Merge pull request #300 from balhoff/upstream-disjoint-partof

Make causally_upstream_of and causally_downstream_of disjoint with overlaps.

src/ontology/ro-edit.owl

@@ -5873,12 +5873,14 @@ 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>))))
 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_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_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>))))
 AnnotationAssertion(owl:deprecated obo:BFO_0000060 "true"^^xsd:boolean)