Merge pull request #2134 from obophenotype/anitacaron/issue1815

Add OMO as import

docs/odk-workflows/RepositoryFileStructure.md

@@ -23,6 +23,7 @@ These are the current imports in CL
 | ro | http://purl.obolibrary.org/obo/ro.owl | None |
 | pato | http://purl.obolibrary.org/obo/pato.owl | None |
 | ncbitaxon | http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl | None |
+| omo | http://purl.obolibrary.org/obo/omo.owl | mirror |
 
 ## Components
 Components, in contrast to imports, are considered full members of the ontology. This means that any axiom in a component is also included in the ontology base - which means it is considered _native_ to the ontology. While this sounds complicated, consider this: conceptually, no component should be part of more than one ontology. If that seems to be the case, we are most likely talking about an import. Components are often not needed for ontologies, but there are some use cases:

src/ontology/Makefile

@@ -113,7 +113,7 @@ all_main: $(MAIN_FILES)
 # ----------------------------------------
 
 
-IMPORTS =  pr go caro uberon ro pato ncbitaxon
+IMPORTS =  pr go caro uberon ro pato ncbitaxon omo
 
 IMPORT_ROOTS =  $(IMPORTDIR)/merged_import
 IMPORT_OWL_FILES = $(foreach n,$(IMPORT_ROOTS), $(n).owl)
@@ -345,6 +345,12 @@ $(IMPORTDIR)/pr_import.owl: $(MIRRORDIR)/merged.owl $(IMPORTDIR)/pr_terms_combin
 		query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru \
 		$(ANNOTATE_CONVERT_FILE); fi
 
+## Module for ontology: omo
+
+$(IMPORTDIR)/omo_import.owl: $(MIRRORDIR)/merged.owl $(IMPORTDIR)/omo_terms_combined.txt
+	if [ $(IMP) = true ]; then $(ROBOT) merge -i $< query --update ../sparql/preprocess-module.ru --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru  \
+    $(ANNOTATE_CONVERT_FILE); fi
+
 
 .PHONY: refresh-imports
 refresh-imports:
@@ -489,6 +495,15 @@ mirror-ncbitaxon: | $(TMPDIR)
 	if [ $(MIR) = true ] && [ $(IMP) = true ]; then $(ROBOT) convert -I http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl -o $@.tmp.owl &&\
 		mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
 
+
+## ONTOLOGY: omo
+.PHONY: mirror-omo
+.PRECIOUS: $(MIRRORDIR)/omo.owl
+mirror-omo: | $(TMPDIR)
+	if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/omo.owl --create-dirs -o $(MIRRORDIR)/omo.owl --retry 4 --max-time 200 &&\
+		$(ROBOT) convert -i $(MIRRORDIR)/omo.owl -o $@.tmp.owl &&\
+		mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
+
 ALL_MIRRORS = $(patsubst %, $(MIRRORDIR)/%.owl, $(IMPORTS))
 MERGE_MIRRORS = true
 

src/ontology/cl-odk.yaml

@@ -68,6 +68,8 @@ import_group:
       use_base: TRUE
     - id: ncbitaxon
       mirror_from: http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl
+    - id: omo
+      module_type: mirror
 pattern_pipelines_group:
   products:
     - id: clustering