Merge pull request #237 from oborel/issue-235-redux2

Obsoleted "related via dependence to"

src/ontology/ro-edit.owl

@@ -3384,7 +3384,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different
 AnnotationAssertion(obo:IAO_0000117 obo:RO_0002410 "Chris Mungall")
 AnnotationAssertion(obo:IAO_0000232 obo:RO_0002410 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.")
 AnnotationAssertion(rdfs:label obo:RO_0002410 "causally related to"@en)
-SubObjectPropertyOf(obo:RO_0002410 obo:RO_0002609)
 
 # Object Property: obo:RO_0002411 (causally upstream of)
 
@@ -4763,18 +4762,18 @@ AnnotationAssertion(obo:IAO_0000119 obo:RO_0002608 <http://purl.obolibrary.org/o
 AnnotationAssertion(rdfs:label obo:RO_0002608 "process has causal agent")
 SubObjectPropertyOf(obo:RO_0002608 obo:RO_0002410)
 
-# Object Property: obo:RO_0002609 (related via dependence to)
+# Object Property: obo:RO_0002609 (obsolete related via dependence to)
 
 AnnotationAssertion(obo:IAO_0000115 obo:RO_0002609 "A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes.")
 AnnotationAssertion(obo:IAO_0000232 obo:RO_0002609 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.")
-AnnotationAssertion(rdfs:label obo:RO_0002609 "related via dependence to")
+AnnotationAssertion(rdfs:label obo:RO_0002609 "obsolete related via dependence to"^^xsd:string)
+AnnotationAssertion(owl:deprecated obo:RO_0002609 "true"^^xsd:boolean)
 
 # Object Property: obo:RO_0002610 (correlated with)
 
 AnnotationAssertion(obo:IAO_0000115 obo:RO_0002610 "A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes.")
 AnnotationAssertion(obo:IAO_0000232 obo:RO_0002610 "Groups both positive and negative correlation")
 AnnotationAssertion(rdfs:label obo:RO_0002610 "correlated with")
-SubObjectPropertyOf(obo:RO_0002610 obo:RO_0002609)
 
 # Object Property: obo:RO_0002614 (is evidence with support from)
 
@@ -5744,7 +5743,7 @@ 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>))))