fixed obi pruning

Author: hrshdhgd

docs/odk-workflows/RepositoryFileStructure.md

@@ -20,7 +20,6 @@ These are the current imports in BERO
 | po | http://purl.obolibrary.org/obo/po.owl | None |
 | omo | http://purl.obolibrary.org/obo/omo.owl | None |
 | ecocore | http://purl.obolibrary.org/obo/ecocore.owl | None |
-| obi | http://purl.obolibrary.org/obo/obi.owl | None |
 | to | http://purl.obolibrary.org/obo/to.owl | None |
 | chebi | http://purl.obolibrary.org/obo/chebi.owl | None |
 | ncbitaxon | http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl | None |
@@ -30,6 +29,7 @@ These are the current imports in BERO
 | edam | https://edamontology.org/EDAM_1.25.owl | custom |
 | pato | http://purl.obolibrary.org/obo/pato.owl | custom |
 | mesh | https://raw.githubusercontent.com/cmungall/mesh2owl/master/mesh-obo.obo | custom |
+| obi | http://purl.obolibrary.org/obo/obi.owl | custom |
 
 ## 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

@@ -97,7 +97,7 @@ all_main: $(MAIN_FILES)
 # ----------------------------------------
 
 
-IMPORTS =  mop po omo ecocore obi to chebi ncbitaxon envo go ncit edam pato mesh
+IMPORTS =  mop po omo ecocore to chebi ncbitaxon envo go ncit edam pato mesh obi
 
 IMPORT_ROOTS = $(patsubst %, $(IMPORTDIR)/%_import, $(IMPORTS))
 IMPORT_OWL_FILES = $(foreach n,$(IMPORT_ROOTS), $(n).owl)
@@ -288,6 +288,10 @@ $(IMPORTDIR)/pato_import.owl: $(MIRRORDIR)/pato.owl
 
 $(IMPORTDIR)/mesh_import.owl: $(MIRRORDIR)/mesh.owl
 	echo "ERROR: You have configured your default module type to be custom; this behavior needs to be overwritten in bero.Makefile!" && false
+## Module for ontology: obi
+
+$(IMPORTDIR)/obi_import.owl: $(MIRRORDIR)/obi.owl
+	echo "ERROR: You have configured your default module type to be custom; this behavior needs to be overwritten in bero.Makefile!" && false
 
 .PHONY: refresh-imports
 refresh-imports:
@@ -356,16 +360,6 @@ mirror-ecocore: | $(TMPDIR)
 		$(ROBOT) convert -i $(MIRRORDIR)/ecocore.owl -o $@.tmp.owl && mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
 
 
-## ONTOLOGY: obi
-.PHONY: mirror-obi
-.PRECIOUS: $(MIRRORDIR)/obi.owl
-mirror-obi: | $(TMPDIR)
-	if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(URIBASE)/obi.owl --create-dirs -o $(MIRRORDIR)/obi.owl --retry 4 --max-time 200 &&\
-		$(ROBOT) convert -i $(MIRRORDIR)/obi.owl -o $@.tmp.owl && \
-		$(ROBOT) remove -i $@.tmp.owl --base-iri $(URIBASE)/OBI --axioms external --preserve-structure false --trim false -o $@.tmp.owl &&\
-		mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
-
-
 ## ONTOLOGY: to
 .PHONY: mirror-to
 .PRECIOUS: $(MIRRORDIR)/to.owl
@@ -444,6 +438,16 @@ mirror-mesh: | $(TMPDIR)
 		mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
 
 
+## ONTOLOGY: obi
+.PHONY: mirror-obi
+.PRECIOUS: $(MIRRORDIR)/obi.owl
+mirror-obi: | $(TMPDIR)
+	if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(URIBASE)/obi.owl --create-dirs -o $(MIRRORDIR)/obi.owl --retry 4 --max-time 200 &&\
+		$(ROBOT) convert -i $(MIRRORDIR)/obi.owl -o $@.tmp.owl && \
+		$(ROBOT) remove -i $@.tmp.owl --base-iri $(URIBASE)/OBI --axioms external --preserve-structure false --trim false -o $@.tmp.owl &&\
+		mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
+
+
 $(MIRRORDIR)/%.owl: mirror-% | $(MIRRORDIR)
 	if [ $(IMP) = true ] && [ $(MIR) = true ] && [ -f $(TMPDIR)/mirror-$*.owl ]; then if cmp -s $(TMPDIR)/mirror-$*.owl $@ ; then echo "Mirror identical, ignoring."; else echo "Mirrors different, updating." &&\
 		cp $(TMPDIR)/mirror-$*.owl $@; fi; fi

src/ontology/bero.Makefile

@@ -66,7 +66,6 @@ $(IMPORTDIR)/obi_import.owl: $(MIRRORDIR)/obi.owl $(IMPORTDIR)/obi_terms_combine
 	if [ $(IMP) = true ]; then $(ROBOT) remove -i $< \
 		--term OBI:0000011 \
 		--select "self descendants" \
-		--select "owl:deprecated='true'^^xsd:boolean" \
 		--signature true \
 		query --update ../sparql/preprocess-module.ru --update ../sparql/inject-subset-declaration.ru --update ../sparql/postprocess-module.ru \
 		annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) --output $@.tmp.owl && mv $@.tmp.owl $@; fi