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Quick and dirty test of chemessence import. #29175

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Quick and dirty test of chemessence import. #29175

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e6754ae
Quick and dirty test of chemessence import.
balhoff Nov 7, 2024
d56df9d
Run robot repair to migrate to replacement CHEBI terms.
balhoff Nov 14, 2024
fb00507
Remove disjoint.
balhoff Nov 15, 2024
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12 changes: 5 additions & 7 deletions src/ontology/Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -409,11 +409,6 @@ CHEBIRELS = RO:0004007 RO:0004009 RO:0004008 RO:0000057 RO:0002233 RO:0002234 RO
# See: https://github.com/ontodev/robot/issues/175
seed.owl: $(SRC)
$(OWLTOOLS) $(USECAT) $< --remove-imports-declarations -o $@
imports/chebi_import_nogci.owl: bio-chebi.owl imports/chebi_terms_combined.txt $(SRC)
$(ROBOT) extract -i bio-chebi.owl -T imports/chebi_terms_combined.txt --method BOT -O $(BASE)/$@ annotate -V $(RELEASE_URIBASE)/$@ -o $@
imports/chebi_import.owl: imports/chebi_import_nogci.owl seed.owl bio-chebi.owl
$(OWLTOOLS) $(USECAT) seed.owl $< --merge-support-ontologies bio-chebi.owl --add-imports-from-supports --extract-module -s $(OBO)/go/extensions/bio-chebi.owl -c --make-subset-by-properties -n $(CHEBIRELS) // --remove-annotation-assertions -r -l -p 'http://www.geneontology.org/formats/oboInOwl#inSubset' --add-obo-shorthand-to-properties --set-ontology-id $(OBO)/go/$@ -o $@
.PRECIOUS: imports/chebi_import.owl

imports/%_import.obo: imports/%_import.owl
$(ROBOT) convert --input $< --format obo --check false --output [email protected] && grep -v ^owl-axioms: [email protected] > $@
Expand All @@ -423,7 +418,7 @@ imports/%_import.obo: imports/%_import.owl
# ----------------------------------------

# Fix external ontologies to specific versions. These should be updated regularly!
CHEBI_SOURCE=http://purl.obolibrary.org/obo/chebi.owl.gz
CHEBI_SOURCE=https://github.com/cmungall/chemessence/releases/download/v2024-08-23/chemessence.owl
CL_SOURCE=http://purl.obolibrary.org/obo/cl/cl-base.owl
UBERON_SOURCE=http://purl.obolibrary.org/obo/uberon/uberon-base.owl
WBBT_SOURCE=http://purl.obolibrary.org/obo/wbbt/wbbt-base.owl
Expand Down Expand Up @@ -457,7 +452,7 @@ mirror/pr-download.owl: $(SRC)

# special case: download gz for speed for chebi
mirror/chebi-download.owl: $(SRC)
wget --no-check-certificate $(CHEBI_SOURCE) -O [email protected].gz && mv [email protected].gz $@.gz && gunzip -f [email protected] && touch $@
wget --no-check-certificate $(CHEBI_SOURCE) -O [email protected] && mv [email protected] $@ && touch $@
.PRECIOUS: mirror/chebi-download.owl

# special case: use ext for uberon
Expand Down Expand Up @@ -556,6 +551,9 @@ mirror/%.owl: mirror/%-download.owl
$(OWLTOOLS) $< $(FILTER_EXTERNAL) -o $@
.PRECIOUS: mirror/%.owl

mirror/chebi.owl: mirror/chebi-download.owl
cp $< $@

# ----------------------------------------
# CHEBI ROLES
# ----------------------------------------
Expand Down
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