weakening domain constraint for has-modifier

oborel · Mar 28, 2018 · 7a3e01a · 7a3e01a
1 parent ec9e133
commit 7a3e01a
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Showing 22 changed files with 62 additions and 58 deletions.
diff --git a/ro.json b/ro.json
@@ -15822,7 +15822,7 @@
         "pred" : "http://purl.org/dc/elements/1.1/title",
         "val" : "OBO Relations Ontology"
       } ],
-      "version" : "http://purl.obolibrary.org/obo/ro/releases/2018-03-13/ro.owl"
+      "version" : "http://purl.obolibrary.org/obo/ro/releases/2018-03-27/ro.owl"
     },
     "equivalentNodesSets" : [ ],
     "logicalDefinitionAxioms" : [ ],
@@ -15842,7 +15842,7 @@
       "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ]
     }, {
       "predicateId" : "http://purl.obolibrary.org/obo/RO_0002573",
-      "domainClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0000001" ]
+      "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000020" ]
     }, {
       "predicateId" : "http://purl.obolibrary.org/obo/RO_0002211",
       "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ],

diff --git a/ro.obo b/ro.obo
diff --git a/ro.owl b/ro.owl
@@ -17,7 +17,7 @@
      xmlns:dc="http://purl.org/dc/elements/1.1/"
      xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#">
     <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/ro.owl">
-        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/ro/releases/2018-03-13/ro.owl"/>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/ro/releases/2018-03-27/ro.owl"/>
         <owl:imports rdf:resource="http://purl.obolibrary.org/obo/ro/annotations.owl"/>
         <owl:imports rdf:resource="http://purl.obolibrary.org/obo/ro/pato_import.owl"/>
         <owl:imports rdf:resource="http://purl.obolibrary.org/obo/ro/temporal-intervals.owl"/>
@@ -6567,7 +6567,7 @@ the a supports either the existence of b, or the truth value of b.</obo:IAO_0000
     <!-- http://purl.obolibrary.org/obo/RO_0002573 -->
 
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002573">
-        <rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/PATO_0000001"/>
+        <rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/BFO_0000020"/>
         <obo:IAO_0000115>A relation that holds between an attribute or a qualifier and another attribute.</obo:IAO_0000115>
         <obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
         <obo:IAO_0000119 rdf:resource="http://www.ncbi.nlm.nih.gov/pubmed/20064205"/>
@@ -9042,9 +9042,9 @@ e.g.  if GP X enables ATPase coupled transporter activity&apos; and &apos;ATPase
                 <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_0002327"/>
-                        <swrl:argument1 rdf:resource="urn:swrl#y"/>
-                        <swrl:argument2 rdf:resource="urn:swrl#z"/>
+                        <swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0002019"/>
+                        <swrl:argument1 rdf:resource="urn:swrl#x"/>
+                        <swrl:argument2 rdf:resource="urn:swrl#y"/>
                     </rdf:Description>
                 </rdf:first>
                 <rdf:rest>
@@ -9053,9 +9053,9 @@ e.g.  if GP X enables ATPase coupled transporter activity&apos; and &apos;ATPase
                         <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_0002019"/>
-                                <swrl:argument1 rdf:resource="urn:swrl#x"/>
-                                <swrl:argument2 rdf:resource="urn:swrl#y"/>
+                                <swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0002327"/>
+                                <swrl:argument1 rdf:resource="urn:swrl#y"/>
+                                <swrl:argument2 rdf:resource="urn:swrl#z"/>
                             </rdf:Description>
                         </rdf:first>
                         <rdf:rest rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>

diff --git a/src/ontology/ro-edit.owl b/src/ontology/ro-edit.owl
@@ -2169,7 +2169,6 @@ AnnotationAssertion(rdfs:label obo:RO_0002214 "has prototype"@en)
 
 AnnotationAssertion(obo:IAO_0000112 obo:RO_0002215 "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)")
 AnnotationAssertion(obo:IAO_0000112 obo:RO_0002215 "osteoclast SubClassOf 'capable of' some 'bone resorption'")
-AnnotationAssertion(obo:IAO_0000114 obo:RO_0002215 obo:IAO_0000125)
 AnnotationAssertion(obo:IAO_0000115 obo:RO_0002215 "A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. ")
 AnnotationAssertion(obo:IAO_0000117 obo:RO_0002215 "Chris Mungall")
 AnnotationAssertion(obo:IAO_0000118 obo:RO_0002215 "has function realized in")
@@ -2185,7 +2184,6 @@ ObjectPropertyRange(obo:RO_0002215 obo:BFO_0000015)
 
 # Object Property: obo:RO_0002216 (capable of part of)
 
-AnnotationAssertion(obo:IAO_0000114 obo:RO_0002216 obo:IAO_0000125)
 AnnotationAssertion(obo:IAO_0000115 obo:RO_0002216 "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p.")
 AnnotationAssertion(obo:IAO_0000117 obo:RO_0002216 "Chris Mungall")
 AnnotationAssertion(obo:IAO_0000118 obo:RO_0002216 "has function in")
@@ -3508,13 +3506,15 @@ SubObjectPropertyOf(obo:RO_0002428 obo:RO_0002431)
 
 # Object Property: obo:RO_0002429 (involved in positive regulation of)
 
+AnnotationAssertion(obo:IAO_0000115 obo:RO_0002429 "c involved in regulation of p if c is involved in some p' and p' positively regulates some p")
 AnnotationAssertion(obo:IAO_0000117 obo:RO_0002429 "Chris Mungall")
 AnnotationAssertion(obo:RO_0004049 obo:RO_0002429 obo:RO_0002428)
 AnnotationAssertion(rdfs:label obo:RO_0002429 "involved in positive regulation of")
 SubObjectPropertyOf(obo:RO_0002429 obo:RO_0002428)
 
 # Object Property: obo:RO_0002430 (involved in negative regulation of)
 
+AnnotationAssertion(obo:IAO_0000115 obo:RO_0002430 "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p")
 AnnotationAssertion(obo:IAO_0000117 obo:RO_0002430 "Chris Mungall")
 AnnotationAssertion(obo:RO_0004050 obo:RO_0002430 obo:RO_0002428)
 AnnotationAssertion(rdfs:label obo:RO_0002430 "involved in negative regulation of")

diff --git a/src/ontology/ro.obo b/src/ontology/ro.obo
diff --git a/src/ontology/ro.owl b/src/ontology/ro.owl
@@ -17,7 +17,7 @@
      xmlns:dc="http://purl.org/dc/elements/1.1/"
      xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#">
     <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/ro.owl">
-        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/ro/releases/2018-03-13/ro.owl"/>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/ro/releases/2018-03-27/ro.owl"/>
         <owl:imports rdf:resource="http://purl.obolibrary.org/obo/ro/annotations.owl"/>
         <owl:imports rdf:resource="http://purl.obolibrary.org/obo/ro/pato_import.owl"/>
         <owl:imports rdf:resource="http://purl.obolibrary.org/obo/ro/temporal-intervals.owl"/>
@@ -2696,7 +2696,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.</obo:I
         </owl:propertyChainAxiom>
         <obo:IAO_0000112>mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)</obo:IAO_0000112>
         <obo:IAO_0000112>osteoclast SubClassOf &apos;capable of&apos; some &apos;bone resorption&apos;</obo:IAO_0000112>
-        <obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
         <obo:IAO_0000115>A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. </obo:IAO_0000115>
         <obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
         <obo:IAO_0000118>has function realized in</obo:IAO_0000118>
@@ -2719,7 +2718,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.</obo:I
             <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002215"/>
             <rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000050"/>
         </owl:propertyChainAxiom>
-        <obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
         <obo:IAO_0000115>c stands in this relationship to p if and only if there exists some p&apos; such that c is capable_of p&apos;, and p&apos; is part_of p.</obo:IAO_0000115>
         <obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
         <obo:IAO_0000118>has function in</obo:IAO_0000118>
@@ -4808,6 +4806,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different
             <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002331"/>
             <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002213"/>
         </owl:propertyChainAxiom>
+        <obo:IAO_0000115>c involved in regulation of p if c is involved in some p&apos; and p&apos; positively regulates some p</obo:IAO_0000115>
         <obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
         <obo:RO_0004049 rdf:resource="http://purl.obolibrary.org/obo/RO_0002428"/>
         <rdfs:label>involved in positive regulation of</rdfs:label>
@@ -4827,6 +4826,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different
             <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002331"/>
             <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002212"/>
         </owl:propertyChainAxiom>
+        <obo:IAO_0000115>c involved in regulation of p if c is involved in some p&apos; and p&apos; negatively regulates some p</obo:IAO_0000115>
         <obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
         <obo:RO_0004050 rdf:resource="http://purl.obolibrary.org/obo/RO_0002428"/>
         <rdfs:label>involved in negative regulation of</rdfs:label>
@@ -6567,7 +6567,7 @@ the a supports either the existence of b, or the truth value of b.</obo:IAO_0000
     <!-- http://purl.obolibrary.org/obo/RO_0002573 -->
 
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002573">
-        <rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/PATO_0000001"/>
+        <rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/BFO_0000020"/>
         <obo:IAO_0000115>A relation that holds between an attribute or a qualifier and another attribute.</obo:IAO_0000115>
         <obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
         <obo:IAO_0000119 rdf:resource="http://www.ncbi.nlm.nih.gov/pubmed/20064205"/>
@@ -9042,9 +9042,9 @@ e.g.  if GP X enables ATPase coupled transporter activity&apos; and &apos;ATPase
                 <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_0002327"/>
-                        <swrl:argument1 rdf:resource="urn:swrl#y"/>
-                        <swrl:argument2 rdf:resource="urn:swrl#z"/>
+                        <swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0002019"/>
+                        <swrl:argument1 rdf:resource="urn:swrl#x"/>
+                        <swrl:argument2 rdf:resource="urn:swrl#y"/>
                     </rdf:Description>
                 </rdf:first>
                 <rdf:rest>
@@ -9053,9 +9053,9 @@ e.g.  if GP X enables ATPase coupled transporter activity&apos; and &apos;ATPase
                         <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_0002019"/>
-                                <swrl:argument1 rdf:resource="urn:swrl#x"/>
-                                <swrl:argument2 rdf:resource="urn:swrl#y"/>
+                                <swrl:propertyPredicate rdf:resource="http://purl.obolibrary.org/obo/RO_0002327"/>
+                                <swrl:argument1 rdf:resource="urn:swrl#y"/>
+                                <swrl:argument2 rdf:resource="urn:swrl#z"/>
                             </rdf:Description>
                         </rdf:first>
                         <rdf:rest rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>

diff --git a/src/ontology/subsets/ro-causal.obo b/src/ontology/subsets/ro-causal.obo
@@ -288,7 +288,6 @@ subset: ro-eco
 xref: RO:0002215
 property_value: IAO:0000112 "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" xsd:string
 property_value: IAO:0000112 "osteoclast SubClassOf 'capable of' some 'bone resorption'" xsd:string
-property_value: IAO:0000114 IAO:0000125
 property_value: IAO:0000117 "Chris Mungall" xsd:string
 property_value: IAO:0000118 "has function realized in" xsd:string
 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20123131
@@ -323,7 +322,6 @@ id: capable_of_part_of
 name: capable of part of
 def: "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." []
 xref: RO:0002216
-property_value: IAO:0000114 IAO:0000125
 property_value: IAO:0000117 "Chris Mungall" xsd:string
 property_value: IAO:0000118 "has function in" xsd:string
 is_a: causal_agent_in_process ! causal agent in process
@@ -2395,6 +2393,7 @@ is_a: involved_in_or_involved_in_regulation_of ! involved in or involved in regu
 [Typedef]
 id: involved_in_negative_regulation_of
 name: involved in negative regulation of
+def: "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" []
 xref: RO:0002430
 property_value: IAO:0000117 "Chris Mungall" xsd:string
 property_value: RO:0004050 RO:0002428
@@ -2414,6 +2413,7 @@ is_a: functionally_related_to ! functionally related to
 [Typedef]
 id: involved_in_positive_regulation_of
 name: involved in positive regulation of
+def: "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" []
 xref: RO:0002429
 property_value: IAO:0000117 "Chris Mungall" xsd:string
 property_value: RO:0004049 RO:0002428

diff --git a/src/ontology/subsets/ro-causal.owl b/src/ontology/subsets/ro-causal.owl
@@ -1511,7 +1511,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.</obo:I
         <rdfs:range rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
         <obo:IAO_0000112>mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)</obo:IAO_0000112>
         <obo:IAO_0000112>osteoclast SubClassOf &apos;capable of&apos; some &apos;bone resorption&apos;</obo:IAO_0000112>
-        <obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
         <obo:IAO_0000115>A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. </obo:IAO_0000115>
         <obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
         <obo:IAO_0000118>has function realized in</obo:IAO_0000118>
@@ -1532,7 +1531,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.</obo:I
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002216">
         <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002328"/>
         <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002500"/>
-        <obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
         <obo:IAO_0000115>c stands in this relationship to p if and only if there exists some p&apos; such that c is capable_of p&apos;, and p&apos; is part_of p.</obo:IAO_0000115>
         <obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
         <obo:IAO_0000118>has function in</obo:IAO_0000118>
@@ -3450,6 +3448,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different
 
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002429">
         <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002428"/>
+        <obo:IAO_0000115>c involved in regulation of p if c is involved in some p&apos; and p&apos; positively regulates some p</obo:IAO_0000115>
         <obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
         <obo:RO_0004049 rdf:resource="http://purl.obolibrary.org/obo/RO_0002428"/>
         <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RO:0002429</oboInOwl:hasDbXref>
@@ -3463,6 +3462,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different
 
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002430">
         <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002428"/>
+        <obo:IAO_0000115>c involved in regulation of p if c is involved in some p&apos; and p&apos; negatively regulates some p</obo:IAO_0000115>
         <obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
         <obo:RO_0004050 rdf:resource="http://purl.obolibrary.org/obo/RO_0002428"/>
         <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RO:0002430</oboInOwl:hasDbXref>

diff --git a/src/ontology/subsets/ro-chado.obo b/src/ontology/subsets/ro-chado.obo
@@ -1753,13 +1753,15 @@ is_a: RO:0002431 ! involved in or involved in regulation of
 [Typedef]
 id: RO:0002429
 name: involved_in_positive_regulation_of
+def: "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" []
 holds_over_chain: RO:0002327 RO:0002213
 holds_over_chain: RO:0002331 RO:0002213
 is_a: RO:0002428 ! involved in regulation of
 
 [Typedef]
 id: RO:0002430
 name: involved_in_negative_regulation_of
+def: "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" []
 holds_over_chain: RO:0002327 RO:0002212
 holds_over_chain: RO:0002331 RO:0002212
 is_a: RO:0002428 ! involved in regulation of

diff --git a/src/ontology/subsets/ro-chado.obo.tmp b/src/ontology/subsets/ro-chado.obo.tmp
@@ -1753,13 +1753,15 @@ is_a: RO:0002431 ! involved in or involved in regulation of
 [Typedef]
 id: RO:0002429
 name: involved in positive regulation of
+def: "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" []
 holds_over_chain: RO:0002327 RO:0002213
 holds_over_chain: RO:0002331 RO:0002213
 is_a: RO:0002428 ! involved in regulation of
 
 [Typedef]
 id: RO:0002430
 name: involved in negative regulation of
+def: "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" []
 holds_over_chain: RO:0002327 RO:0002212
 holds_over_chain: RO:0002331 RO:0002212
 is_a: RO:0002428 ! involved in regulation of

diff --git a/src/ontology/subsets/ro-developmental.obo b/src/ontology/subsets/ro-developmental.obo
@@ -288,7 +288,6 @@ subset: ro-eco
 xref: RO:0002215
 property_value: IAO:0000112 "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" xsd:string
 property_value: IAO:0000112 "osteoclast SubClassOf 'capable of' some 'bone resorption'" xsd:string
-property_value: IAO:0000114 IAO:0000125
 property_value: IAO:0000117 "Chris Mungall" xsd:string
 property_value: IAO:0000118 "has function realized in" xsd:string
 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20123131
@@ -323,7 +322,6 @@ id: capable_of_part_of
 name: capable of part of
 def: "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." []
 xref: RO:0002216
-property_value: IAO:0000114 IAO:0000125
 property_value: IAO:0000117 "Chris Mungall" xsd:string
 property_value: IAO:0000118 "has function in" xsd:string
 is_a: causal_agent_in_process ! causal agent in process
@@ -2395,6 +2393,7 @@ is_a: involved_in_or_involved_in_regulation_of ! involved in or involved in regu
 [Typedef]
 id: involved_in_negative_regulation_of
 name: involved in negative regulation of
+def: "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" []
 xref: RO:0002430
 property_value: IAO:0000117 "Chris Mungall" xsd:string
 property_value: RO:0004050 RO:0002428
@@ -2414,6 +2413,7 @@ is_a: functionally_related_to ! functionally related to
 [Typedef]
 id: involved_in_positive_regulation_of
 name: involved in positive regulation of
+def: "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" []
 xref: RO:0002429
 property_value: IAO:0000117 "Chris Mungall" xsd:string
 property_value: RO:0004049 RO:0002428