Merge pull request #3129 from obophenotype/new-composite-pipeline

New composite pipeline

.gitignore

@@ -194,6 +194,7 @@ composite-metazoan.*
 composite-metazoan-basic.*
 composite-vertebrate.*
 composite-vertebrate-basic.*
+collected-metazoan.*
 ext.json
 ext.obo
 ext.owl
@@ -215,4 +216,4 @@ src/ontology/subsets/*.json
 src/ontology/subsets/*.obo
 src/ontology/subsets/*.owl
 src/ontology/subsets/*.tsv
-src/ontology/imports/*_import.owl
+src/ontology/imports/*_import.owl

src/ontology/Makefile

@@ -62,7 +62,7 @@ PATTERN_RELEASE_FILES=      $(PATTERNDIR)/definitions.owl $(PATTERNDIR)/pattern.
 
 FORMATS = $(sort  owl obo json owl)
 FORMATS_INCL_TSV = $(sort $(FORMATS) tsv)
-RELEASE_ARTEFACTS = $(sort $(ONT)-base $(ONT)-full $(ONT)-simple $(ONT)-basic basic composite-metazoan composite-metazoan-basic composite-vertebrate composite-vertebrate-basic common-anatomy )
+RELEASE_ARTEFACTS = $(sort $(ONT)-base $(ONT)-full $(ONT)-simple $(ONT)-basic basic collected-metazoan composite-metazoan composite-metazoan-basic composite-vertebrate composite-vertebrate-basic common-anatomy )
 
 # ----------------------------------------
 # Top-level targets
@@ -706,6 +706,12 @@ basic.json: basic.owl
 	$(ROBOT) annotate --input $< --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \
 		convert --check false -f json -o $@.tmp.json &&\
 		mv $@.tmp.json $@
+collected-metazoan.obo: collected-metazoan.owl
+	$(ROBOT) convert --input $< --check false -f obo $(OBO_FORMAT_OPTIONS) -o $@.tmp.obo && grep -v ^owl-axioms $@.tmp.obo > $@ && rm $@.tmp.obo
+collected-metazoan.json: collected-metazoan.owl
+	$(ROBOT) annotate --input $< --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \
+		convert --check false -f json -o $@.tmp.json &&\
+		mv $@.tmp.json $@
 composite-metazoan.obo: composite-metazoan.owl
 	$(ROBOT) convert --input $< --check false -f obo $(OBO_FORMAT_OPTIONS) -o $@.tmp.obo && grep -v ^owl-axioms $@.tmp.obo > $@ && rm $@.tmp.obo
 composite-metazoan.json: composite-metazoan.owl
@@ -810,6 +816,9 @@ $(ONT)-basic.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) $(SIMPLESEED) $(KEEPRELATION
 basic.owl:
 	echo "ERROR: You have configured a custom release artefact ($@); this release artefact needs to be define in uberon.Makefile!" && false
 
+collected-metazoan.owl:
+	echo "ERROR: You have configured a custom release artefact ($@); this release artefact needs to be define in uberon.Makefile!" && false
+
 composite-metazoan.owl:
 	echo "ERROR: You have configured a custom release artefact ($@); this release artefact needs to be define in uberon.Makefile!" && false
 

src/ontology/bridge/collected-adult-mammal-hdr.owl

@@ -0,0 +1,51 @@
+<?xml version="1.0"?>
+<rdf:RDF xmlns="http://purl.obolibrary.org/obo/uberon/bridge/collected-adult-mammal.owl#"
+     xml:base="http://purl.obolibrary.org/obo/uberon/bridge/collected-adult-mammal.owl"
+     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:xsd="http://www.w3.org/2001/XMLSchema#"
+     xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
+     xmlns:terms="http://purl.org/dc/terms/">
+    <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/uberon/bridge/collected-adult-mammal.owl">
+        <terms:creator>Uberon editors</terms:creator>
+        <terms:description>This is an ontology that collects all of the core Uberon, plus the adult anatomy ontology for mouse (MA). Note that it does no longer include the adult anatomy ontology for human (FMA).</terms:description>
+        <terms:title>Collected anatomy ontology for post-natal mammals</terms:title>
+        <rdfs:comment>Uberon ontologies with the prefix ‘collected’ are ontologies that import the core Uberon ontology together with one or more external, typically species-centric, ontologies plus bridging axioms that connect Uberon to those external ontologies. Uberon ontologies with the prefix ‘composite’ are variations of the corresponding ‘collected’ ontologies with additional reasoning performed.</rdfs:comment>
+        <rdfs:seeAlso rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://genomebiology.com/2012/13/1/R5</rdfs:seeAlso>
+    </owl:Ontology>
+
+
+
+    <!-- 
+    ///////////////////////////////////////////////////////////////////////////////////////
+    //
+    // Annotation properties
+    //
+    ///////////////////////////////////////////////////////////////////////////////////////
+     -->
+
+
+
+
+    <!-- http://purl.org/dc/terms/creator -->
+
+    <owl:AnnotationProperty rdf:about="http://purl.org/dc/terms/creator"/>
+
+
+
+    <!-- http://purl.org/dc/terms/description -->
+
+    <owl:AnnotationProperty rdf:about="http://purl.org/dc/terms/description"/>
+
+
+
+    <!-- http://purl.org/dc/terms/title -->
+
+    <owl:AnnotationProperty rdf:about="http://purl.org/dc/terms/title"/>
+</rdf:RDF>
+
+
+
+<!-- Generated by the OWL API (version 4.5.26) https://github.com/owlcs/owlapi -->
+