From b12d0ff24f52203e5e6d0f5c6b1fcc9644988ab1 Mon Sep 17 00:00:00 2001
From: Jim Balhoff <jim@balhoff.org>
Date: Fri, 25 Oct 2024 15:55:06 -0400
Subject: [PATCH] Filter out related xrefs. (#29117)

---
 src/ontology/Makefile              |  2 +-
 src/sparql/remove-related-xrefs.ru | 16 ++++++++++++++++
 2 files changed, 17 insertions(+), 1 deletion(-)
 create mode 100644 src/sparql/remove-related-xrefs.ru

diff --git a/src/ontology/Makefile b/src/ontology/Makefile
index 870eed4697..bc580b6ca4 100644
--- 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
new file mode 100644
index 0000000000..35b9c7354e
--- /dev/null
+++ 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 .
+}