Associate EnvO classes with NMDC environmental context subset properties

[turbomam]

via ROBOT templates

for example

modules/ebi_biomes.owl: modules/ebi_biomes.csv
	$(ROBOT) template --template $< -i imports/ro_import.owl -o $@.tmp.owl && mv $@.tmp.owl $@

[turbomam]

related?

MODS = entity_attribute_location entity_quality_location entity_attribute process_attribute chemical_concentration
ALL_MODS_OWL = $(patsubst %, modules/%.owl, $(MODS))

$(SRC): $(PRE_SRC)
	$(OWLTOOLS) $(USECAT) $<  $(patsubst %, --remove-import-declaration $(OBO)/envo/modules/%.owl, $(MODS)) -o $@.tmp
	$(OWLTOOLS) $(USECAT) $@.tmp  $(ALL_MODS_OWL) --merge-support-ontologies -o $@

modules/%.owl: modules/%.csv patterns/%.yaml curie_map.yaml 
	@perl -pe 's/\r\n/\n/' $< > $<.tmp && mv $<.tmp $< # replace crlf with lf
	if [ true = true ]; then dosdp-tools generate --table-format=csv --template=./patterns/$*.yaml --outfile=modules/$*.tmp.owl --obo-prefixes=true --infile=modules/$*.csv; fi
	$(ROBOT) annotate --input modules/$*.tmp.owl -O http://purl.obolibrary.org/obo/envo/modules/$*.owl --output modules/$*.owl && rm modules/$*.tmp.owl

modules/%.obo: modules/%.owl
	$(OWLTOOLS) $< -o -f obo $@.tmp && grep -v ^owl-axioms $@.tmp > $@

modules/ebi_biomes.owl: modules/ebi_biomes.csv
	$(ROBOT) template --template $< -i imports/ro_import.owl -o $@.tmp.owl && mv $@.tmp.owl $@

this seems most relevant:

$(SRC): $(PRE_SRC)
	$(OWLTOOLS) $(USECAT) $<  $(patsubst %, --remove-import-declaration $(OBO)/envo/modules/%.owl, $(MODS)) -o $@.tmp
	$(OWLTOOLS) $(USECAT) $@.tmp  $(ALL_MODS_OWL) --merge-support-ontologies -o $@

[turbomam]

closed due to

• NMDC environmental context bindings, Protege 5.6.4 (current) #1599