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oborel · May 11, 2018 · 65a29ef · 65a29ef
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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/2018-03-27/ro.owl"/>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/ro/releases/2018-05-11/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"/>
@@ -2741,7 +2741,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.</obo:I
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002217">
         <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000056"/>
         <owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002218"/>
-        <obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
         <obo:IAO_0000115>x actively participates in y if and only if x participates in y and x realizes some active role</obo:IAO_0000115>
         <obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
         <obo:IAO_0000118>agent in</obo:IAO_0000118>
@@ -3289,7 +3288,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.</obo:I
             <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002411"/>
         </owl:propertyChainAxiom>
         <obo:IAO_0000112>A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision.</obo:IAO_0000112>
-        <obo:IAO_0000115>c involved in regulation of p if c enables f and f causally upstream of p</obo:IAO_0000115>
+        <obo:IAO_0000115>c acts upstream of p if and only if c enables some f that is involved in p&apos; and p&apos; occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p&apos; are processes.</obo:IAO_0000115>
         <rdfs:label>acts upstream of</rdfs:label>
         <rdfs:seeAlso rdf:resource="http://wiki.geneontology.org/index.php/Acts_upstream_of"/>
     </owl:ObjectProperty>
@@ -3834,6 +3833,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati
     <!-- http://purl.obolibrary.org/obo/RO_0002331 -->
 
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002331">
+        <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002217"/>
         <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002431"/>
         <owl:propertyChainAxiom rdf:parseType="Collection">
             <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002327"/>
@@ -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_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>
@@ -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_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 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
@@ -30,7 +30,6 @@ id: actively_participates_in
 name: actively participates in
 def: "x actively participates in y if and only if x participates in y and x realizes some active role" []
 xref: RO:0002217
-property_value: IAO:0000114 IAO:0000125
 property_value: IAO:0000117 "Chris Mungall" xsd:string
 property_value: IAO:0000118 "agent in" xsd:string
 is_a: participates_in
@@ -69,7 +68,7 @@ is_a: molecularly_interacts_with ! molecularly interacts with
 [Typedef]
 id: acts_upstream_of
 name: acts upstream of
-def: "c involved in regulation of p if c enables f and f causally upstream of p" []
+def: "c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes." []
 xref: RO:0002263
 property_value: IAO:0000112 "A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision." xsd:string
 property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of
@@ -2388,6 +2387,7 @@ property_value: IAO:0000117 "Chris Mungall" xsd:string
 property_value: IAO:0000118 "actively involved in" xsd:string
 property_value: IAO:0000118 "enables part of" xsd:string
 property_value: seeAlso Involved:in
+is_a: actively_participates_in ! actively participates in
 is_a: involved_in_or_involved_in_regulation_of ! involved in or involved in regulation of
 
 [Typedef]

diff --git a/src/ontology/subsets/ro-causal.owl b/src/ontology/subsets/ro-causal.owl
@@ -1547,7 +1547,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.</obo:I
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002217">
         <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000056"/>
         <owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002218"/>
-        <obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
         <obo:IAO_0000115>x actively participates in y if and only if x participates in y and x realizes some active role</obo:IAO_0000115>
         <obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
         <obo:IAO_0000118>agent in</obo:IAO_0000118>
@@ -2079,7 +2078,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.</obo:I
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002263">
         <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002264"/>
         <obo:IAO_0000112>A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision.</obo:IAO_0000112>
-        <obo:IAO_0000115>c involved in regulation of p if c enables f and f causally upstream of p</obo:IAO_0000115>
+        <obo:IAO_0000115>c acts upstream of p if and only if c enables some f that is involved in p&apos; and p&apos; occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p&apos; are processes.</obo:IAO_0000115>
         <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RO:0002263</oboInOwl:hasDbXref>
         <oboInOwl:shorthand rdf:datatype="http://www.w3.org/2001/XMLSchema#string">acts_upstream_of</oboInOwl:shorthand>
         <rdfs:label>acts upstream of</rdfs:label>
@@ -2536,6 +2535,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati
     <!-- http://purl.obolibrary.org/obo/RO_0002331 -->
 
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002331">
+        <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002217"/>
         <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002431"/>
         <obo:IAO_0000115>c involved_in p if and only if c enables some process p&apos;, and p&apos; is part of p</obo:IAO_0000115>
         <obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>

diff --git a/src/ontology/subsets/ro-chado.obo b/src/ontology/subsets/ro-chado.obo
@@ -1155,7 +1155,7 @@ is_a: RO:0000087 ! has role
 [Typedef]
 id: RO:0002263
 name: acts_upstream_of
-def: "c involved in regulation of p if c enables f and f causally upstream of p" []
+def: "c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes." []
 holds_over_chain: RO:0002327 RO:0002411
 is_a: RO:0002264 ! acts upstream of or within
 
@@ -1327,6 +1327,7 @@ id: RO:0002331
 name: involved_in
 def: "c involved_in p if and only if c enables some process p', and p' is part of p" []
 holds_over_chain: RO:0002327 BFO:0000050
+is_a: RO:0002217 ! actively participates in
 is_a: RO:0002431 ! involved in or involved in regulation of
 transitive_over: BFO:0000050 ! part of
 

diff --git a/src/ontology/subsets/ro-chado.obo.tmp b/src/ontology/subsets/ro-chado.obo.tmp
@@ -1155,7 +1155,7 @@ is_a: RO:0000087 ! has role
 [Typedef]
 id: RO:0002263
 name: acts upstream of
-def: "c involved in regulation of p if c enables f and f causally upstream of p" []
+def: "c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes." []
 holds_over_chain: RO:0002327 RO:0002411
 is_a: RO:0002264 ! acts upstream of or within
 
@@ -1327,6 +1327,7 @@ id: RO:0002331
 name: involved in
 def: "c involved_in p if and only if c enables some process p', and p' is part of p" []
 holds_over_chain: RO:0002327 BFO:0000050
+is_a: RO:0002217 ! actively participates in
 is_a: RO:0002431 ! involved in or involved in regulation of
 transitive_over: BFO:0000050 ! part of
 

diff --git a/src/ontology/subsets/ro-developmental.obo b/src/ontology/subsets/ro-developmental.obo
@@ -30,7 +30,6 @@ id: actively_participates_in
 name: actively participates in
 def: "x actively participates in y if and only if x participates in y and x realizes some active role" []
 xref: RO:0002217
-property_value: IAO:0000114 IAO:0000125
 property_value: IAO:0000117 "Chris Mungall" xsd:string
 property_value: IAO:0000118 "agent in" xsd:string
 is_a: participates_in
@@ -69,7 +68,7 @@ is_a: molecularly_interacts_with ! molecularly interacts with
 [Typedef]
 id: acts_upstream_of
 name: acts upstream of
-def: "c involved in regulation of p if c enables f and f causally upstream of p" []
+def: "c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes." []
 xref: RO:0002263
 property_value: IAO:0000112 "A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision." xsd:string
 property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of
@@ -2388,6 +2387,7 @@ property_value: IAO:0000117 "Chris Mungall" xsd:string
 property_value: IAO:0000118 "actively involved in" xsd:string
 property_value: IAO:0000118 "enables part of" xsd:string
 property_value: seeAlso Involved:in
+is_a: actively_participates_in ! actively participates in
 is_a: involved_in_or_involved_in_regulation_of ! involved in or involved in regulation of
 
 [Typedef]

diff --git a/src/ontology/subsets/ro-developmental.owl b/src/ontology/subsets/ro-developmental.owl
@@ -1547,7 +1547,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.</obo:I
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002217">
         <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000056"/>
         <owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002218"/>
-        <obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
         <obo:IAO_0000115>x actively participates in y if and only if x participates in y and x realizes some active role</obo:IAO_0000115>
         <obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
         <obo:IAO_0000118>agent in</obo:IAO_0000118>
@@ -2079,7 +2078,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.</obo:I
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002263">
         <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002264"/>
         <obo:IAO_0000112>A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision.</obo:IAO_0000112>
-        <obo:IAO_0000115>c involved in regulation of p if c enables f and f causally upstream of p</obo:IAO_0000115>
+        <obo:IAO_0000115>c acts upstream of p if and only if c enables some f that is involved in p&apos; and p&apos; occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p&apos; are processes.</obo:IAO_0000115>
         <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RO:0002263</oboInOwl:hasDbXref>
         <oboInOwl:shorthand rdf:datatype="http://www.w3.org/2001/XMLSchema#string">acts_upstream_of</oboInOwl:shorthand>
         <rdfs:label>acts upstream of</rdfs:label>
@@ -2536,6 +2535,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati
     <!-- http://purl.obolibrary.org/obo/RO_0002331 -->
 
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002331">
+        <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002217"/>
         <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002431"/>
         <obo:IAO_0000115>c involved_in p if and only if c enables some process p&apos;, and p&apos; is part of p</obo:IAO_0000115>
         <obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>

diff --git a/src/ontology/subsets/ro-eco.obo b/src/ontology/subsets/ro-eco.obo
@@ -1007,7 +1007,6 @@ expand_expression_to: "RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y))"
 id: RO:0002217
 name: actively participates in
 def: "x actively participates in y if and only if x participates in y and x realizes some active role" []
-property_value: IAO:0000114 IAO:0000125
 property_value: IAO:0000117 "Chris Mungall" xsd:string
 property_value: IAO:0000118 "agent in" xsd:string
 inverse_of: RO:0002218 ! has active participant
@@ -1330,7 +1329,7 @@ def: "c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:510
 [Typedef]
 id: RO:0002263
 name: acts upstream of
-def: "c involved in regulation of p if c enables f and f causally upstream of p" []
+def: "c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes." []
 property_value: IAO:0000112 "A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision." xsd:string
 property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of
 holds_over_chain: RO:0002327 RO:0002411
@@ -1594,6 +1593,7 @@ property_value: IAO:0000118 "actively involved in" xsd:string
 property_value: IAO:0000118 "enables part of" xsd:string
 property_value: seeAlso Involved:in
 holds_over_chain: RO:0002327 BFO:0000050
+is_a: RO:0002217 ! actively participates in
 is_a: RO:0002431 ! involved in or involved in regulation of
 transitive_over: BFO:0000050
 

diff --git a/src/ontology/subsets/ro-eco.owl b/src/ontology/subsets/ro-eco.owl
@@ -2567,7 +2567,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.</obo:I
 
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002217">
         <owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002218"/>
-        <obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
         <obo:IAO_0000115>x actively participates in y if and only if x participates in y and x realizes some active role</obo:IAO_0000115>
         <obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
         <obo:IAO_0000118>agent in</obo:IAO_0000118>
@@ -3074,7 +3073,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.</obo:I
             <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002411"/>
         </owl:propertyChainAxiom>
         <obo:IAO_0000112>A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision.</obo:IAO_0000112>
-        <obo:IAO_0000115>c involved in regulation of p if c enables f and f causally upstream of p</obo:IAO_0000115>
+        <obo:IAO_0000115>c acts upstream of p if and only if c enables some f that is involved in p&apos; and p&apos; occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p&apos; are processes.</obo:IAO_0000115>
         <rdfs:label>acts upstream of</rdfs:label>
         <rdfs:seeAlso rdf:resource="http://wiki.geneontology.org/index.php/Acts_upstream_of"/>
     </owl:ObjectProperty>
@@ -3584,6 +3583,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati
     <!-- http://purl.obolibrary.org/obo/RO_0002331 -->
 
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002331">
+        <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002217"/>
         <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002431"/>
         <owl:propertyChainAxiom rdf:parseType="Collection">
             <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002327"/>

diff --git a/src/ontology/subsets/ro-interaction.obo b/src/ontology/subsets/ro-interaction.obo
@@ -30,7 +30,6 @@ id: actively_participates_in
 name: actively participates in
 def: "x actively participates in y if and only if x participates in y and x realizes some active role" []
 xref: RO:0002217
-property_value: IAO:0000114 IAO:0000125
 property_value: IAO:0000117 "Chris Mungall" xsd:string
 property_value: IAO:0000118 "agent in" xsd:string
 is_a: participates_in
@@ -69,7 +68,7 @@ is_a: molecularly_interacts_with ! molecularly interacts with
 [Typedef]
 id: acts_upstream_of
 name: acts upstream of
-def: "c involved in regulation of p if c enables f and f causally upstream of p" []
+def: "c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes." []
 xref: RO:0002263
 property_value: IAO:0000112 "A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision." xsd:string
 property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of
@@ -2388,6 +2387,7 @@ property_value: IAO:0000117 "Chris Mungall" xsd:string
 property_value: IAO:0000118 "actively involved in" xsd:string
 property_value: IAO:0000118 "enables part of" xsd:string
 property_value: seeAlso Involved:in
+is_a: actively_participates_in ! actively participates in
 is_a: involved_in_or_involved_in_regulation_of ! involved in or involved in regulation of
 
 [Typedef]