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Add OBA integration and SSSOM mapping steps #1001

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17 changes: 17 additions & 0 deletions src/ontology/upheno.Makefile
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Expand Up @@ -47,6 +47,23 @@ $(REPORTDIR)/upheno-associated-entities.csv: upheno.owl
#$(ROBOT) query -i tmp/mat_upheno.owl -f csv --query ../sparql/phenotype_entity_associations.sparql $@
touch $@

$(TMPDIR)/oba.owl:
wget -O $@ "http://purl.obolibrary.org/obo/oba.owl"

$(TMPDIR)/upheno-oba.owl: upheno.owl $(TMPDIR)/oba.owl $(COMPONENTSDIR)/upheno-haspart-characteristicofpartof-chain.owl
$(ROBOT) merge -i upheno.owl -i $(TMPDIR)/oba.owl -i $(COMPONENTSDIR)/upheno-haspart-characteristicofpartof-chain.owl \
remove --axioms DisjointClasses \
remove --term rdfs:label --select complement --select annotation-properties \
materialize --term BFO:0000051 \
query --update ../sparql/pheno_trait.ru \
reason reduce \
query --update ../sparql/pheno_trait_materialise.ru -o $@

$(TMPDIR)/upheno-oba.json: $(TMPDIR)/upheno-oba.owl
$(ROBOT) convert -i $(TMPDIR)/upheno-oba.owl -o $@

$(MAPPINGDIR)/upheno-oba.sssom.tsv: $(TMPDIR)/upheno-oba.json
sssom parse $(TMPDIR)/upheno-oba.json -I obographs-json -C merged -F UPHENO:phenotypeToTrait -o $@

# NOT USED IN PIPELINE
#$(MAPPINGDIR)/upheno-oba.kgx: $(TMPDIR)/upheno-oba.json
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