Add QC to ensure that if we provide evidence for a subset, the mappin…

…g must be exact (#7689) * Create qc-ordo-subset-exact-mapping.sparql * Update src/sparql/qc/mondo/qc-ordo-subset-exact-mapping.sparql * Update src/sparql/qc/mondo/qc-ordo-subset-exact-mapping.sparql Co-authored-by: Nico Matentzoglu <[email protected]> * add back MONDO:obsoleteEquivalent * change annotation to source * fix proxy merge/qc issue * add ordo subset to correct term --------- Co-authored-by: Trish Whetzel <[email protected]> Co-authored-by: Trish Whetzel <[email protected]>
monarch-initiative · Jul 31, 2024 · f49262c · f49262c
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diff --git a/src/ontology/mondo-edit.obo b/src/ontology/mondo-edit.obo
@@ -322116,7 +322116,7 @@ synonym: "susceptibility to autism 18" RELATED DEPRECATED [OMIM:615032]
 xref: MEDGEN:767287 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"}
 xref: OMIM:615032 {source="MONDO:equivalentTo"}
 xref: Orphanet:106 {source="OMIM:615032"}
-xref: Orphanet:642675 {xref="MONDO:equivalentTo"}
+xref: Orphanet:642675 {source="MONDO:equivalentTo"}
 xref: UMLS:C3554373 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:767287"}
 is_a: MONDO:0020836 {source="OMIM:615032"} ! autism, susceptiblity to
 intersection_of: MONDO:0020573 ! inherited disease susceptibility
@@ -328540,6 +328540,7 @@ id: MONDO:0014269
 name: combined oxidative phosphorylation deficiency 19
 def: "Any combined oxidative phosphorylation deficiency in which the cause of the disease is a mutation in the LYRM4 gene." [MONDO:patterns/disease_series_by_gene]
 subset: gard_rare {source="GARD:18466", source="MONDO:GARD"}
+subset: ordo_disorder {source="Orphanet:397593"}
 subset: rare
 synonym: "combined oxidative phosphorylation deficiency 19" EXACT [MONDO:Lexical, OMIM:615595]
 synonym: "combined oxidative phosphorylation deficiency caused by mutation in LYRM4" EXACT [MONDO:design_pattern]
@@ -334441,7 +334442,7 @@ xref: ICD10CM:L50.2 {source="DOID:0090065"}
 xref: MEDGEN:863713 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"}
 xref: OMIM:616115 {source="DOID:0090065", source="MONDO:equivalentTo"}
 xref: Orphanet:47045 {source="DOID:0090065"}
-xref: Orphanet:576349 {xref="MONDO:equivalentTo"}
+xref: Orphanet:576349 {source="MONDO:equivalentTo"}
 xref: UMLS:C4015276 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:863713"}
 is_a: MONDO:0017953 {source="Orphanet:576349"} ! hereditary periodic fever syndrome
 is_a: MONDO:0018768 {source="DC-OMIM:616115", source="DOID:0090065", source="MONDO:Redundant", source="OMIM:616115"} ! familial cold autoinflammatory syndrome
@@ -415705,7 +415706,6 @@ consider: MONDO:0008394
 [Term]
 id: MONDO:0018337
 name: obsolete severe neonatal lactic acidosis due to NFS1-ISD11 complex deficiency
-subset: ordo_disorder {source="Orphanet:397593"}
 subset: otar {source="MONDO:OTAR"}
 xref: GARD:17629 {source="MONDO:obsoleteEquivalent"}
 xref: ICD10CM:E88.8 {source="Orphanet:397593", source="Orphanet:397593/attributed", source="Orphanet:397593/ntbt"}
@@ -505540,7 +505540,7 @@ xref: DOID:0112182 {source="MONDO:equivalentTo"}
 xref: GARD:17217 {source="MONDO:GARD"}
 xref: MEDGEN:78553 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"}
 xref: OMIMPS:276300 {source="MONDO:equivalentTo"}
-xref: Orphanet:252202 {xref="MONDO:equivalentTo"}
+xref: Orphanet:252202 {source="MONDO:equivalentTo"}
 xref: UMLS:C0265325 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:78553"}
 is_a: MONDO:0021190 {source="OMIMPS:276300"} ! DNA repair disease
 relationship: has_characteristic MONDO:0021152 {source="OMIMPS:276300"} ! inherited
@@ -512586,7 +512586,7 @@ synonym: "spinocerebellar ataxia 44" EXACT [OMIM:617691]
 xref: DOID:0080286 {source="MONDO:equivalentTo"}
 xref: MEDGEN:1611168 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"}
 xref: OMIM:617691 {source="DOID:0080286", source="MONDO:equivalentTo"}
-xref: Orphanet:631095 {xref="MONDO:equivalentTo"}
+xref: Orphanet:631095 {source="MONDO:equivalentTo"}
 xref: UMLS:C4521563 {source="MEDGEN:1611168", source="MONDO:equivalentTo", source="MONDO:MEDGEN"}
 is_a: MONDO:0000437 {source="OMIM:617691"} ! cerebellar ataxia
 is_a: MONDO:0020380 {source="DOID:0080286", source="MONDO:Redundant", source="OMIM:617691"} ! autosomal dominant cerebellar ataxia
@@ -525159,7 +525159,7 @@ synonym: "invasive candidiasis" EXACT [NCIT:C116813, Orphanet:636945]
 xref: MEDGEN:296300 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"}
 xref: MESH:D058365 {source="MONDO:equivalentTo"}
 xref: NCIT:C116813 {source="MONDO:equivalentTo"}
-xref: Orphanet:636945 {xref="MONDO:equivalentTo"}
+xref: Orphanet:636945 {source="MONDO:equivalentTo"}
 xref: UMLS:C1609535 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:296300"}
 is_a: MONDO:0002026 {source="MESH:D058365", source="NCIT:C116813"} ! candidiasis
 
@@ -557704,7 +557704,7 @@ synonym: "MRD72" EXACT ABBREVIATION [OMIM:620439]
 synonym: "SRRM2-related neurodevelopmental disorder" EXACT [https://orcid.org/0000-0001-9310-0163]
 xref: MEDGEN:1841248 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"}
 xref: OMIM:620439 {source="MONDO:equivalentTo"}
-xref: Orphanet:652487 {xref="MONDO:equivalentTo"}
+xref: Orphanet:652487 {source="MONDO:equivalentTo"}
 xref: UMLS:C5830612 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:1841248"}
 is_a: MONDO:0100172 {source="OMIM:620439"} ! intellectual disability, autosomal dominant
 

diff --git a/src/sparql/qc/mondo/qc-ordo-subset-exact-mapping.sparql b/src/sparql/qc/mondo/qc-ordo-subset-exact-mapping.sparql
@@ -0,0 +1,37 @@
+prefix owl: <http://www.w3.org/2002/07/owl#>
+prefix oboInOwl: <http://www.geneontology.org/formats/oboInOwl#>
+prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+
+## This QC check ensures that if we have a source for subset, it must 
+## also be mapped to the same term as the subset
+
+SELECT DISTINCT ?entity ?property ?value WHERE {
+    VALUES ?subset {
+        <http://purl.obolibrary.org/obo/mondo#ordo_disorder>
+    }
+    ?entity oboInOwl:inSubset ?subset .
+
+    ?subset_anno a owl:Axiom ;
+           owl:annotatedSource ?entity ;
+           owl:annotatedProperty oboInOwl:inSubset ;
+           owl:annotatedTarget ?subset ;
+           oboInOwl:source ?xref .
+
+    FILTER NOT EXISTS {
+        ?entity oboInOwl:hasDbXref ?xref .
+        VALUES ?mondo_source {
+            "MONDO:obsoleteEquivalent"
+            "MONDO:equivalentTo"
+        }
+        ?xref_anno a owl:Axiom ;
+            owl:annotatedSource ?entity ;
+            owl:annotatedProperty oboInOwl:hasDbXref ;
+            owl:annotatedTarget ?xref ;
+            oboInOwl:source ?mondo_source .
+    }
+    FILTER (STRSTARTS(str(?xref), "Orphanet:"))
+    FILTER (isIRI(?entity) && STRSTARTS(str(?entity), "http://purl.obolibrary.org/obo/MONDO_"))
+    BIND(?xref as ?value)
+    BIND(str(?subset) as ?property)
+}
+ORDER BY ?entity