Updated imports to large file repo

obophenotype · Feb 22, 2019 · e4e84d3 · e4e84d3
1 parent bfc6ce6
commit e4e84d3
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diff --git a/src/metadata/cl-odk.yaml b/src/metadata/cl-odk.yaml
@@ -0,0 +1,34 @@
+id: cl
+title: "Cell Ontology"
+github_org: obophenotype
+repo: cell-ontology
+#report_fail_on: ERROR
+report_fail_on: None
+use_dosdps: TRUE
+export_formats:
+  - owl
+  - obo
+  - json
+import_group:
+  products:
+    - id: pr
+      mirror_from: https://raw.githubusercontent.com/matentzn/large-ontology-dependencies/master/pr.owl.gz
+      use_base: FALSE
+    - id: go
+    - id: uberon 
+    - id: ro
+    - id: chebi
+      mirror_from: https://raw.githubusercontent.com/matentzn/large-ontology-dependencies/master/chebi.owl.gz
+      use_base: FALSE
+    - id: clo
+    - id: pato
+    - id: ncbitaxon
+      mirror_from: https://raw.githubusercontent.com/matentzn/large-ontology-dependencies/master/ncbitaxon.owl.gz
+      use_base: FALSE
+pattern_pipelines_group:
+  products:
+    - id: clustering
+      dosdp_tools_options: "--obo-prefixes=true"
+
+
+
diff --git a/src/ontology/Makefile b/src/ontology/Makefile
@@ -36,7 +36,7 @@ PATTERN_RELEASE_FILES=       $(PATTERNDIR)/definitions.owl $(PATTERNDIR)/pattern
 # ----------------------------------------
 
 all: all_imports patterns all_main all_subsets sparql_test all_reports all_assets
-test: all_reports cl.obo
+test: all_reports cl.owl
 
 ## -- main targets --
 ##
@@ -213,8 +213,7 @@ imports/%_import.obo: imports/%_import.owl
 mirror/pr.trigger: $(SRC)
 
 mirror/pr.owl: mirror/pr.trigger
-	echo "MIRROR skipped: Version contained unsatisfiable classes which need to be fixed first"
-	#$(ROBOT) convert -I https://raw.githubusercontent.com/monarch-ebi-dev/ontologies/master/pr.owl.gz -o $@
+	$(ROBOT) convert -I https://raw.githubusercontent.com/matentzn/large-ontology-dependencies/master/pr.owl.gz -o $@
 
 .PRECIOUS: mirror/%.owl
 
@@ -254,7 +253,7 @@ mirror/ro.owl: mirror/ro.trigger
 mirror/chebi.trigger: $(SRC)
 
 mirror/chebi.owl: mirror/chebi.trigger
-	$(ROBOT) convert -I $(URIBASE)/chebi.owl -o $@
+	$(ROBOT) convert -I https://raw.githubusercontent.com/matentzn/large-ontology-dependencies/master/chebi.owl.gz -o $@
 
 .PRECIOUS: mirror/%.owl
 
@@ -284,7 +283,7 @@ mirror/pato.owl: mirror/pato.trigger
 mirror/ncbitaxon.trigger: $(SRC)
 
 mirror/ncbitaxon.owl: mirror/ncbitaxon.trigger
-	$(ROBOT) convert -I $(URIBASE)/ncbitaxon.owl -o $@
+	$(ROBOT) convert -I https://raw.githubusercontent.com/matentzn/large-ontology-dependencies/master/ncbitaxon.owl.gz -o $@
 
 .PRECIOUS: mirror/%.owl
 

diff --git a/src/ontology/imports/ro_import.owl b/src/ontology/imports/ro_import.owl
@@ -1,20 +1,20 @@
 <?xml version="1.0"?>
 <rdf:RDF xmlns="http://purl.obolibrary.org/obo/cl/imports/ro_import.owl#"
      xml:base="http://purl.obolibrary.org/obo/cl/imports/ro_import.owl"
-     xmlns:dc="http://purl.org/dc/elements/1.1/"
-     xmlns:obo="http://purl.obolibrary.org/obo/"
      xmlns:owl="http://www.w3.org/2002/07/owl#"
-     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
-     xmlns:xml="http://www.w3.org/XML/1998/namespace"
+     xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"
+     xmlns:swrlb="http://www.w3.org/2003/11/swrlb#"
+     xmlns:swrl="http://www.w3.org/2003/11/swrl#"
      xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
-     xmlns:cito="http://purl.org/spar/cito/"
-     xmlns:foaf="http://xmlns.com/foaf/0.1/"
      xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
-     xmlns:swrl="http://www.w3.org/2003/11/swrl#"
+     xmlns:cito="http://purl.org/spar/cito/"
      xmlns:swrla="http://swrl.stanford.edu/ontologies/3.3/swrla.owl#"
-     xmlns:swrlb="http://www.w3.org/2003/11/swrlb#"
-     xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#"
-     xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
+     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+     xmlns:xml="http://www.w3.org/XML/1998/namespace"
+     xmlns:obo="http://purl.obolibrary.org/obo/"
+     xmlns:foaf="http://xmlns.com/foaf/0.1/"
+     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/cl/imports/ro_import.owl">
         <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/cl/releases/2019-02-21/imports/ro_import.owl"/>
     </owl:Ontology>
@@ -5996,118 +5996,6 @@ 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>
@@ -6200,5 +6088,5 @@ 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 4.2.8.20170104-2310) https://github.com/owlcs/owlapi -->