Merge pull request #63 from obophenotype/wmbo_integration

Wmbo integration

src/ontology/Makefile

@@ -50,7 +50,7 @@ OBODATE ?=                  $(shell date +'%d:%m:%Y %H:%M')
 VERSION=                    $(TODAY)
 ANNOTATE_ONTOLOGY_VERSION = annotate -V $(ONTBASE)/releases/$(VERSION)/$@ --annotation owl:versionInfo $(VERSION)
 ANNOTATE_CONVERT_FILE =     annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) convert -f ofn --output $@.tmp.owl && mv $@.tmp.owl $@
-OTHER_SRC =                 $(PATTERNDIR)/definitions.owl $(COMPONENTSDIR)/bdso-pcl-comp.owl $(COMPONENTSDIR)/whbo-pcl-comp.owl 
+OTHER_SRC =                 $(PATTERNDIR)/definitions.owl $(COMPONENTSDIR)/bdso-pcl-comp.owl $(COMPONENTSDIR)/whbo-pcl-comp.owl $(COMPONENTSDIR)/wmbo-pcl-comp.owl 
 ONTOLOGYTERMS =             $(TMPDIR)/ontologyterms.txt
 EDIT_PREPROCESSED =         $(TMPDIR)/$(ONT)-preprocess.owl
 PATTERNDIR=                 ../patterns
@@ -405,6 +405,7 @@ $(COMPONENTSDIR)/%: | $(COMPONENTSDIR)
 
 
 
+
 # ----------------------------------------
 # Mirroring upstream ontologies
 # ----------------------------------------

src/ontology/catalog-v001.xml

@@ -4,6 +4,7 @@
   <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/pcl/patterns/definitions.owl" uri="../patterns/definitions.owl"/>
   <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/pcl/components/bdso-pcl-comp.owl" uri="components/bdso-pcl-comp.owl"/>
   <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/pcl/components/whbo-pcl-comp.owl" uri="components/whbo-pcl-comp.owl"/>
+  <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/pcl/components/wmbo-pcl-comp.owl" uri="components/wmbo-pcl-comp.owl"/>
 
   <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/pcl.owl" uri="pcl.owl"/>
   <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/pcl/imports/pr_import.owl" uri="imports/pr_import.owl"/>

src/ontology/components/wmbo-pcl-comp.owl

@@ -0,0 +1,14 @@
+<?xml version="1.0"?>
+<rdf:RDF 
+     xml:base="http://purl.obolibrary.org/obo/"
+     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+     xmlns:owl="http://www.w3.org/2002/07/owl#"
+     xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"
+     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/">
+    <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/pcl/components/wmbo-pcl-comp.owl"/>
+
+    <!-- This is a placeholder, it will be regenerated when makefile is first executed -->
+</rdf:RDF>

src/ontology/pcl-edit.owl

@@ -11,6 +11,7 @@ Prefix(dcterms:=<http://purl.org/dc/terms/>)
 Ontology(<http://purl.obolibrary.org/obo/pcl.owl>
 Import(<http://purl.obolibrary.org/obo/pcl/components/bdso-pcl-comp.owl>)
 Import(<http://purl.obolibrary.org/obo/pcl/components/whbo-pcl-comp.owl>)
+Import(<http://purl.obolibrary.org/obo/pcl/components/wmbo-pcl-comp.owl>)
 Import(<http://purl.obolibrary.org/obo/pcl/imports/merged_import.owl>)
 Import(<http://purl.obolibrary.org/obo/pcl/patterns/definitions.owl>)
 Annotation(dce:contributor "https://orcid.org/0000-0001-7258-9596")

src/ontology/pcl-odk.yaml

@@ -66,4 +66,5 @@ robot_java_args: '-Xmx12G'
 components:
   products:
     - filename: bdso-pcl-comp.owl
-    - filename: whbo-pcl-comp.owl
+    - filename: whbo-pcl-comp.owl
+    - filename: wmbo-pcl-comp.owl

src/ontology/pcl.Makefile

@@ -2,18 +2,26 @@
 ## 
 ## If you need to customize your Makefile, make
 ## changes here rather than in the main Makefile
+##
+## Delete files under src/ontology/components
+## Run `sh run.sh make all_components`
+## Run `sh run.sh make prepare_release`
 
-$(SRCMERGED): $(SRC) $(COMPONENTSDIR)/bdso-pcl-comp.owl $(COMPONENTSDIR)/whbo-pcl-comp.owl
+$(SRCMERGED): $(SRC) $(COMPONENTSDIR)/bdso-pcl-comp.owl $(COMPONENTSDIR)/whbo-pcl-comp.owl $(COMPONENTSDIR)/wmbo-pcl-comp.owl
 	$(ROBOT) remove --input $< --select imports --trim false \
 		merge  $(patsubst %, -i %, $(OTHER_SRC)) -o $@
 
 BDSO_BASE_EXT_URL = "https://raw.githubusercontent.com/obophenotype/brain_data_standards_ontologies/master/bdso-pcl-comp.owl"
 $(COMPONENTSDIR)/bdso-pcl-comp.owl: $(SRC)
 	$(ROBOT) annotate -I $(BDSO_BASE_EXT_URL) --ontology-iri $(ONTBASE)/$@ -o $@
 
-WHBO_BASE_EXT_URL = "https://github.com/hkir-dev/whole_human_brain_ontology/raw/main/whbo-pcl-comp.owl"
+WHBO_BASE_EXT_URL = "https://github.com/Cellular-Semantics/whole_human_brain_ontology/raw/main/whbo-pcl-comp.owl"
 $(COMPONENTSDIR)/whbo-pcl-comp.owl: $(SRC)
 	$(ROBOT) annotate -I $(WHBO_BASE_EXT_URL) --ontology-iri $(ONTBASE)/$@ -o $@
+
+WMBO_BASE_EXT_URL = "https://github.com/Cellular-Semantics/whole_mouse_brain_ontology/raw/main/wmbo-pcl-comp.owl"
+$(COMPONENTSDIR)/wmbo-pcl-comp.owl: $(SRC)
+	$(ROBOT) annotate -I $(WMBO_BASE_EXT_URL) --ontology-iri $(ONTBASE)/$@ -o $@
 
 #######################################
 #  Make Combined CL and PCL Product  #

src/ontology/run.sh

@@ -67,7 +67,7 @@ else
     BIND_OPTIONS="-v $(echo $VOLUME_BIND | sed 's/,/ -v /')"
     docker run $ODK_DOCKER_OPTIONS $BIND_OPTIONS -w $WORK_DIR \
         -e ROBOT_JAVA_ARGS="$ODK_JAVA_OPTS" -e JAVA_OPTS="$ODK_JAVA_OPTS" \
-        --rm -ti obolibrary/$ODK_IMAGE:$ODK_TAG $TIMECMD "$@"
+        --rm -ti obolibrary/$ODK_IMAGE:v1.4.3 $TIMECMD "$@"
 fi
 
 case "$@" in