Filter out related xrefs. (#29117)

geneontology · Oct 25, 2024 · b12d0ff · b12d0ff
1 parent cf91365
commit b12d0ff
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diff --git 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 (generate-mappings) prior to filtering narrow xrefs, but broad xrefs are filtered here
 $(ONT)-pre.owl: reasoned.owl
-	$(ROBOT) materialize --input $< --reasoner ELK $(addprefix --term ,$(GO_MAIN_RELATIONS)) remove --select imports --trim true remove --select '<http://purl.obolibrary.org/obo/GO_*>' --select complement --select classes --signature true --trim true remove $(addprefix --term ,$(GO_MAIN_RELATIONS)) --select complement --select object-properties --signature true --trim true query --update ../sparql/remove-broad-xrefs.ru annotate -O $(OBO)/$(ONT).owl -V $(RELEASE_URIBASE)/$(ONT).owl convert -f owl --output $@.tmp && mv $@.tmp $@
+	$(ROBOT) materialize --input $< --reasoner ELK $(addprefix --term ,$(GO_MAIN_RELATIONS)) remove --select imports --trim true remove --select '<http://purl.obolibrary.org/obo/GO_*>' --select complement --select classes --signature true --trim true remove $(addprefix --term ,$(GO_MAIN_RELATIONS)) --select complement --select object-properties --signature true --trim true query --update ../sparql/remove-broad-xrefs.ru --update ../sparql/remove-related-xrefs.ru 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 $@

diff --git a/src/sparql/remove-related-xrefs.ru b/src/sparql/remove-related-xrefs.ru
@@ -0,0 +1,16 @@
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX owl: <http://www.w3.org/2002/07/owl#>
+prefix xsd: <http://www.w3.org/2001/XMLSchema#>
+PREFIX oio: <http://www.geneontology.org/formats/oboInOwl#>
+
+DELETE
+WHERE { 
+  ?term oio:hasDbXref ?xref .
+  ?axiom rdf:type owl:Axiom ;
+         owl:annotatedSource ?term ;
+         owl:annotatedProperty oio:hasDbXref ;
+         owl:annotatedTarget ?xref ;
+         oio:source "skos:relatedMatch"^^xsd:string ;
+         ?p ?o .
+}