Add obsoletion pipeline sparql queries

monarch-initiative · Aug 16, 2023 · 3f53fd8 · 3f53fd8
1 parent a0b8ca8
commit 3f53fd8
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Showing 3 changed files with 43 additions and 1 deletion.
diff --git a/src/sparql/qc/general/qc-obsoletion-reason.sparql b/src/sparql/qc/general/qc-obsoletion-reason.sparql
@@ -10,7 +10,7 @@ SELECT ?entity ?property ?value WHERE {
   VALUES ?property { IAO:0000231 }
   ?entity ?property ?value .
   FILTER(!isIRI(?value))
-  FILTER(?value!=OMO:00001000 || 
+  FILTER(?value!=OMO:0001000 || 
     ?value!=IAO:0000423 ||
     ?value!=IAO:0000229 ||
     ?value!=MONDO:TermsMerged )

diff --git a/src/sparql/reports/not-under-a-grouping.sparql b/src/sparql/reports/not-under-a-grouping.sparql
@@ -0,0 +1,36 @@
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+prefix IAO: <http://purl.obolibrary.org/obo/IAO_>
+prefix MONDO: <http://purl.obolibrary.org/obo/MONDO_>
+prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+prefix oio: <http://www.geneontology.org/formats/oboInOwl#>
+prefix def: <http://purl.obolibrary.org/obo/IAO_0000115>
+prefix owl: <http://www.w3.org/2002/07/owl#>
+PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
+
+SELECT ?mondo_id ?label ?definition
+
+WHERE
+{
+  ?mondo_id a owl:Class .
+  OPTIONAL {
+  	?mondo_id rdfs:label ?label .
+  }
+  OPTIONAL {
+  	?mondo_id IAO:0000115 ?definition .
+  }
+
+  FILTER((STRSTARTS(STR(?mondo_id),"http://purl.obolibrary.org/obo/MONDO_")))
+
+  FILTER NOT EXISTS { ?mondo_id owl:deprecated true }
+
+  FILTER NOT EXISTS {
+    VALUES ?grouping { 
+        MONDO:0000001
+      MONDO:0042489
+      MONDO:0021178
+      MONDO:0021125
+  }
+    ?mondo_id rdfs:subClassOf* ?grouping .
+  }
+
+}
diff --git a/src/sparql/update/mondo-obsolete-simple.ru b/src/sparql/update/mondo-obsolete-simple.ru
@@ -21,6 +21,12 @@ INSERT {
   ?entity <http://purl.obolibrary.org/obo/IAO_0000231> "out of scope" .
   ?entity <http://purl.obolibrary.org/obo/IAO_0000115> ?obsolete_definition .
   ?def_anno owl:annotatedTarget ?obsolete_definition.
+  ?entity <http://purl.obolibrary.org/obo/IAO_0000231> <http://purl.obolibrary.org/obo/OMO_0001000> .
+  ?xref_anno a owl:Axiom ;
+           owl:annotatedSource ?entity ;
+           owl:annotatedProperty <http://purl.obolibrary.org/obo/IAO_0000231> ;
+           owl:annotatedTarget <http://purl.obolibrary.org/obo/OMO_0001000> ;
+           oboInOwl:source "MONDO:excludeGrouping" .
 }
 
 WHERE {