091,18 +3098,20 @@ AnnotationAssertion(rdfs:label obo:RO_0002373 "has muscle insertion"@en)
AnnotationAssertion(rdfs:seeAlso obo:RO_0002373 <http://dbpedia.org/property/insertion>)
SubObjectPropertyOf(obo:RO_0002373 obo:RO_0002371)
SubObjectPropertyOf(obo:RO_0002373 obo:RO_0002567)
ObjectPropertyDomain(Annotation(obo:IAO_0000116 "We need to import uberon muscle into RO to use as a stricter domain constraint") obo:RO_0002373 obo:CARO_0000003)

# Object Property: obo:RO_0002374 (has fused element)
# Object Property: obo:RO_0002374 (derived from ancestral fusion of)

AnnotationAssertion(obo:IAO_0000112 obo:RO_0002374 "false"^^xsd:boolean)
AnnotationAssertion(obo:IAO_0000114 obo:RO_0002374 obo:IAO_0000428)
AnnotationAssertion(obo:IAO_0000115 obo:RO_0002374 "x has_fused_element y iff: there exists some z : x has_part z, z homologous_to y, and y is a distinct element, the boundary between x and z is largely fiat"@en)
AnnotationAssertion(obo:IAO_0000117 obo:RO_0002374 "Chris Mungall")
AnnotationAssertion(obo:IAO_0000117 obo:RO_0002374 "Chris Mungall"@en)
AnnotationAssertion(obo:IAO_0000119 obo:RO_0002374 <http://www.ncbi.nlm.nih.gov/pubmed/22293552>)
AnnotationAssertion(oboInOwl:hasBroadSynonym obo:RO_0002374 "has fused element")
AnnotationAssertion(rdfs:comment obo:RO_0002374 "A has_fused_element B does not imply that A has_part some B: rather than A has_part some B', where B' that has some evolutionary relationship to B."@en)
AnnotationAssertion(rdfs:label obo:RO_0002374 "has fused element"@en)
SubObjectPropertyOf(obo:RO_0002374 obo:RO_0002320)
AnnotationAssertion(rdfs:label obo:RO_0002374 "derived from ancestral fusion of"@en)
SubObjectPropertyOf(obo:RO_0002374 obo:RO_0002156)

# Object Property: obo:RO_0002375 (in branching relationship with)

Expand Down Expand Up @@ -3492,6 +3501,7 @@ SubObjectPropertyOf(obo:RO_0002430 obo:RO_0002428)
# Object Property: obo:RO_0002431 (involved in or involved in regulation of)

AnnotationAssertion(obo:IAO_0000115 obo:RO_0002431 "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p")
AnnotationAssertion(obo:IAO_0000116 obo:RO_0002431 "OWL does not allow defining object properties via a Union")
AnnotationAssertion(obo:IAO_0000117 obo:RO_0002431 "Chris Mungall")
AnnotationAssertion(obo:IAO_0000118 obo:RO_0002431 "involved in or reguates")
AnnotationAssertion(rdfs:label obo:RO_0002431 "involved in or involved in regulation of")
Expand Down Expand Up @@ -4520,6 +4530,8 @@ AnnotationAssertion(obo:IAO_0000117 obo:RO_0002567 "Chris Mungall")
AnnotationAssertion(obo:IAO_0000232 obo:RO_0002567 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes.")
AnnotationAssertion(rdfs:label obo:RO_0002567 "biomechanically related to")
SubObjectPropertyOf(obo:RO_0002567 obo:RO_0002328)
ObjectPropertyDomain(obo:RO_0002567 obo:CARO_0000003)
ObjectPropertyRange(obo:RO_0002567 obo:CARO_0000003)

# Object Property: obo:RO_0002568 (has muscle antagonist)

Expand Down Expand Up @@ -4578,6 +4590,7 @@ AnnotationAssertion(obo:IAO_0000232 obo:RO_0002573 "This relation is intended to
AnnotationAssertion(oboInOwl:inSubset obo:RO_0002573 subsets:ro-eco)
AnnotationAssertion(rdfs:label obo:RO_0002573 "has modifier")
ObjectPropertyDomain(obo:RO_0002573 obo:BFO_0000020)
ObjectPropertyRange(obo:RO_0002573 obo:BFO_0000020)

# Object Property: obo:RO_0002574 (participates in a biotic-biotic interaction with)

Expand All @@ -4586,6 +4599,8 @@ AnnotationAssertion(oboInOwl:inSubset obo:RO_0002574 subsets:ro-eco)
AnnotationAssertion(rdfs:label obo:RO_0002574 "participates in a biotic-biotic interaction with")
AnnotationAssertion(rdfs:seeAlso obo:RO_0002574 <http://dx.doi.org/10.1016/j.ecoinf.2014.08.005>)
SubObjectPropertyOf(obo:RO_0002574 obo:RO_0002437)
ObjectPropertyDomain(obo:RO_0002574 obo:CARO_0001010)
ObjectPropertyRange(obo:RO_0002574 obo:CARO_0001010)

# Object Property: obo:RO_0002576 (skeleton of)

Expand Down Expand Up @@ -5405,13 +5420,17 @@ SubObjectPropertyOf(obo:RO_0008504 obo:RO_0002445)
AnnotationAssertion(obo:IAO_0000115 obo:RO_0008505 "An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism.")
AnnotationAssertion(rdfs:label obo:RO_0008505 "creates habitat for")
SubObjectPropertyOf(obo:RO_0008505 obo:RO_0002321)
ObjectPropertyDomain(obo:RO_0008505 obo:CARO_0001010)
ObjectPropertyRange(obo:RO_0008505 obo:CARO_0001010)

# Object Property: obo:RO_0008506 (ecologically co-occurs with)

AnnotationAssertion(obo:IAO_0000115 obo:RO_0008506 "An interaction relationship describing organisms that often occur together at the same time and space or in the same environment.")
AnnotationAssertion(rdfs:label obo:RO_0008506 "ecologically co-occurs with")
SubObjectPropertyOf(obo:RO_0008506 obo:RO_0002321)
SymmetricObjectProperty(obo:RO_0008506)
ObjectPropertyDomain(obo:RO_0008506 obo:CARO_0001010)
ObjectPropertyRange(obo:RO_0008506 obo:CARO_0001010)

# Object Property: obo:RO_0008507 (lays eggs on)

Expand Down Expand Up @@ -5551,10 +5570,6 @@ SubClassOf(obo:BFO_0000002 ObjectAllValuesFrom(obo:RO_0002214 obo:BFO_0000002))

SubClassOf(obo:BFO_0000015 ObjectAllValuesFrom(obo:RO_0002214 obo:BFO_0000015))

# Class: obo:CARO_0001010 (organism or virus or viroid)

AnnotationAssertion(rdfs:label obo:CARO_0001010 "organism or virus or viroid"^^xsd:string)

# Class: obo:GO_0004842 (ubiquitin-protein ligase activity)

SubClassOf(obo:GO_0004842 ObjectHasSelf(obo:RO_0002482))
Expand Down Expand Up @@ -5768,7 +5783,7 @@ DLSafeRule(Annotation(rdfs:comment "This rule is dubious: added as a quick fix f
DLSafeRule(Annotation(rdfs:comment "If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.") Annotation(rdfs:label "inferring direct reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom(obo:RO_0002352 Variable(<urn:swrl#B>) Variable(<urn:swrl#C>)) ObjectPropertyAtom(obo:RO_0002333 Variable(<urn:swrl#A>) Variable(<urn:swrl#B>)) ObjectPropertyAtom(obo:RO_0002013 Variable(<urn:swrl#D>) Variable(<urn:swrl#C>)))Head(ObjectPropertyAtom(obo:RO_0002578 Variable(<urn:swrl#A>) Variable(<urn:swrl#D>))))
DLSafeRule(Annotation(rdfs:label "inferring direct neg reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom(obo:RO_0002352 Variable(<urn:swrl#B>) Variable(<urn:swrl#C>)) ObjectPropertyAtom(obo:RO_0002333 Variable(<urn:swrl#A>) Variable(<urn:swrl#B>)) ObjectPropertyAtom(obo:RO_0002014 Variable(<urn:swrl#D>) Variable(<urn:swrl#C>)))Head(ObjectPropertyAtom(obo:RO_0002630 Variable(<urn:swrl#A>) Variable(<urn:swrl#D>))))
DLSafeRule(Annotation(rdfs:label "inferring direct positive reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom(obo:RO_0002352 Variable(<urn:swrl#B>) Variable(<urn:swrl#C>)) ObjectPropertyAtom(obo:RO_0002333 Variable(<urn:swrl#A>) Variable(<urn:swrl#B>)) ObjectPropertyAtom(obo:RO_0002015 Variable(<urn:swrl#D>) Variable(<urn:swrl#C>)))Head(ObjectPropertyAtom(obo:RO_0002629 Variable(<urn:swrl#A>) Variable(<urn:swrl#D>))))
DLSafeRule(Annotation(rdfs:label "From has_ligand to ligand activity") Body(ObjectPropertyAtom(obo:RO_0002327 Variable(<urn:swrl#y>) Variable(<urn:swrl#z>)) ObjectPropertyAtom(obo:RO_0002019 Variable(<urn:swrl#x>) Variable(<urn:swrl#y>)))Head(ClassAtom(obo:GO_0048018 Variable(<urn:swrl#z>)) ObjectPropertyAtom(obo:RO_0002578 Variable(<urn:swrl#z>) Variable(<urn:swrl#x>))))
DLSafeRule(Annotation(rdfs:label "From has_ligand to ligand activity") Body(ObjectPropertyAtom(obo:RO_0002019 Variable(<urn:swrl#x>) Variable(<urn:swrl#y>)) ObjectPropertyAtom(obo:RO_0002327 Variable(<urn:swrl#y>) Variable(<urn:swrl#z>)))Head(ClassAtom(obo:GO_0048018 Variable(<urn:swrl#z>)) ObjectPropertyAtom(obo:RO_0002578 Variable(<urn:swrl#z>) Variable(<urn:swrl#x>))))
DLSafeRule(Annotation(rdfs:label "effector input is compound function input") Body(ObjectPropertyAtom(obo:RO_0002233 Variable(<urn:swrl#eff>) Variable(<urn:swrl#in>)) ObjectPropertyAtom(obo:RO_0002025 Variable(<urn:swrl#mf>) Variable(<urn:swrl#eff>)))Head(ObjectPropertyAtom(obo:RO_0002233 Variable(<urn:swrl#mf>) Variable(<urn:swrl#in>))))
DLSafeRule(Annotation(rdfs:label "Input of effector is input of its parent MF") Body(ObjectPropertyAtom(obo:RO_0002233 Variable(<urn:swrl#mf>) Variable(<urn:swrl#in>)) ObjectPropertyAtom(obo:RO_0002025 Variable(<urn:swrl#mf>) Variable(<urn:swrl#eff>)))Head(ObjectPropertyAtom(obo:RO_0002233 Variable(<urn:swrl#eff>) Variable(<urn:swrl#in>))))
DLSafeRule(Annotation(rdfs:comment "if effector directly regulates X, its parent MF directly regulates X") Body(ObjectPropertyAtom(obo:RO_0002025 Variable(<urn:swrl#mf>) Variable(<urn:swrl#eff>)) ObjectPropertyAtom(obo:RO_0002578 Variable(<urn:swrl#mf>) Variable(<urn:swrl#mf2>)))Head(ObjectPropertyAtom(obo:RO_0002578 Variable(<urn:swrl#eff>) Variable(<urn:swrl#mf2>))))
Expand Down
134 changes: 109 additions & 25 deletions src/ontology/ro.obo
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