Merge pull request #13 from microbiomedata/issue-12

Issue 12: remove equivalents as subclasses

nmdco.owl

@@ -26,7 +26,7 @@
      xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"
      xmlns:process_attribute="http://purl.obolibrary.org/obo/envo-p/patterns/process_attribute/">
     <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/nmdco.owl">
-        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/nmdco/releases/2021-08-17/nmdco.owl"/>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/nmdco/releases/2021-08-24/nmdco.owl"/>
         <dc:description>The NMDC Ontology (NMDCO) is used  by the National Micrbiome Data Collaborative (NMDC, https://microbiomedata.org) to to annotate metagemoic metadata. 
 
 It is maintained using Github at https://github.com/microbiomedata/nmdc-ontology.
@@ -35,7 +35,7 @@ Please use this GitHub repository&apos;s Issue tracker to request new terms/clas
         <dc:title>NMDC Ontology</dc:title>
         <terms:creator>Bill Duncan (https://orcid.org/0000-0001-9625-1899)</terms:creator>
         <terms:license rdf:resource="https://creativecommons.org/publicdomain/zero/1.0/"/>
-        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2021-08-17</owl:versionInfo>
+        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2021-08-24</owl:versionInfo>
     </owl:Ontology>
 
 

src/ontology/Makefile

@@ -139,7 +139,7 @@ $(ONT)-relation-graph.owl: $(ONT).owl $(ONT)-merged-labels.ttl
 	@echo "\n** building $@ **"
 	relation-graph --ontology-file $< \
 	    --reflexive-subclasses false \
-	    --equivalence-as-subclass true \
+	    --equivalence-as-subclass false \
 	    --non-redundant-output-file $(ONT)-nonredundant.ttl \
 	    --redundant-output-file $(ONT)-redundant.ttl \
 	    --mode rdf
@@ -158,15 +158,21 @@ $(ONT).json: $(ONT)-relation-graph.owl
 	    $(ANNOTATE_ONTOLOGY_VERSION) \
 	    convert --output $@
 
-$(ONT)-classes.json: $(ONT)-relation-graph.owl $(ONT)-merged-labels.ttl
-# select classes, merge with the labels, and convert ontology to json
+$(ONT)-classes.owl: $(ONT)-relation-graph.owl $(ONT)-merged-labels.ttl
+# select classes and merge with the labels
 	@echo "\n** building $@ **"
 	$(ROBOT) filter --input $< \
 	    --select classes \
 	    merge --input $(word 2, $^) \
 	    annotate --ontology-iri $(ONTBASE)/$@ \
 	    $(ANNOTATE_ONTOLOGY_VERSION) \
-	    convert --output $@
+	    --output $@
+
+$(ONT)-classes.json: $(ONT)-classes.owl
+# convert ontology to json
+	@echo "\n** building $@ **"
+	$(ROBOT) annotate --input $< --ontology-iri $(URIBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \
+		convert -o [email protected] && mv [email protected] $@
 
 # -----------------------------------------------------
 # Variant artefacts

src/ontology/imports/envo_import.owl

@@ -19,8 +19,8 @@
      xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"
      xmlns:process_attribute="http://purl.obolibrary.org/obo/envo-p/patterns/process_attribute/">
     <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/nmdco/imports/envo_import.owl">
-        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/nmdco/releases/2021-08-17/imports/envo_import.owl"/>
-        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2021-08-17</owl:versionInfo>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/nmdco/releases/2021-08-24/imports/envo_import.owl"/>
+        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2021-08-24</owl:versionInfo>
     </owl:Ontology>
 
 

src/ontology/imports/po_import.owl

@@ -14,8 +14,8 @@
      xmlns:swrlb="http://www.w3.org/2003/11/swrlb#"
      xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
     <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/nmdco/imports/po_import.owl">
-        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/nmdco/releases/2021-08-17/imports/po_import.owl"/>
-        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2021-08-17</owl:versionInfo>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/nmdco/releases/2021-08-24/imports/po_import.owl"/>
+        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2021-08-24</owl:versionInfo>
     </owl:Ontology>
 
 

src/ontology/imports/ro_import.owl

@@ -18,8 +18,8 @@
      xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#"
      xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
     <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/nmdco/imports/ro_import.owl">
-        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/nmdco/releases/2021-08-17/imports/ro_import.owl"/>
-        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2021-08-17</owl:versionInfo>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/nmdco/releases/2021-08-24/imports/ro_import.owl"/>
+        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2021-08-24</owl:versionInfo>
     </owl:Ontology>