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Update chmo.Makefile to fix failing QC workflow #66

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Merged
StroemPhi merged 2 commits into from
Mar 4, 2026
Merged

Update chmo.Makefile to fix failing QC workflow #66

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cb8c478
Update chmo.Makefile
StroemPhi Mar 4, 2026
ed96aaf
Fix dependency on mirrors being there
StroemPhi Mar 4, 2026
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14 changes: 7 additions & 7 deletions src/ontology/chmo.Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -6,10 +6,10 @@
## Module for ontology: ms
# Using ROBOT extract MIREOT here, as CHMO only reuses one class from MS

$(IMPORTDIR)/ms_import.owl: $(MIRRORDIR)/ms.owl $(IMPORTDIR)/ms_terms_combined.txt
$(IMPORTDIR)/ms_import.owl: $(IMPORTDIR)/ms_terms.txt
if [ $(IMP) = true ]; then $(ROBOT) query -i $< --update ../sparql/preprocess-module.ru \
extract -T $(IMPORTDIR)/ms_terms_combined.txt --copy-ontology-annotations true --force true \
--upper-terms $(IMPORTDIR)/ms_terms_combined.txt --lower-terms $(IMPORTDIR)/ms_terms_combined.txt \
extract -T $(IMPORTDIR)/ms_terms.txt --copy-ontology-annotations true --force true \
--upper-terms $(IMPORTDIR)/ms_terms.txt --lower-terms $(IMPORTDIR)/ms_terms.txt \
--individuals include --method MIREOT \
query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru \
$(ANNOTATE_CONVERT_FILE); fi
Expand All @@ -29,9 +29,9 @@ $(IMPORTDIR)/ms_import.owl: $(MIRRORDIR)/ms.owl $(IMPORTDIR)/ms_terms_combined.t
# and classes used in these, which is quite a time consuming task, but needed, as ROBOT extract pulls in too much
# and the CHEBI module would otherwise be too big to load.

$(IMPORTDIR)/chebi_import.owl: $(MIRRORDIR)/chebi.owl $(IMPORTDIR)/chebi_terms_combined.txt
$(IMPORTDIR)/chebi_import.owl: $(IMPORTDIR)/chebi_terms.txt
if [ $(IMP) = true ] && [ $(IMP_LARGE) = true ]; then $(ROBOT) \
filter -i $< -T $(IMPORTDIR)/chebi_terms_combined.txt --signature true --select "annotations self" \
filter -i $< -T $(IMPORTDIR)/chebi_terms.txt --signature true --select "annotations self" \
--exclude-term http://purl.obolibrary.org/obo/CHEBI_24431 \
--exclude-term http://purl.obolibrary.org/obo/CHEBI_36342 \
query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru \
Expand All @@ -43,9 +43,9 @@ $(IMPORTDIR)/chebi_import.owl: $(MIRRORDIR)/chebi.owl $(IMPORTDIR)/chebi_terms_c
## We need to use the ODK default ROBOT 'extract' method plus 'filter' in here to remove out-of-scope terms that
## get also pulled in. And we remove the NCBITaxon intermediates between OBI:organism and NCBITaxon:Homo Sapiens.

$(IMPORTDIR)/obi_import.owl: $(MIRRORDIR)/obi.owl $(IMPORTDIR)/obi_terms_combined.txt
$(IMPORTDIR)/obi_import.owl: $(IMPORTDIR)/obi_terms.txt
if [ $(IMP) = true ]; then $(ROBOT) query -i $< --update ../sparql/preprocess-module.ru \
extract -T $(IMPORTDIR)/obi_terms_combined.txt --copy-ontology-annotations true --force true \
extract -T $(IMPORTDIR)/obi_terms.txt --copy-ontology-annotations true --force true \
--individuals include --method BOT \
remove --term OBI:0100026 --select "descendants" --exclude-term NCBITaxon:9606 \
remove -T $(IMPORTDIR)/obi_terms_to_remove.txt --select "self instances descendants" \
Expand Down