Merge pull request #25 from monarch-initiative/16-include-emapa

Add EMAPA
monarch-initiative · Oct 14, 2022 · 973997d · 973997d
2 parents 61afa3b + e87dfab
commit 973997d
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diff --git a/docs/odk-workflows/RepositoryFileStructure.md b/docs/odk-workflows/RepositoryFileStructure.md
@@ -23,12 +23,14 @@ These are the current imports in PHENIO
 | oba | http://purl.obolibrary.org/obo/oba.owl | None |
 | pato | http://purl.obolibrary.org/obo/pato.owl | None |
 | stato | http://purl.obolibrary.org/obo/stato.owl | None |
+| uberon-bridge-to-emapa | http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-emapa.owl | None |
 | uberon-bridge-to-zfa | http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-zfa.owl | None |
 | uberon-bridge-to-ma | http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-ma.owl | None |
 | uberon-bridge-to-wbbt | http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-wbbt.owl | None |
 | uberon-bridge-to-fbbt | http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-fbbt.owl | None |
 | uberon-bridge-to-fma | http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-fma.owl | None |
 | uberon-bridge-to-nifstd | http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-nifstd.owl | None |
+| cl-bridge-to-emapa | http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-emapa.owl | None |
 | cl-bridge-to-ma | http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-ma.owl | None |
 | cl-bridge-to-fma | http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-fma.owl | None |
 | cl-bridge-to-wbbt | http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-wbbt.owl | None |
@@ -48,6 +50,7 @@ These are the components in PHENIO
 | -------- | --- |
 | bfo.owl | http://purl.obolibrary.org/obo/bfo.owl |
 | fao.owl | http://purl.obolibrary.org/obo/fao.owl |
+| emapa.owl | http://purl.obolibrary.org/obo/emapa.owl |
 | fbbt.owl | http://purl.obolibrary.org/obo/fbbt.owl |
 | go.owl | http://purl.obolibrary.org/obo/go.owl |
 | hsapdv.owl | http://purl.obolibrary.org/obo/hsapdv.owl |

diff --git a/src/ontology/Makefile b/src/ontology/Makefile
@@ -47,7 +47,7 @@ TODAY ?=                    $(shell date +%Y-%m-%d)
 OBODATE ?=                  $(shell date +'%d:%m:%Y %H:%M')
 VERSION=                    $(TODAY)
 ANNOTATE_ONTOLOGY_VERSION = annotate -V $(ONTBASE)/releases/$(VERSION)/$@ --annotation owl:versionInfo $(VERSION)
-OTHER_SRC =                 $(COMPONENTSDIR)/bfo.owl $(COMPONENTSDIR)/fao.owl $(COMPONENTSDIR)/fbbt.owl $(COMPONENTSDIR)/go.owl $(COMPONENTSDIR)/hsapdv.owl $(COMPONENTSDIR)/mondo.owl $(COMPONENTSDIR)/mpath.owl $(COMPONENTSDIR)/nbo.owl $(COMPONENTSDIR)/ro.owl $(COMPONENTSDIR)/uberon.owl $(COMPONENTSDIR)/upheno.owl $(COMPONENTSDIR)/wbbt.owl $(COMPONENTSDIR)/zfa.owl 
+OTHER_SRC =                 $(COMPONENTSDIR)/bfo.owl $(COMPONENTSDIR)/fao.owl $(COMPONENTSDIR)/emapa.owl $(COMPONENTSDIR)/fbbt.owl $(COMPONENTSDIR)/go.owl $(COMPONENTSDIR)/hsapdv.owl $(COMPONENTSDIR)/mondo.owl $(COMPONENTSDIR)/mpath.owl $(COMPONENTSDIR)/nbo.owl $(COMPONENTSDIR)/ro.owl $(COMPONENTSDIR)/uberon.owl $(COMPONENTSDIR)/upheno.owl $(COMPONENTSDIR)/wbbt.owl $(COMPONENTSDIR)/zfa.owl 
 ONTOLOGYTERMS =             $(TMPDIR)/ontologyterms.txt
 
 FORMATS = $(sort  owl json owl)
@@ -98,7 +98,7 @@ all_main: $(MAIN_FILES)
 # ----------------------------------------
 
 
-IMPORTS =  caro chebi eco ncbitaxon-taxslim oba pato stato uberon-bridge-to-zfa uberon-bridge-to-ma uberon-bridge-to-wbbt uberon-bridge-to-fbbt uberon-bridge-to-fma uberon-bridge-to-nifstd cl-bridge-to-ma cl-bridge-to-fma cl-bridge-to-wbbt cl-bridge-to-fbbt cl-bridge-to-zfa
+IMPORTS =  caro chebi eco ncbitaxon-taxslim oba pato stato uberon-bridge-to-emapa uberon-bridge-to-zfa uberon-bridge-to-ma uberon-bridge-to-wbbt uberon-bridge-to-fbbt uberon-bridge-to-fma uberon-bridge-to-nifstd cl-bridge-to-emapa cl-bridge-to-ma cl-bridge-to-fma cl-bridge-to-wbbt cl-bridge-to-fbbt cl-bridge-to-zfa
 
 IMPORT_ROOTS =  $(IMPORTDIR)/merged_import
 IMPORT_OWL_FILES = $(foreach n,$(IMPORT_ROOTS), $(n).owl)
@@ -356,6 +356,17 @@ $(COMPONENTSDIR)/fao.owl:  component-download-fao.owl
 .PRECIOUS: $(COMPONENTSDIR)/fao.owl
 
 
+.PHONY: component-download-emapa.owl
+component-download-emapa.owl: | $(TMPDIR)
+	if [ $(MIR) = true ] && [ $(COMP) = true ]; then $(ROBOT) merge -I http://purl.obolibrary.org/obo/emapa.owl \
+	annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) -o $(TMPDIR)/$@.owl; fi
+
+$(COMPONENTSDIR)/emapa.owl:  component-download-emapa.owl
+	if [ $(COMP) = true ] ; then if cmp -s $(TMPDIR)/component-download-emapa.owl.owl $@ ; then echo "Component identical."; else echo "Component is different, updating." && cp $(TMPDIR)/component-download-emapa.owl.owl $@; fi; fi
+
+.PRECIOUS: $(COMPONENTSDIR)/emapa.owl
+
+
 .PHONY: component-download-fbbt.owl
 component-download-fbbt.owl: | $(TMPDIR)
 	if [ $(MIR) = true ] && [ $(COMP) = true ]; then $(ROBOT) merge -I http://purl.obolibrary.org/obo/fbbt.owl \
@@ -548,6 +559,14 @@ mirror-stato: | $(TMPDIR)
 		mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
 
 
+## ONTOLOGY: uberon-bridge-to-emapa
+.PHONY: mirror-uberon-bridge-to-emapa
+.PRECIOUS: $(MIRRORDIR)/uberon-bridge-to-emapa.owl
+mirror-uberon-bridge-to-emapa: | $(TMPDIR)
+	if [ $(MIR) = true ] && [ $(IMP) = true ]; then $(ROBOT) convert -I http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-emapa.owl -o $@.tmp.owl &&\
+		mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
+
+
 ## ONTOLOGY: uberon-bridge-to-zfa
 .PHONY: mirror-uberon-bridge-to-zfa
 .PRECIOUS: $(MIRRORDIR)/uberon-bridge-to-zfa.owl
@@ -596,6 +615,14 @@ mirror-uberon-bridge-to-nifstd: | $(TMPDIR)
 		mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
 
 
+## ONTOLOGY: cl-bridge-to-emapa
+.PHONY: mirror-cl-bridge-to-emapa
+.PRECIOUS: $(MIRRORDIR)/cl-bridge-to-emapa.owl
+mirror-cl-bridge-to-emapa: | $(TMPDIR)
+	if [ $(MIR) = true ] && [ $(IMP) = true ]; then $(ROBOT) convert -I http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-emapa.owl -o $@.tmp.owl &&\
+		mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
+
+
 ## ONTOLOGY: cl-bridge-to-ma
 .PHONY: mirror-cl-bridge-to-ma
 .PRECIOUS: $(MIRRORDIR)/cl-bridge-to-ma.owl

diff --git a/src/ontology/_import.owl b/src/ontology/_import.owl
diff --git a/src/ontology/phenio-odk.yaml b/src/ontology/phenio-odk.yaml
@@ -33,6 +33,8 @@ import_group:
     - id: oba
     - id: pato
     - id: stato
+    - id: uberon-bridge-to-emapa
+      mirror_from: http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-emapa.owl
     - id: uberon-bridge-to-zfa
       mirror_from: http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-zfa.owl
     - id: uberon-bridge-to-ma
@@ -45,6 +47,8 @@ import_group:
       mirror_from: http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-fma.owl
     - id: uberon-bridge-to-nifstd
       mirror_from: http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-nifstd.owl
+    - id: cl-bridge-to-emapa
+      mirror_from: http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-emapa.owl
     - id: cl-bridge-to-ma
       mirror_from: http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-ma.owl
     - id: cl-bridge-to-fma
@@ -68,6 +72,12 @@ components:
       make_base: TRUE
       base_iris:
         - http://purl.obolibrary.org/obo/FAO_
+    - filename: emapa.owl
+      source: http://purl.obolibrary.org/obo/emapa.owl
+      make_base: TRUE
+      base_iris:
+        - http://purl.obolibrary.org/obo/emapa#
+        - http://purl.obolibrary.org/obo/EMAPA_
     - filename: fbbt.owl
       source: http://purl.obolibrary.org/obo/fbbt.owl
       make_base: TRUE

diff --git a/src/ontology/reports/validate_profile_owl2dl_phenio.owl.txt b/src/ontology/reports/validate_profile_owl2dl_phenio.owl.txt
diff --git a/src/ontology/run.bat b/src/ontology/run.bat
@@ -1 +1 @@
-docker run -v %cd%\..\..\:/work -w /work/src/ontology -e ROBOT_JAVA_ARGS='-Xmx18G' -e JAVA_OPTS='-Xmx18G' --rm -ti obolibrary/odkfull %*
+docker run -v %cd%\..\..\:/work -w /work/src/ontology -e 'ROBOT_JAVA_ARGS=-Xmx24G' -e 'JAVA_OPTS=-Xmx24G' --rm -ti obolibrary/odkfull %*
Original file line number	Diff line number	Diff line change
		@@ -1 +1 @@
		docker run -v %cd%\..\..\:/work -w /work/src/ontology -e ROBOT_JAVA_ARGS='-Xmx18G' -e JAVA_OPTS='-Xmx18G' --rm -ti obolibrary/odkfull %*
		docker run -v %cd%\..\..\:/work -w /work/src/ontology -e 'ROBOT_JAVA_ARGS=-Xmx24G' -e 'JAVA_OPTS=-Xmx24G' --rm -ti obolibrary/odkfull %*