actual fix for #233

src/envo/Makefile

@@ -184,7 +184,7 @@ mirror/ro-classes.owl: envo-edit.owl
 	owltools $(OBO)/ro.owl --merge-imports-closure --make-subset-by-properties -f // --remove-external-classes -k RO --remove-annotation-assertions -l -s -d  -o $@
 
 mirror/bfo.owl: envo-edit.owl
-	owltools $(OBO)/ro.owl --merge-imports-closure --make-subset-by-properties -f // --remove-external-classes BFO --remove-annotation-assertions -l -s -d  --remove-dangling --set-ontology-id $(OBO)/bfo.owl -o $@
+	owltools $(OBO)/bfo.owl --merge-imports-closure --make-subset-by-properties -f // --remove-external-classes BFO --remove-annotation-assertions -l -s -d  --remove-dangling --set-ontology-id $(OBO)/bfo.owl -o $@
 .PRECIOUS: mirror/%.owl
 
 mirror/uberon.owl: envo-edit.owl

src/envo/imports/bfo_import.owl

@@ -3,13 +3,11 @@
      xml:base="http://purl.obolibrary.org/obo/envo/imports/bfo_import.owl"
      xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
      xmlns:owl="http://www.w3.org/2002/07/owl#"
+     xmlns:xml="http://www.w3.org/XML/1998/namespace"
      xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
      xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
-     xmlns:obo="http://purl.obolibrary.org/obo/"
-     xmlns:dc="http://purl.org/dc/elements/1.1/">
-    <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/envo/imports/bfo_import.owl">
-        <dc:source rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
-    </owl:Ontology>
+     xmlns:obo="http://purl.obolibrary.org/obo/">
+    <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/envo/imports/bfo_import.owl"/>
     
 
 
@@ -30,6 +28,12 @@
     
 
 
+    <!-- http://purl.obolibrary.org/obo/IAO_0010000 -->
+
+    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0010000"/>
+    
+
+
     <!-- 
     ///////////////////////////////////////////////////////////////////////////////////////
     //
@@ -41,96 +45,202 @@
     
 
 
+    <!-- http://purl.obolibrary.org/obo/BFO_0000001 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000001">
+        <rdfs:label xml:lang="en">entity</rdfs:label>
+    </owl:Class>
+    
+
+
     <!-- http://purl.obolibrary.org/obo/BFO_0000002 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000002">
-        <rdfs:label xml:lang="en">continuant</rdfs:label>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000001"/>
         <owl:disjointWith rdf:resource="http://purl.obolibrary.org/obo/BFO_0000003"/>
-        <obo:IAO_0000115 xml:lang="en">An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.</obo:IAO_0000115>
+        <rdfs:label xml:lang="en">continuant</rdfs:label>
     </owl:Class>
     
 
 
     <!-- http://purl.obolibrary.org/obo/BFO_0000003 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000003">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000001"/>
         <rdfs:label xml:lang="en">occurrent</rdfs:label>
-        <obo:IAO_0000115 xml:lang="en">An entity that has temporal parts and that happens, unfolds or develops through time.</obo:IAO_0000115>
     </owl:Class>
     
 
 
     <!-- http://purl.obolibrary.org/obo/BFO_0000004 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000004">
-        <rdfs:label xml:lang="en">independent continuant</rdfs:label>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000002"/>
         <owl:disjointWith rdf:resource="http://purl.obolibrary.org/obo/BFO_0000020"/>
-        <obo:IAO_0000115 xml:lang="en">A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.</obo:IAO_0000115>
+        <obo:IAO_0000115 xml:lang="en">b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])</obo:IAO_0000115>
+        <rdfs:label xml:lang="en">independent continuant</rdfs:label>
+    </owl:Class>
+    <owl:Axiom>
+        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000004"/>
+        <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
+        <owl:annotatedTarget xml:lang="en">b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])</owl:annotatedTarget>
+        <obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/017-002"/>
+    </owl:Axiom>
+    
+
+
+    <!-- http://purl.obolibrary.org/obo/BFO_0000006 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000006">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000141"/>
+        <owl:disjointWith rdf:resource="http://purl.obolibrary.org/obo/BFO_0000140"/>
+        <rdfs:label xml:lang="en">spatial region</rdfs:label>
     </owl:Class>
     
 
 
     <!-- http://purl.obolibrary.org/obo/BFO_0000015 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000015">
-        <rdfs:label xml:lang="en">process</rdfs:label>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000003"/>
-        <obo:IAO_0000115 xml:lang="en">An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.</obo:IAO_0000115>
+        <obo:IAO_0000115 xml:lang="en">p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])</obo:IAO_0000115>
+        <rdfs:label xml:lang="en">process</rdfs:label>
     </owl:Class>
+    <owl:Axiom>
+        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
+        <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
+        <owl:annotatedTarget xml:lang="en">p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])</owl:annotatedTarget>
+        <obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/083-003"/>
+    </owl:Axiom>
     
 
 
     <!-- http://purl.obolibrary.org/obo/BFO_0000016 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000016">
-        <rdfs:label xml:lang="en">disposition</rdfs:label>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000017"/>
         <owl:disjointWith rdf:resource="http://purl.obolibrary.org/obo/BFO_0000023"/>
+        <rdfs:label xml:lang="en">disposition</rdfs:label>
     </owl:Class>
     
 
 
     <!-- http://purl.obolibrary.org/obo/BFO_0000017 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000017">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000020"/>
+        <owl:disjointWith rdf:resource="http://purl.obolibrary.org/obo/BFO_0000019"/>
         <rdfs:label xml:lang="en">realizable entity</rdfs:label>
+    </owl:Class>
+    
+
+
+    <!-- http://purl.obolibrary.org/obo/BFO_0000019 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000019">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000020"/>
-        <obo:IAO_0000115 xml:lang="en">A specifically dependent continuant  that inheres in continuant  entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.</obo:IAO_0000115>
+        <rdfs:label xml:lang="en">quality</rdfs:label>
     </owl:Class>
     
 
 
     <!-- http://purl.obolibrary.org/obo/BFO_0000020 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000020">
-        <rdfs:label xml:lang="en">specifically dependent continuant</rdfs:label>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000002"/>
-        <obo:IAO_0000115 xml:lang="en">A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.</obo:IAO_0000115>
+        <obo:IAO_0000115 xml:lang="en">b is a specifically dependent continuant = Def. b is a continuant &amp; there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])</obo:IAO_0000115>
+        <rdfs:label xml:lang="en">specifically dependent continuant</rdfs:label>
     </owl:Class>
+    <owl:Axiom>
+        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000020"/>
+        <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
+        <owl:annotatedTarget xml:lang="en">b is a specifically dependent continuant = Def. b is a continuant &amp; there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])</owl:annotatedTarget>
+        <obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/050-003"/>
+    </owl:Axiom>
     
 
 
     <!-- http://purl.obolibrary.org/obo/BFO_0000023 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000023">
-        <rdfs:label xml:lang="en">role</rdfs:label>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000017"/>
-        <obo:IAO_0000115 xml:lang="en">A realizable entity  the manifestation of which brings about some result or end that is not essential to a continuant  in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant  in some kinds of natural, social or institutional contexts.</obo:IAO_0000115>
+        <rdfs:label xml:lang="en">role</rdfs:label>
+    </owl:Class>
+    
+
+
+    <!-- http://purl.obolibrary.org/obo/BFO_0000024 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000024">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
+        <rdfs:label xml:lang="en">fiat object part</rdfs:label>
+    </owl:Class>
+    
+
+
+    <!-- http://purl.obolibrary.org/obo/BFO_0000034 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000034">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000016"/>
+        <rdfs:label xml:lang="en">function</rdfs:label>
     </owl:Class>
     
 
 
     <!-- http://purl.obolibrary.org/obo/BFO_0000040 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000040">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000004"/>
+        <owl:disjointWith rdf:resource="http://purl.obolibrary.org/obo/BFO_0000141"/>
         <rdfs:label xml:lang="en">material entity</rdfs:label>
+    </owl:Class>
+    
+
+
+    <!-- http://purl.obolibrary.org/obo/BFO_0000140 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000140">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000141"/>
+        <obo:IAO_0000115 xml:lang="en">b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001])</obo:IAO_0000115>
+        <rdfs:label xml:lang="en">continuant fiat boundary</rdfs:label>
+    </owl:Class>
+    <owl:Axiom>
+        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000140"/>
+        <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
+        <owl:annotatedTarget xml:lang="en">b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001])</owl:annotatedTarget>
+        <obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/029-001"/>
+    </owl:Axiom>
+    
+
+
+    <!-- http://purl.obolibrary.org/obo/BFO_0000141 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000141">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000004"/>
-        <obo:IAO_0000115 xml:lang="en">An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.</obo:IAO_0000115>
+        <rdfs:label xml:lang="en">immaterial entity</rdfs:label>
+    </owl:Class>
+    
+
+
+    <!-- http://purl.obolibrary.org/obo/BFO_0000142 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000142">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000140"/>
+        <owl:disjointWith rdf:resource="http://purl.obolibrary.org/obo/BFO_0000146"/>
+        <rdfs:label xml:lang="en">one-dimensional continuant fiat boundary</rdfs:label>
+    </owl:Class>
+    
+
+
+    <!-- http://purl.obolibrary.org/obo/BFO_0000146 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000146">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000140"/>
+        <rdfs:label xml:lang="en">two-dimensional continuant fiat boundary</rdfs:label>
     </owl:Class>
 </rdf:RDF>
 
 
 
-<!-- Generated by the OWL API (version 0.2.2-SNAPSHOT) http://owlapi.sourceforge.net -->
+<!-- Generated by the OWL API (version 4.2.6) https://github.com/owlcs/owlapi -->