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Remove owl:nothing per issue AgriculturalSemantics#129
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@KrishnaTO
KrishnaTO committed Nov 2, 2021
1 parent 6724739 commit df4453c
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Showing 4 changed files with 11 additions and 459 deletions.
112 changes: 0 additions & 112 deletions src/ontology/imports/pato_import.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -3785,118 +3785,6 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase
</rdf:Description>
</swrl:head>
</rdf:Description>
<rdf:Description>
<rdfs:label>&apos;causally downstream of&apos; and &apos;overlaps&apos; should be disjoint properties (a SWRL rule is required because these are non-simple properties).</rdfs:label>
<rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#Imp"/>
<swrl:body>
<rdf:Description>
<rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#AtomList"/>
<rdf:first>
<rdf:Description>
<rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#IndividualPropertyAtom"/>
<swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0002131"/>
<swrl:argument1 rdf:resource="urn:swrl#x"/>
<swrl:argument2 rdf:resource="urn:swrl#y"/>
</rdf:Description>
</rdf:first>
<rdf:rest>
<rdf:Description>
<rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#AtomList"/>
<rdf:first>
<rdf:Description>
<rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#IndividualPropertyAtom"/>
<swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0002404"/>
<swrl:argument1 rdf:resource="urn:swrl#x"/>
<swrl:argument2 rdf:resource="urn:swrl#y"/>
</rdf:Description>
</rdf:first>
<rdf:rest rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>
</rdf:Description>
</rdf:rest>
</rdf:Description>
</swrl:body>
<swrl:head>
<rdf:Description>
<rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#AtomList"/>
<rdf:first>
<rdf:Description>
<rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#ClassAtom"/>
<swrl:classPredicate rdf:resource="http://www.w3.org/2002/07/owl#Nothing"/>
<swrl:argument1 rdf:resource="urn:swrl#y"/>
</rdf:Description>
</rdf:first>
<rdf:rest>
<rdf:Description>
<rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#AtomList"/>
<rdf:first>
<rdf:Description>
<rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#ClassAtom"/>
<swrl:classPredicate rdf:resource="http://www.w3.org/2002/07/owl#Nothing"/>
<swrl:argument1 rdf:resource="urn:swrl#x"/>
</rdf:Description>
</rdf:first>
<rdf:rest rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>
</rdf:Description>
</rdf:rest>
</rdf:Description>
</swrl:head>
</rdf:Description>
<rdf:Description>
<rdfs:label>&apos;causally upstream of&apos; and &apos;overlaps&apos; should be disjoint properties (a SWRL rule is required because these are non-simple properties).</rdfs:label>
<rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#Imp"/>
<swrl:body>
<rdf:Description>
<rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#AtomList"/>
<rdf:first>
<rdf:Description>
<rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#IndividualPropertyAtom"/>
<swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0002131"/>
<swrl:argument1 rdf:resource="urn:swrl#x"/>
<swrl:argument2 rdf:resource="urn:swrl#y"/>
</rdf:Description>
</rdf:first>
<rdf:rest>
<rdf:Description>
<rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#AtomList"/>
<rdf:first>
<rdf:Description>
<rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#IndividualPropertyAtom"/>
<swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0002411"/>
<swrl:argument1 rdf:resource="urn:swrl#x"/>
<swrl:argument2 rdf:resource="urn:swrl#y"/>
</rdf:Description>
</rdf:first>
<rdf:rest rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>
</rdf:Description>
</rdf:rest>
</rdf:Description>
</swrl:body>
<swrl:head>
<rdf:Description>
<rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#AtomList"/>
<rdf:first>
<rdf:Description>
<rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#ClassAtom"/>
<swrl:classPredicate rdf:resource="http://www.w3.org/2002/07/owl#Nothing"/>
<swrl:argument1 rdf:resource="urn:swrl#y"/>
</rdf:Description>
</rdf:first>
<rdf:rest>
<rdf:Description>
<rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#AtomList"/>
<rdf:first>
<rdf:Description>
<rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#ClassAtom"/>
<swrl:classPredicate rdf:resource="http://www.w3.org/2002/07/owl#Nothing"/>
<swrl:argument1 rdf:resource="urn:swrl#x"/>
</rdf:Description>
</rdf:first>
<rdf:rest rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>
</rdf:Description>
</rdf:rest>
</rdf:Description>
</swrl:head>
</rdf:Description>
<rdf:Description>
<rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#Imp"/>
<swrl:body>
Expand Down
122 changes: 5 additions & 117 deletions src/ontology/imports/po_import.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -428,7 +428,7 @@ A continuant cannot have an occurrent as part: use &apos;participates in&apos;.
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/RO_0002023"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
<owl:annotatedTarget>Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.</owl:annotatedTarget>
<oboInOwl:hasDbXref>GOC:dos</oboInOwl:hasDbXref>
<oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GOC:dos</oboInOwl:hasDbXref>
</owl:Axiom>


Expand All @@ -445,7 +445,7 @@ A continuant cannot have an occurrent as part: use &apos;participates in&apos;.
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/RO_0002024"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
<owl:annotatedTarget>Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.</owl:annotatedTarget>
<oboInOwl:hasDbXref>GOC:dos</oboInOwl:hasDbXref>
<oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GOC:dos</oboInOwl:hasDbXref>
</owl:Axiom>


Expand All @@ -462,7 +462,7 @@ A continuant cannot have an occurrent as part: use &apos;participates in&apos;.
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/RO_0002025"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
<owl:annotatedTarget>A &apos;has effector activity&apos; B if A and B are GO molecular functions (GO_0003674), A &apos;has component activity&apos; B and B is the effector (output function) of B. Each compound function has only one effector activity.</owl:annotatedTarget>
<oboInOwl:hasDbXref>GOC:dos</oboInOwl:hasDbXref>
<oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GOC:dos</oboInOwl:hasDbXref>
</owl:Axiom>


Expand Down Expand Up @@ -1201,7 +1201,7 @@ A continuant cannot have an occurrent as part: use &apos;participates in&apos;.
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
<owl:annotatedTarget>c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.</owl:annotatedTarget>
<oboInOwl:hasDbXref>GOC:cjm</oboInOwl:hasDbXref>
<oboInOwl:hasDbXref>GOC:dos</oboInOwl:hasDbXref>
<oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GOC:dos</oboInOwl:hasDbXref>
</owl:Axiom>


Expand Down Expand Up @@ -6334,118 +6334,6 @@ e.g. if GP X enables ATPase coupled transporter activity&apos; and &apos;ATPase
</rdf:Description>
</swrl:head>
</rdf:Description>
<rdf:Description>
<rdfs:label>&apos;causally downstream of&apos; and &apos;overlaps&apos; should be disjoint properties (a SWRL rule is required because these are non-simple properties).</rdfs:label>
<rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#Imp"/>
<swrl:body>
<rdf:Description>
<rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#AtomList"/>
<rdf:first>
<rdf:Description>
<rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#IndividualPropertyAtom"/>
<swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0002131"/>
<swrl:argument1 rdf:resource="urn:swrl#x"/>
<swrl:argument2 rdf:resource="urn:swrl#y"/>
</rdf:Description>
</rdf:first>
<rdf:rest>
<rdf:Description>
<rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#AtomList"/>
<rdf:first>
<rdf:Description>
<rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#IndividualPropertyAtom"/>
<swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0002404"/>
<swrl:argument1 rdf:resource="urn:swrl#x"/>
<swrl:argument2 rdf:resource="urn:swrl#y"/>
</rdf:Description>
</rdf:first>
<rdf:rest rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>
</rdf:Description>
</rdf:rest>
</rdf:Description>
</swrl:body>
<swrl:head>
<rdf:Description>
<rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#AtomList"/>
<rdf:first>
<rdf:Description>
<rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#ClassAtom"/>
<swrl:classPredicate rdf:resource="http://www.w3.org/2002/07/owl#Nothing"/>
<swrl:argument1 rdf:resource="urn:swrl#y"/>
</rdf:Description>
</rdf:first>
<rdf:rest>
<rdf:Description>
<rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#AtomList"/>
<rdf:first>
<rdf:Description>
<rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#ClassAtom"/>
<swrl:classPredicate rdf:resource="http://www.w3.org/2002/07/owl#Nothing"/>
<swrl:argument1 rdf:resource="urn:swrl#x"/>
</rdf:Description>
</rdf:first>
<rdf:rest rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>
</rdf:Description>
</rdf:rest>
</rdf:Description>
</swrl:head>
</rdf:Description>
<rdf:Description>
<rdfs:label>&apos;causally upstream of&apos; and &apos;overlaps&apos; should be disjoint properties (a SWRL rule is required because these are non-simple properties).</rdfs:label>
<rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#Imp"/>
<swrl:body>
<rdf:Description>
<rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#AtomList"/>
<rdf:first>
<rdf:Description>
<rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#IndividualPropertyAtom"/>
<swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0002131"/>
<swrl:argument1 rdf:resource="urn:swrl#x"/>
<swrl:argument2 rdf:resource="urn:swrl#y"/>
</rdf:Description>
</rdf:first>
<rdf:rest>
<rdf:Description>
<rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#AtomList"/>
<rdf:first>
<rdf:Description>
<rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#IndividualPropertyAtom"/>
<swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0002411"/>
<swrl:argument1 rdf:resource="urn:swrl#x"/>
<swrl:argument2 rdf:resource="urn:swrl#y"/>
</rdf:Description>
</rdf:first>
<rdf:rest rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>
</rdf:Description>
</rdf:rest>
</rdf:Description>
</swrl:body>
<swrl:head>
<rdf:Description>
<rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#AtomList"/>
<rdf:first>
<rdf:Description>
<rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#ClassAtom"/>
<swrl:classPredicate rdf:resource="http://www.w3.org/2002/07/owl#Nothing"/>
<swrl:argument1 rdf:resource="urn:swrl#y"/>
</rdf:Description>
</rdf:first>
<rdf:rest>
<rdf:Description>
<rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#AtomList"/>
<rdf:first>
<rdf:Description>
<rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#ClassAtom"/>
<swrl:classPredicate rdf:resource="http://www.w3.org/2002/07/owl#Nothing"/>
<swrl:argument1 rdf:resource="urn:swrl#x"/>
</rdf:Description>
</rdf:first>
<rdf:rest rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>
</rdf:Description>
</rdf:rest>
</rdf:Description>
</swrl:head>
</rdf:Description>
<rdf:Description>
<rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#Imp"/>
<swrl:body>
Expand Down Expand Up @@ -6538,5 +6426,5 @@ e.g. if GP X enables ATPase coupled transporter activity&apos; and &apos;ATPase



<!-- Generated by the OWL API (version 4.5.6) https://github.com/owlcs/owlapi -->
<!-- Generated by the OWL API (version 4.5.9.2019-02-01T07:24:44Z) https://github.com/owlcs/owlapi -->

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