From a3764a0e39661c7577ebba15c1d30f233130d316 Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Sat, 16 Aug 2025 21:17:37 +0300 Subject: [PATCH] Add OBA integration and SSSOM mapping steps Introduces Makefile targets to download oba.owl, merge it with upheno.owl, process with ROBOT, convert to JSON, and generate SSSOM mappings. This extends the pipeline to support phenotype-to-trait mapping using OBA. --- src/ontology/upheno.Makefile | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) diff --git a/src/ontology/upheno.Makefile b/src/ontology/upheno.Makefile index 44fdaf64..774c1014 100644 --- a/src/ontology/upheno.Makefile +++ b/src/ontology/upheno.Makefile @@ -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