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Obsoleting contains and contained in 693 #739

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merged 5 commits into from
Aug 16, 2023
Merged

Obsoleting contains and contained in 693 #739

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e5aad84
Obsoleting contains and contained in.
cmungall Jul 18, 2023
6e44222
adding seeAlso to issue
cmungall Jul 18, 2023
7515788
Merge branch 'master' into issue-693
Aug 7, 2023
6d3e45d
Merge branch 'master' into issue-693
Aug 16, 2023
a33cbb0
Merge branch 'master' into issue-693
Aug 16, 2023
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45 changes: 22 additions & 23 deletions src/ontology/ro-edit.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -1327,7 +1327,7 @@ AnnotationAssertion(rdfs:label obo:RO_0000302 "obsolete downstream in neural cir
AnnotationAssertion(owl:deprecated obo:RO_0000302 "true"^^xsd:boolean)
TransitiveObjectProperty(obo:RO_0000302)

# Object Property: obo:RO_0001018 (contained in)
# Object Property: obo:RO_0001018 (obsolete contained in)

AnnotationAssertion(obo:IAO_0000111 obo:RO_0001018 "contained in"@en)
AnnotationAssertion(obo:IAO_0000116 obo:RO_0001018 "Containment is location not involving parthood, and arises only where some immaterial continuant is involved.")
Expand All @@ -1337,19 +1337,18 @@ domain: material entity
range: spatial region or site (immaterial continuant)
"@en)
AnnotationAssertion(obo:IAO_0000118 obo:RO_0001018 "contained_in"@en)
AnnotationAssertion(obo:RO_0001900 obo:RO_0001018 obo:RO_0001901)
AnnotationAssertion(oboInOwl:inSubset obo:RO_0001018 subsets:ro-eco)
AnnotationAssertion(rdfs:label obo:RO_0001018 "contained in"@en)
InverseObjectProperties(obo:RO_0001018 obo:RO_0001019)
AnnotationAssertion(rdfs:label obo:RO_0001018 "obsolete contained in")
AnnotationAssertion(rdfs:seeAlso obo:RO_0001018 <https://github.com/oborel/obo-relations/issues/693>)
AnnotationAssertion(owl:deprecated obo:RO_0001018 "true"^^xsd:boolean)
ObjectPropertyDomain(obo:RO_0001018 obo:BFO_0000040)
ObjectPropertyRange(obo:RO_0001018 obo:BFO_0000004)

# Object Property: obo:RO_0001019 (contains)
# Object Property: obo:RO_0001019 (obsolete contains)

AnnotationAssertion(obo:IAO_0000111 obo:RO_0001019 "contains"@en)
AnnotationAssertion(obo:RO_0001900 obo:RO_0001019 obo:RO_0001901)
AnnotationAssertion(oboInOwl:inSubset obo:RO_0001019 subsets:ro-eco)
AnnotationAssertion(rdfs:label obo:RO_0001019 "contains"@en)
AnnotationAssertion(rdfs:label obo:RO_0001019 "obsolete contains")
AnnotationAssertion(rdfs:seeAlso obo:RO_0001019 <https://github.com/oborel/obo-relations/issues/693>)
AnnotationAssertion(owl:deprecated obo:RO_0001019 "true"^^xsd:boolean)

# Object Property: obo:RO_0001020 (is allergic trigger for)

Expand Down Expand Up @@ -1420,7 +1419,7 @@ SubObjectPropertyOf(obo:RO_0002003 obo:RO_0002170)
AnnotationAssertion(obo:IAO_0000115 obo:RO_0002004 "The relationship that holds between a trachea or tracheole and an antomical structure that is contained in (and so provides an oxygen supply to).")
AnnotationAssertion(obo:IAO_0000117 obo:RO_0002004 <https://orcid.org/0000-0002-7073-9172>)
AnnotationAssertion(rdfs:label obo:RO_0002004 "tracheates"@en)
SubObjectPropertyOf(obo:RO_0002004 obo:RO_0001018)
SubObjectPropertyOf(obo:RO_0002004 obo:RO_0001025)
ObjectPropertyDomain(obo:RO_0002004 obo:UBERON_0000061)
ObjectPropertyRange(obo:RO_0002004 obo:UBERON_0000061)

Expand Down Expand Up @@ -7073,19 +7072,19 @@ DLSafeRule(Annotation(rdfs:seeAlso <https://github.com/oborel/obo-relations/issu
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 "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>))))
DLSafeRule(Annotation(rdfs:comment "if effector directly positively regulates X, its parent MF directly positively regulates X") Body(ObjectPropertyAtom(obo:RO_0002629 Variable(<urn:swrl#mf>) Variable(<urn:swrl#mf2>)) ObjectPropertyAtom(obo:RO_0002025 Variable(<urn:swrl#mf>) Variable(<urn:swrl#eff>)))Head(ObjectPropertyAtom(obo:RO_0002629 Variable(<urn:swrl#eff>) Variable(<urn:swrl#mf2>))))
DLSafeRule(Annotation(rdfs:label "if effector directly negatively regulates X, its parent MF directly negatively regulates X") Body(ObjectPropertyAtom(obo:RO_0002025 Variable(<urn:swrl#mf>) Variable(<urn:swrl#eff>)) ObjectPropertyAtom(obo:RO_0002630 Variable(<urn:swrl#mf>) Variable(<urn:swrl#mf2>)))Head(ObjectPropertyAtom(obo:RO_0002630 Variable(<urn:swrl#eff>) Variable(<urn:swrl#mf2>))))
DLSafeRule(Annotation(rdfs:label "'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom(obo:RO_0002404 Variable(<urn:swrl#x>) Variable(<urn:swrl#y>)) ObjectPropertyAtom(obo:RO_0002131 Variable(<urn:swrl#x>) Variable(<urn:swrl#y>)))Head(ClassAtom(owl:Nothing Variable(<urn:swrl#x>)) ClassAtom(owl:Nothing Variable(<urn:swrl#y>))))
DLSafeRule(Annotation(rdfs:label "'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom(obo:RO_0002411 Variable(<urn:swrl#x>) Variable(<urn:swrl#y>)) ObjectPropertyAtom(obo:RO_0002131 Variable(<urn:swrl#x>) Variable(<urn:swrl#y>)))Head(ClassAtom(owl:Nothing Variable(<urn:swrl#x>)) ClassAtom(owl:Nothing Variable(<urn:swrl#y>))))
DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0012011 Variable(<urn:swrl:var#p>) Variable(<urn:swrl:var#q>)) ObjectPropertyAtom(obo:RO_0002211 Variable(<urn:swrl:var#p>) Variable(<urn:swrl:var#q>)))Head(ObjectPropertyAtom(obo:RO_0012012 Variable(<urn:swrl:var#p>) Variable(<urn:swrl:var#q>))))
DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002213 Variable(<urn:swrl#y>) Variable(<urn:swrl#z>)) ObjectPropertyAtom(obo:RO_0002212 Variable(<urn:swrl#x>) Variable(<urn:swrl#y>)))Head(ObjectPropertyAtom(obo:RO_0002212 Variable(<urn:swrl#x>) Variable(<urn:swrl#z>))))
DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002213 Variable(<urn:swrl#x>) Variable(<urn:swrl#y>)) ObjectPropertyAtom(obo:RO_0002212 Variable(<urn:swrl#y>) Variable(<urn:swrl#z>)))Head(ObjectPropertyAtom(obo:RO_0002212 Variable(<urn:swrl#x>) Variable(<urn:swrl#z>))))
DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0019002 Variable(<urn:swrl:var#y>) Variable(<urn:swrl:var#z>)) ObjectPropertyAtom(obo:RO_0002212 Variable(<urn:swrl:var#x>) Variable(<urn:swrl:var#y>)))Head(ObjectPropertyAtom(obo:RO_0019001 Variable(<urn:swrl:var#x>) Variable(<urn:swrl:var#z>))))
DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002264 Variable(<urn:swrl:var#x>) Variable(<urn:swrl:var#y>)) ObjectPropertyAtom(obo:RO_0002411 Variable(<urn:swrl:var#y>) Variable(<urn:swrl:var#z>)))Head(ObjectPropertyAtom(obo:RO_0002263 Variable(<urn:swrl:var#x>) Variable(<urn:swrl:var#z>))))
DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002411 Variable(<urn:swrl:var#q>) Variable(<urn:swrl:var#u>)) ObjectPropertyAtom(obo:RO_0002411 Variable(<urn:swrl:var#p>) Variable(<urn:swrl:var#q>)))Head(ObjectPropertyAtom(obo:RO_0012011 Variable(<urn:swrl:var#p>) Variable(<urn:swrl:var#u>))))
DLSafeRule(Annotation(rdfs:label "effector input is compound function input") Body(ObjectPropertyAtom(obo:RO_0002025 Variable(<urn:swrl#mf>) Variable(<urn:swrl#eff>)) ObjectPropertyAtom(obo:RO_0002233 Variable(<urn:swrl#eff>) Variable(<urn:swrl#in>)))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_0002025 Variable(<urn:swrl#mf>) Variable(<urn:swrl#eff>)) ObjectPropertyAtom(obo:RO_0002233 Variable(<urn:swrl#mf>) Variable(<urn:swrl#in>)))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_0002578 Variable(<urn:swrl#mf>) Variable(<urn:swrl#mf2>)) ObjectPropertyAtom(obo:RO_0002025 Variable(<urn:swrl#mf>) Variable(<urn:swrl#eff>)))Head(ObjectPropertyAtom(obo:RO_0002578 Variable(<urn:swrl#eff>) Variable(<urn:swrl#mf2>))))
DLSafeRule(Annotation(rdfs:comment "if effector directly positively regulates X, its parent MF directly positively regulates X") Body(ObjectPropertyAtom(obo:RO_0002025 Variable(<urn:swrl#mf>) Variable(<urn:swrl#eff>)) ObjectPropertyAtom(obo:RO_0002629 Variable(<urn:swrl#mf>) Variable(<urn:swrl#mf2>)))Head(ObjectPropertyAtom(obo:RO_0002629 Variable(<urn:swrl#eff>) Variable(<urn:swrl#mf2>))))
DLSafeRule(Annotation(rdfs:label "if effector directly negatively regulates X, its parent MF directly negatively regulates X") Body(ObjectPropertyAtom(obo:RO_0002630 Variable(<urn:swrl#mf>) Variable(<urn:swrl#mf2>)) ObjectPropertyAtom(obo:RO_0002025 Variable(<urn:swrl#mf>) Variable(<urn:swrl#eff>)))Head(ObjectPropertyAtom(obo:RO_0002630 Variable(<urn:swrl#eff>) Variable(<urn:swrl#mf2>))))
DLSafeRule(Annotation(rdfs:label "'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom(obo:RO_0002131 Variable(<urn:swrl#x>) Variable(<urn:swrl#y>)) ObjectPropertyAtom(obo:RO_0002404 Variable(<urn:swrl#x>) Variable(<urn:swrl#y>)))Head(ClassAtom(owl:Nothing Variable(<urn:swrl#y>)) ClassAtom(owl:Nothing Variable(<urn:swrl#x>))))
DLSafeRule(Annotation(rdfs:label "'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom(obo:RO_0002131 Variable(<urn:swrl#x>) Variable(<urn:swrl#y>)) ObjectPropertyAtom(obo:RO_0002411 Variable(<urn:swrl#x>) Variable(<urn:swrl#y>)))Head(ClassAtom(owl:Nothing Variable(<urn:swrl#y>)) ClassAtom(owl:Nothing Variable(<urn:swrl#x>))))
DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002211 Variable(<urn:swrl:var#p>) Variable(<urn:swrl:var#q>)) ObjectPropertyAtom(obo:RO_0012011 Variable(<urn:swrl:var#p>) Variable(<urn:swrl:var#q>)))Head(ObjectPropertyAtom(obo:RO_0012012 Variable(<urn:swrl:var#p>) Variable(<urn:swrl:var#q>))))
DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002212 Variable(<urn:swrl#x>) Variable(<urn:swrl#y>)) ObjectPropertyAtom(obo:RO_0002213 Variable(<urn:swrl#y>) Variable(<urn:swrl#z>)))Head(ObjectPropertyAtom(obo:RO_0002212 Variable(<urn:swrl#x>) Variable(<urn:swrl#z>))))
DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002212 Variable(<urn:swrl#y>) Variable(<urn:swrl#z>)) ObjectPropertyAtom(obo:RO_0002213 Variable(<urn:swrl#x>) Variable(<urn:swrl#y>)))Head(ObjectPropertyAtom(obo:RO_0002212 Variable(<urn:swrl#x>) Variable(<urn:swrl#z>))))
DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002212 Variable(<urn:swrl:var#x>) Variable(<urn:swrl:var#y>)) ObjectPropertyAtom(obo:RO_0019002 Variable(<urn:swrl:var#y>) Variable(<urn:swrl:var#z>)))Head(ObjectPropertyAtom(obo:RO_0019001 Variable(<urn:swrl:var#x>) Variable(<urn:swrl:var#z>))))
DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002411 Variable(<urn:swrl:var#y>) Variable(<urn:swrl:var#z>)) ObjectPropertyAtom(obo:RO_0002264 Variable(<urn:swrl:var#x>) Variable(<urn:swrl:var#y>)))Head(ObjectPropertyAtom(obo:RO_0002263 Variable(<urn:swrl:var#x>) Variable(<urn:swrl:var#z>))))
DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002411 Variable(<urn:swrl:var#p>) Variable(<urn:swrl:var#q>)) ObjectPropertyAtom(obo:RO_0002411 Variable(<urn:swrl:var#q>) Variable(<urn:swrl:var#u>)))Head(ObjectPropertyAtom(obo:RO_0012011 Variable(<urn:swrl:var#p>) Variable(<urn:swrl:var#u>))))
AnnotationAssertion(owl:deprecated obo:BFO_0000060 "true"^^xsd:boolean)
AnnotationAssertion(obo:IAO_0000115 obo:RO_0000092 "inverse of has disposition")
AnnotationAssertion(oboInOwl:inSubset obo:RO_0000092 obo:RO_0002259)
Expand Down
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