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Including additional CARO classes in import, in particular the more g…
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…eneral 'anatomical structure'

Broadening range for some developmental relations to AS. See obophenotype/uberon#1455
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@cmungall
cmungall committed Oct 19, 2018
1 parent 77d7387 commit d852a55
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Showing 2 changed files with 23 additions and 6 deletions.
19 changes: 17 additions & 2 deletions src/ontology/other_import.owl
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Expand Up @@ -122,20 +122,28 @@
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000141"/>


<!-- http://purl.obolibrary.org/obo/CARO_0000000 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/CARO_0000000">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CARO_0030000"/>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/caro.owl"/>
<rdfs:label xml:lang="en">anatomical entity</rdfs:label>
</owl:Class>

<!-- http://purl.obolibrary.org/obo/CARO_0000003 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/CARO_0000003">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CARO_0000006"/>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/caro.owl"/>
<rdfs:label xml:lang="en">anatomical structure</rdfs:label>
<rdfs:label xml:lang="en">connected anatomical structure</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/CARO_0000006 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/CARO_0000006">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CARO_0000000"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/caro.owl"/>
<rdfs:label xml:lang="en">material anatomical entity</rdfs:label>
Expand All @@ -155,7 +163,7 @@
<!-- http://purl.obolibrary.org/obo/CARO_0000011 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/CARO_0000011">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CARO_0000006"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CARO_0010000"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002577"/>
<rdfs:label>connected anatomical system</rdfs:label>
</owl:Class>
Expand Down Expand Up @@ -201,6 +209,13 @@
</owl:Class>


<!-- http://purl.obolibrary.org/obo/CARO_0030000 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/CARO_0030000">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000004"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">biological entity</rdfs:label>
</owl:Class>


<!-- http://purl.obolibrary.org/obo/CARO_0010000 -->

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10 changes: 6 additions & 4 deletions src/ontology/ro-edit.owl
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Expand Up @@ -2282,7 +2282,7 @@ AnnotationAssertion(obo:IAO_0000119 obo:RO_0002226 "EHDAA2")
AnnotationAssertion(obo:IAO_0000119 obo:RO_0002226 "Jonathan Bard, EHDAA2")
AnnotationAssertion(rdfs:label obo:RO_0002226 "develops in"@en)
SubObjectPropertyOf(obo:RO_0002226 obo:RO_0002258)
ObjectPropertyDomain(obo:RO_0002226 obo:CARO_0000003)
ObjectPropertyDomain(obo:RO_0002226 obo:CARO_0000000)

# Object Property: obo:RO_0002227 (obligate parasite of)

Expand Down Expand Up @@ -2462,8 +2462,8 @@ AnnotationAssertion(obo:IAO_0000117 obo:RO_0002254 "Chris Mungall")
AnnotationAssertion(rdfs:label obo:RO_0002254 "has developmental contribution from"@en)
SubObjectPropertyOf(obo:RO_0002254 obo:RO_0002258)
InverseObjectProperties(obo:RO_0002254 obo:RO_0002255)
ObjectPropertyDomain(obo:RO_0002254 obo:BFO_0000004)
ObjectPropertyRange(obo:RO_0002254 obo:CARO_0000003)
ObjectPropertyDomain(obo:RO_0002254 obo:CARO_0000000)
ObjectPropertyRange(obo:RO_0002254 obo:CARO_0000000)

# Object Property: obo:RO_0002255 (developmentally contributes to)

Expand Down Expand Up @@ -3237,6 +3237,8 @@ AnnotationAssertion(obo:IAO_0000115 obo:RO_0002384 "x has developmental potentia
AnnotationAssertion(obo:IAO_0000117 obo:RO_0002384 "Chris Mungall")
AnnotationAssertion(rdfs:label obo:RO_0002384 "has developmental potential involving"@en)
SubObjectPropertyOf(obo:RO_0002384 obo:RO_0002324)
ObjectPropertyDomain(obo:RO_0002384 obo:CARO_0000000)
ObjectPropertyRange(obo:RO_0002384 obo:CARO_0000000)

# Object Property: obo:RO_0002385 (has potential to developmentally contribute to)

Expand Down Expand Up @@ -5809,7 +5811,7 @@ DLSafeRule(Annotation(swrla:isRuleEnabled "true"^^xsd:boolean) Annotation(rdfs:c
DLSafeRule(Annotation(rdfs:comment "GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z),
e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'") Annotation(rdfs:label "enabling an MF enables its parts") Body(ClassAtom(obo:GO_0003674 Variable(<urn:swrl#y>)) ObjectPropertyAtom(obo:RO_0002327 Variable(<urn:swrl#x>) Variable(<urn:swrl#y>)) ObjectPropertyAtom(obo:BFO_0000051 Variable(<urn:swrl#y>) Variable(<urn:swrl#z>)))Head(ObjectPropertyAtom(obo:RO_0002327 Variable(<urn:swrl#x>) Variable(<urn:swrl#z>))))
DLSafeRule(Annotation(swrla:isRuleEnabled "true"^^xsd:boolean) Annotation(rdfs:comment "GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'"^^xsd:string) Annotation(rdfs:label "involved in BP"^^xsd:string) Body(ClassAtom(obo:GO_0008150 Variable(<urn:swrl#z>)) ObjectPropertyAtom(obo:BFO_0000050 Variable(<urn:swrl#y>) Variable(<urn:swrl#z>)) ObjectPropertyAtom(obo:RO_0002327 Variable(<urn:swrl#x>) Variable(<urn:swrl#y>)))Head(ObjectPropertyAtom(obo:RO_0002331 Variable(<urn:swrl#x>) Variable(<urn:swrl#z>))))
DLSafeRule(Annotation(rdfs:seeAlso <https://github.com/oborel/obo-relations/issues/259>) Body(ObjectPropertyAtom(obo:RO_0002333 Variable(<urn:swrl#a1>) Variable(<urn:swrl#g1>)) ClassAtom(obo:GO_0016301 Variable(<urn:swrl#a1>)) ObjectPropertyAtom(obo:RO_0002578 Variable(<urn:swrl#a1>) Variable(<urn:swrl#a2>)) ObjectPropertyAtom(obo:RO_0002333 Variable(<urn:swrl#a2>) Variable(<urn:swrl#g2>)))Head(ObjectPropertyAtom(obo:RO_0002447 Variable(<urn:swrl#g1>) Variable(<urn:swrl#g2>))))
DLSafeRule(Annotation(rdfs:seeAlso <https://github.com/oborel/obo-relations/issues/259>) Body(ObjectPropertyAtom(obo:RO_0002578 Variable(<urn:swrl#a1>) Variable(<urn:swrl#a2>)) ClassAtom(obo:GO_0016301 Variable(<urn:swrl#a1>)) ObjectPropertyAtom(obo:RO_0002333 Variable(<urn:swrl#a1>) Variable(<urn:swrl#g1>)) ObjectPropertyAtom(obo:RO_0002333 Variable(<urn:swrl#a2>) Variable(<urn:swrl#g2>)))Head(ObjectPropertyAtom(obo:RO_0002447 Variable(<urn:swrl#g1>) Variable(<urn:swrl#g2>))))
DLSafeRule(Annotation(rdfs:label "From ligand activity to has_ligand") Body(ObjectPropertyAtom(obo:RO_0002327 Variable(<urn:swrl#y>) Variable(<urn:swrl#z>)) ObjectPropertyAtom(obo:RO_0002578 Variable(<urn:swrl#z>) Variable(<urn:swrl#x>)) ClassAtom(obo:GO_0048018 Variable(<urn:swrl#z>)))Head(ObjectPropertyAtom(obo:RO_0002019 Variable(<urn:swrl#x>) Variable(<urn:swrl#y>))))
DLSafeRule(Annotation(rdfs:comment "This rule is dubious: added as a quick fix for expected inference in GO-CAM. The problem is most acute for transmembrane proteins, such as receptors or cell adhesion molecules, which have some subfunctions inside the cell (e.g. kinase activity) and some subfunctions outside (e.g. ligand binding). Correct annotation of where these functions occurs leads to incorrect inference about the location of the whole protein. This should probably be weakened to \"... -> overlaps\"") Body(ObjectPropertyAtom(obo:BFO_0000066 Variable(<urn:swrl#y>) Variable(<urn:swrl#z>)) ObjectPropertyAtom(obo:RO_0002327 Variable(<urn:swrl#x>) Variable(<urn:swrl#y>)))Head(ObjectPropertyAtom(obo:BFO_0000050 Variable(<urn:swrl#x>) Variable(<urn:swrl#z>))))
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>))))
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