diff --git a/src/ontology/uberon.Makefile b/src/ontology/uberon.Makefile index 7f377d609..85210aa77 100644 --- a/src/ontology/uberon.Makefile +++ b/src/ontology/uberon.Makefile @@ -30,15 +30,6 @@ all: uberon-qc .SECONDEXPANSION: -# ---------------------------------------- -# COMMANDS -# ---------------------------------------- - -# FIXME: Is a custom OBO generation rule needed? -# https://github.com/obophenotype/uberon/issues/3014 -MAKEOBO= $(OWLTOOLS) $< --add-obo-shorthand-to-properties -o -f obo --no-check $@.tmp1 && grep -v ^property_value: $@.tmp1 | perl -npe 's@relationship: dc-@property_value: dc-@' | grep -v ^owl-axioms: > $@.tmp && mv $@.tmp $@ - - # ---------------------------------------- # XML CATALOG # ---------------------------------------- @@ -166,12 +157,6 @@ uberon.owl: $(OWLSRC) $(BRIDGEDIR)/uberon-bridge-to-bfo.owl $(DEVELOPS_FROM_CHAI unmerge -i $(DEVELOPS_FROM_CHAIN) \ annotate -O $(URIBASE)/$@ -V $(RELEASE)/$@ -o $@ -# Step 2.1: Generating other formats. -# also do OE check here -uberon.obo: uberon.owl - $(MAKEOBO) -.PRECIOUS: uberon.obo - uberon.json.gz: uberon.json gzip -c $< > $@.tmp && mv $@.tmp $@ .PRECIOUS: uberon.json.gz @@ -1004,9 +989,6 @@ $(TMPDIR)/uberon-taxmod-%.owl: uberon.owl subsets/cumbo.owl: uberon-basic.owl $(OWLTOOLS) $< --extract-ontology-subset --subset cumbo --iri $(URIBASE)/uberon/$@ -o $@ -subsets/cumbo.obo: subsets/cumbo.owl - $(MAKEOBO) - # Common anatony subset common-anatomy.owl: $(ONT).owl $(OWLTOOLS) $< --extract-ontology-subset --fill-gaps --subset common_anatomy \ @@ -1200,15 +1182,6 @@ composite-metazoan.owl: $(TMPDIR)/composite-metazoan.owl composite-vertebrate.owl: $(TMPDIR)/composite-vertebrate.owl $(ROBOT) annotate -i $< --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) -o $@ -# Step 4: OBO version -# Here again we are overriding the standard OWL-to-OBO rules set forth -# by the ODK (https://github.com/obophenotype/uberon/issues/3014) -composite-%.obo: composite-%.owl - $(OWLTOOLS) $< --add-obo-shorthand-to-properties \ - --set-ontology-id -v $(RELEASE)/$@ $(ONTBASE)/$@ \ - -o -f obo --no-check $@.tmp && \ - grep -v ^owl-axioms: $@.tmp > $@ - # Some special products derived from the products generated above # ----------------------------------------