Add check for definition xrefs that are not also term xrefs.

src/ontology/Makefile

@@ -643,7 +643,7 @@ imports/go-taxon-groupings.obo: imports/go-taxon-groupings.owl
 # these live in the ../sparql directory, and have suffix -violation.sparql
 # adding the name here will make the violation check live
 
-VCHECKS = equivalent-classes trailing-whitespace owldef-self-reference synonym-label-match replacedby-obsolete replacedby-namespace duplicate-exact-synonym duplicate-synonym non-IRI-value non-anyURI-value obsolete-definition definition-constraints one-to-one-xrefs-by-subject one-to-one-xrefs-by-value xref-syntax
+VCHECKS = equivalent-classes trailing-whitespace owldef-self-reference synonym-label-match replacedby-obsolete replacedby-namespace duplicate-exact-synonym duplicate-synonym non-IRI-value non-anyURI-value obsolete-definition definition-constraints one-to-one-xrefs-by-subject one-to-one-xrefs-by-value xref-syntax missing-defxref-as-xref
 
 # run all violation checks
 VARGS = $(foreach V,$(VCHECKS), $(SPARQLDIR)/$V-violation.sparql)

src/sparql/missing-defxref-as-xref-violation.sparql

@@ -0,0 +1,24 @@
+prefix oio: <http://www.geneontology.org/formats/oboInOwl#>
+prefix definition: <http://purl.obolibrary.org/obo/IAO_0000115>
+prefix owl: <http://www.w3.org/2002/07/owl#>
+
+SELECT DISTINCT ?cls ?defxref
+WHERE 
+{
+  ?cls a owl:Class .
+  [
+   a owl:Axiom ;
+     owl:annotatedSource ?cls ;
+     owl:annotatedProperty definition: ;
+     oio:hasDbXref ?defxref
+  ]
+  FILTER(STRSTARTS(?defxref, "RHEA")
+      || STRSTARTS(?defxref, "EC")
+      || STRSTARTS(?defxref, "MetaCyc")
+      || STRSTARTS(?defxref, "KEGG")
+      || STRSTARTS(?defxref, "UM-BBD")
+      || STRSTARTS(?defxref, "TC"))
+  FILTER NOT EXISTS {
+    ?cls oio:hasDbXref ?defxref .
+  }
+}