From ece699b7ad9ee31fc2ab9fae738686c482c55e4c Mon Sep 17 00:00:00 2001 From: Jim Balhoff Date: Wed, 11 Sep 2024 13:51:35 -0400 Subject: [PATCH] Migrate two owltools steps to robot. (#28902) --- src/ontology/Makefile | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/src/ontology/Makefile b/src/ontology/Makefile index 97beeab44a..e4b9ceacfd 100644 --- a/src/ontology/Makefile +++ b/src/ontology/Makefile @@ -252,7 +252,7 @@ $(GO_LEGO_REACTO).owl: extensions/go-lego-reacto-edit.ofn $(GO_LEGO).owl extensi # go.obo is a simplified; we use oort to remove imports etc # This version of the ontology is used in another step prior to filtering narrow xrefs $(ONT)-pre.owl: reasoned.owl - $(OWLTOOLS) $(USECAT) $< --remove-imports-declarations --remove-dangling --make-subset-by-properties $(GO_MAIN_RELATIONS) --set-ontology-id -v $(RELEASE_URIBASE)/$(ONT).owl $(OBO)/go.owl -o -f owl $@.tmp && mv $@.tmp $@ + $(ROBOT) materialize --input $< --reasoner ELK $(addprefix --term ,$(GO_MAIN_RELATIONS)) remove --select imports --trim true remove --select '' --select complement --select classes --signature true --trim true remove $(addprefix --term ,$(GO_MAIN_RELATIONS)) --select complement --select object-properties --signature true --trim true annotate -O $(OBO)/$(ONT).owl -V $(RELEASE_URIBASE)/$(ONT).owl convert -f owl --output $@.tmp && mv $@.tmp $@ $(ONT)-pre-reduced.owl: $(ONT)-pre.owl $(ROBOT) reduce -r elk -i $< query --update ../sparql/remove-narrow-xrefs.ru -o $@ @@ -275,8 +275,9 @@ go-simple.obo: $(ONT).obo go.owl: $(ONT).obo # remove non-basic relationship types (e.g. has_part) +# assuming materialization step already done for these properties when making go.obo go-simple-filtered.obo: go-simple.obo - $(OWLTOOLS) $< --make-subset-by-properties $(GO_BASIC_RELATIONS) // -o -f obo $@ + $(ROBOT) remove --input $< $(addprefix --term ,$(GO_BASIC_RELATIONS)) --select complement --select object-properties --signature true --trim true convert -f obo --output $@ go-simple-filtered-reduced.obo: go-simple-filtered.obo $(ROBOT) reduce -r elk -i $< -o $@