From 9f43a81c8a26b8f5de6ffe768847c6e17e95a728 Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Fri, 2 Aug 2024 23:12:34 +0300 Subject: [PATCH] Add QC check for proper treatment of preferredExternal annotations (#8012) * Add QC check for proper treatment of preferred external Adding check that ensures that: 1) Xrefs with preferred external must have a corresponding equivalentto on the same class 2) Xrefs with preferred external must be related to another class which are equivalent as well * Add OMIA to xref without source check * remove incorrect xref * remove non-equivalent SCTID:609622007 * remove MONDO:preferredExternal from obsolete OMIM:277610 entry * add MONDO:preferredExternal to DOID:3774, DOID:3773 is obsolete and fix OMIA * remove incorrect xref to Orphanet:3056 * change status of Orphanet:85328 and revert prior change * fix Orphanet:85328 status * add correct orphanet and confirm others are obsolete * add MONDO:equivalentTo OMIA:000605 * remove MONDO:preferredExternal from OMIM:207720 since obsolete * remove prefExt and SCTID that can not be found * fix obsEq * fix proxy merges * edits for MONDO:0010407 * edits for MONDO:0016706 * revert change for MONDO:0010407 --------- Co-authored-by: Trish Whetzel --- src/ontology/mondo-edit.obo | 63 +++++++++---------- .../qc/general/qc-xref-without-source.sparql | 2 +- ...qc-preferred-external-no-equivalent.sparql | 46 ++++++++++++++ 3 files changed, 76 insertions(+), 35 deletions(-) create mode 100644 src/sparql/qc/mondo/qc-preferred-external-no-equivalent.sparql diff --git a/src/ontology/mondo-edit.obo b/src/ontology/mondo-edit.obo index fbba09c5c5..04b17441a9 100644 --- a/src/ontology/mondo-edit.obo +++ b/src/ontology/mondo-edit.obo @@ -8612,8 +8612,7 @@ synonym: "thoracic segment of trunk disease or disorder" EXACT [MONDO:design_pat xref: DOID:0060118 {source="MONDO:obsoleteEquivalent"} xref: MESH:D013896 {source="MONDO:obsoleteEquivalent"} xref: NCIT:C35742 {source="MONDO:obsoleteEquivalent", source="NCIT:C35742"} -xref: SCTID:118946009 {source="MONDO:obsoleteEquivalent", source="MONDO:preferredExternal"} -xref: SCTID:609622007 {source="MONDO:obsoleteEquivalent"} +xref: SCTID:118946009 {source="MONDO:obsoleteEquivalent"} property_value: IAO:0000231 OMO:0001000 property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/4111" xsd:anyURI is_obsolete: true @@ -22840,7 +22839,7 @@ xref: SCTID:10501004 {source="MONDO:equivalentTo", source="DOID:12120"} xref: UMLS:C5400698 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:1763046"} is_a: MONDO:0005275 {source="DOID:12120", source="MESH:D011649", source="MONDO:Entailed", source="NCIT:C85037/inferred"} ! lung disorder relationship: disease_disrupts GO:0007585 ! respiratory gaseous exchange by respiratory system -relationship: disease_has_location CL:0002063 {source="https://orcid.org/0000-0002-6601-2165"} ! pulmonary alveolar type 2 cell +relationship: disease_has_location CL:0002063 {source="https://orcid.org/0000-0002-6601-2165"} ! type II pneumocyte relationship: disease_has_major_feature HP:0006517 ! Intraalveolar phospholipid accumulation [Term] @@ -101110,7 +101109,6 @@ synonym: "pervasive developmental disorders" EXACT [NCIT:C88412] xref: DOID:0060041 {source="MONDO:equivalentTo", source="EFO:0003756"} xref: DOID:0060042 {source="MONDO:relatedTo", source="EFO:0003759"} xref: EFO:0003756 {source="MONDO:equivalentTo", source="MONDO:EFO"} -xref: EFO:0003759 {source="MONDO:preferredExternal"} xref: icd11.foundation:437815624 {source="MONDO:equivalentTo"} xref: MEDGEN:307153 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"} xref: MESH:D002659 {source="EFO:0003756"} @@ -176868,7 +176866,7 @@ xref: MESH:C535776 {source="MONDO:equivalentTo"} xref: MESH:C537494 {source="Orphanet:166100", source="MONDO:equivalentTo", source="MONDO:preferredExternal", source="Orphanet:166100/e"} xref: NORD:1533 {source="MONDO:NORD"} xref: OMIM:184840 {source="Orphanet:166100", source="MONDO:equivalentTo", source="Orphanet:166100/e"} -xref: OMIM:277610 {source="MONDO:equivalentObsolete", source="Orphanet:3450/e", source="MONDO:preferredExternal", source="Orphanet:3450"} +xref: OMIM:277610 {source="MONDO:equivalentObsolete", source="Orphanet:3450/e", source="Orphanet:3450"} xref: Orphanet:166100 {source="MONDO:equivalentTo", source="MONDO:preferredExternal", source="OMIM:184840"} xref: Orphanet:3450 {source="MONDO:equivalentObsolete", source="OMIM:277610"} xref: SCTID:156908005 {source="DOID:4258"} @@ -185331,7 +185329,7 @@ name: obsolete apnea, central sleep synonym: "apnea, central sleep" EXACT [OMIM:107640, OMIM:207720] synonym: "sleep apnea, lethal central" RELATED [OMIM:207720] xref: OMIM:107640 {source="MONDO:obsoleteEquivalent"} -xref: OMIM:207720 {source="MONDO:obsoleteEquivalent", source="MONDO:preferredExternal"} +xref: OMIM:207720 {source="MONDO:obsoleteEquivalent"} property_value: IAO:0000231 OMO:0001000 {source="MONDO:excludeHistoricalDisease"} property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/46" xsd:anyURI property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/6463" xsd:anyURI @@ -230773,7 +230771,7 @@ xref: OMIM:300612 {source="DOID:0060829", source="Orphanet:3056", source="MONDO: xref: OMIM:300706 {source="MONDO:equivalentObsolete", source="DOID:0060811", source="Orphanet:85328", source="Orphanet:85328/e"} xref: OMIM:309590 {source="Orphanet:3056", source="MONDO:equivalentTo"} xref: Orphanet:3056 {source="DOID:0060829", source="MONDO:equivalentObsolete", source="OMIM:300612"} -xref: Orphanet:85328 {source="OMIM:300706", source="MONDO:equivalentObsolete", source="OMIM:309590", source="DOID:0060811", source="MONDO:preferredExternal"} +xref: Orphanet:85328 {source="OMIM:300706", source="MONDO:equivalentObsolete", source="OMIM:309590", source="DOID:0060811"} xref: SCTID:725912001 {source="MONDO:equivalentTo"} xref: UMLS:C2678046 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:394425"} is_a: MONDO:0000001 {source="OMIM:309590"} ! disease @@ -238279,10 +238277,10 @@ xref: GARD:3521 {source="MONDO:GARD"} xref: MEDGEN:1676827 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"} xref: MESH:C537445 {source="MONDO:equivalentTo"} xref: OMIM:309580 {source="Orphanet:73220", source="Orphanet:93971/ntbt", source="Orphanet:93971", source="MONDO:equivalentTo", source="Orphanet:93973", source="Orphanet:73220/e", source="Orphanet:93974", source="GARD:0000081", source="Orphanet:93974/ntbt", source="Orphanet:93973/ntbt"} -xref: Orphanet:73220 {source="MONDO:equivalentObsolete", source="MONDO:preferredExternal", source="OMIM:309580"} -xref: Orphanet:93970 {source="OMIM:309580"} +xref: Orphanet:73220 {source="MONDO:equivalentObsolete", source="OMIM:309580"} +xref: Orphanet:93970 {source="MONDO:equivalentObsolete", source="OMIM:309580"} xref: Orphanet:93971 {source="MONDO:equivalentObsolete", source="OMIM:309580"} -xref: Orphanet:93972 {source="OMIM:309580", source="GARD:0000081"} +xref: Orphanet:93972 {source="MONDO:equivalentObsolete", source="OMIM:309580", source="GARD:0000081"} xref: Orphanet:93973 {source="MONDO:equivalentObsolete", source="OMIM:309580"} xref: Orphanet:93974 {source="MONDO:equivalentObsolete", source="OMIM:309580"} xref: Orphanet:93975 {source="OMIM:309580"} @@ -339557,7 +339555,7 @@ xref: MEDGEN:900671 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"} xref: MESH:C565736 {source="MONDO:equivalentTo"} xref: OMIM:604916 {source="MONDO:equivalentObsolete", source="Orphanet:2729/e", source="Orphanet:2729"} xref: OMIM:616580 {source="MONDO:equivalentTo", source="Orphanet:453504", source="Orphanet:453504/e"} -xref: Orphanet:2729 {source="MONDO:equivalentObsolete", source="MONDO:preferredExternal", source="OMIM:604916"} +xref: Orphanet:2729 {source="MONDO:equivalentObsolete", source="OMIM:604916"} xref: Orphanet:453504 {source="MONDO:equivalentTo"} xref: SCTID:722065002 {source="MONDO:equivalentTo"} xref: UMLS:C4225274 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:900671"} @@ -382188,7 +382186,7 @@ synonym: "chordoid glioma of the third ventricle" EXACT [GARD:0010636] synonym: "chordoid glioma of the third ventricle (WHO grade II)" EXACT [NCIT:C5592] synonym: "chordoid glioma of third ventricle" EXACT [DOID:3773] synonym: "third ventricle chordoid glioma" EXACT [MONDO:patterns/location] -xref: DOID:3773 {source="MONDO:equivalentObsolete", source="MONDO:preferredExternal"} +xref: DOID:3773 {source="MONDO:equivalentObsolete"} xref: DOID:3774 {source="MONDO:equivalentTo"} xref: GARD:20715 {source="MONDO:GARD"} xref: ICD10CM:C71.9 {source="Orphanet:251674", source="Orphanet:251674/ntbt"} @@ -413920,8 +413918,7 @@ xref: NANDO:1201020 {source="MONDO:NANDO", source="https://orcid.org/0000-0003-0 xref: NANDO:2200544 {source="MONDO:NANDO", source="https://orcid.org/0000-0003-0011-764X", source="https://orcid.org/0000-0002-0170-9172"} xref: NCIT:C122662 {source="MONDO:obsoleteEquivalent"} xref: Orphanet:370 {source="MONDO:obsoleteEquivalent"} -xref: SCTID:235908005 {source="MONDO:obsoleteEquivalent", source="MONDO:preferredExternal"} -xref: SCTID:40191005 {source="MONDO:obsoleteEquivalent"} +xref: SCTID:235908005 {source="MONDO:obsoleteEquivalent"} property_value: IAO:0000231 OMO:0001000 property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/3886" xsd:anyURI is_obsolete: true @@ -448371,7 +448368,6 @@ def: "OBSOLETE. Holmes-Gang syndrome is an X-linked mental retardation (XLMR) sy comment: Reason: out of scope. Term to consider: alpha thalassemia-X-linked intellectual disability syndrome' subset: ordo_malformation_syndrome {source="Orphanet:93970"} xref: ICD10CM:Q87.0 {source="Orphanet:93970/attributed", source="Orphanet:93970/ntbt", source="Orphanet:93970"} -xref: Orphanet:93970 {source="MONDO:obsoleteEquivalentObsolete"} property_value: IAO:0000231 OMO:0001000 property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/4130" xsd:anyURI is_obsolete: true @@ -448392,7 +448388,6 @@ def: "OBSOLETE. Juberg-Marsidi syndrome is an X-linked mental retardation (XLMR) subset: ordo_malformation_syndrome {source="Orphanet:93972"} synonym: "juberg Marsidi syndrome" EXACT [] xref: MESH:C537457 {source="Orphanet:93972", source="Orphanet:93972/e"} -xref: Orphanet:93972 {source="MONDO:obsoleteEquivalentObsolete"} xref: SCTID:721875000 {source="MONDO:obsoleteEquivalent"} relationship: excluded_subClassOf MONDO:0001071 {source="https://orcid.org/0000-0001-5208-3432"} ! intellectual disability property_value: IAO:0000231 OMO:0001000 {source="MONDO:excludeHistoricalDisease"} @@ -572872,7 +572867,7 @@ id: MONDO:1011429 name: hepatic lipidosis, non-human animal def: "Hepatic lipidosis that occurs in non-human animals." [MONDO:patterns/nonhuman_disease] xref: OMIA:000548 {source="MONDO:equivalentTo"} -xref: OMIA:000605 {source="MONDO:preferredExternal"} +xref: OMIA:000605 {source="MONDO:equivalentTo", source="MONDO:preferredExternal"} is_a: MONDO:0005583 {source="OMIA:000548", source="OMIA:000605"} ! non-human animal disease intersection_of: MONDO:0005583 ! non-human animal disease intersection_of: MONDO:0700097 MONDO:0004790 ! cross-species analog fatty liver disease @@ -573991,7 +573986,7 @@ id: MONDO:1011527 name: hepatic lipidosis, domestic cat def: "Hepatic lipidosis that occurs in domestic cat." [MONDO:patterns/nonhuman_disease] xref: OMIA:000548-9685 {source="MONDO:equivalentTo"} -xref: OMIA:000605-9685 {source="MONDO:preferredExternal"} +xref: OMIA:000605-9685 {source="MONDO:equivalentTo", source="MONDO:preferredExternal"} is_a: MONDO:1011429 {source="OMIA:000548", source="OMIA:000605", source="https://orcid.org/0000-0002-5002-8648"} ! hepatic lipidosis, non-human animal intersection_of: MONDO:0005583 ! non-human animal disease intersection_of: in_taxon NCBITaxon:9685 ! Felis catus @@ -578890,7 +578885,7 @@ id: MONDO:1012081 name: tetragametic chimerism, bighorn sheep xref: OMIA:000393-37174 {source="MONDO:equivalentTo"} is_a: MONDO:1011918 {source="OMIA:000393", source="https://orcid.org/0000-0002-5002-8648"} ! tetragametic chimerism, non-human animal -relationship: in_taxon NCBITaxon:37174 {source="OMIA:000393-37174", source="https://orcid.org/0000-0002-5002-8648"} ! Ovis canadensis +relationship: in_taxon NCBITaxon:37174 {source="OMIA:000393-37174", source="https://orcid.org/0000-0002-5002-8648"} property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/7225" xsd:anyURI [Term] @@ -578962,7 +578957,7 @@ id: MONDO:1012090 name: gastric dilatation volvulus syndrome, maned wolf xref: OMIA:000404-68728 {source="MONDO:equivalentTo"} is_a: MONDO:1011659 {source="OMIA:000404", source="https://orcid.org/0000-0002-5002-8648"} ! gastric dilatation volvulus syndrome, non-human animal -relationship: in_taxon NCBITaxon:68728 {source="OMIA:000404-68728", source="https://orcid.org/0000-0002-5002-8648"} ! Chrysocyon brachyurus +relationship: in_taxon NCBITaxon:68728 {source="OMIA:000404-68728", source="https://orcid.org/0000-0002-5002-8648"} property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/7225" xsd:anyURI [Term] @@ -579689,7 +579684,7 @@ id: MONDO:1012174 name: myasthenia, Amur tiger xref: OMIA:000684-74533 {source="MONDO:equivalentTo"} is_a: MONDO:1011849 {source="OMIA:000684", source="https://orcid.org/0000-0002-5002-8648"} ! myasthenia, non-human animal -relationship: in_taxon NCBITaxon:74533 {source="OMIA:000684-74533", source="https://orcid.org/0000-0002-5002-8648"} ! Panthera tigris altaica +relationship: in_taxon NCBITaxon:74533 {source="OMIA:000684-74533", source="https://orcid.org/0000-0002-5002-8648"} property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/7225" xsd:anyURI [Term] @@ -579713,7 +579708,7 @@ id: MONDO:1012177 name: myoclonus epilepsy of Lafora, fennec fox xref: OMIA:000690-68732 {source="MONDO:equivalentTo"} is_a: MONDO:1011627 {source="OMIA:000690", source="https://orcid.org/0000-0002-5002-8648"} ! myoclonus epilepsy of Lafora, non-human animal -relationship: in_taxon NCBITaxon:68732 {source="OMIA:000690-68732", source="https://orcid.org/0000-0002-5002-8648"} ! Vulpes zerda +relationship: in_taxon NCBITaxon:68732 {source="OMIA:000690-68732", source="https://orcid.org/0000-0002-5002-8648"} property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/7225" xsd:anyURI [Term] @@ -579737,7 +579732,7 @@ id: MONDO:1012180 name: myoclonus epilepsy of Lafora, Eurasian elk xref: OMIA:000690-9852 {source="MONDO:equivalentTo"} is_a: MONDO:1011627 {source="OMIA:000690", source="https://orcid.org/0000-0002-5002-8648"} ! myoclonus epilepsy of Lafora, non-human animal -relationship: in_taxon NCBITaxon:9852 {source="OMIA:000690-9852", source="https://orcid.org/0000-0002-5002-8648"} ! Alces alces +relationship: in_taxon NCBITaxon:9852 {source="OMIA:000690-9852", source="https://orcid.org/0000-0002-5002-8648"} property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/7225" xsd:anyURI [Term] @@ -580877,7 +580872,7 @@ id: MONDO:1012315 name: congenital erythropoietic porphyria, zebu cattle xref: OMIA:001175-9915 {source="MONDO:equivalentTo"} is_a: MONDO:1011742 {source="OMIA:001175", source="https://orcid.org/0000-0002-5002-8648"} ! congenital erythropoietic porphyria, non-human animal -relationship: in_taxon NCBITaxon:9915 {source="OMIA:001175-9915", source="https://orcid.org/0000-0002-5002-8648"} ! Bos indicus +relationship: in_taxon NCBITaxon:9915 {source="OMIA:001175-9915", source="https://orcid.org/0000-0002-5002-8648"} property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/7225" xsd:anyURI [Term] @@ -581043,7 +581038,7 @@ id: MONDO:1012335 name: bone spavin, red deer xref: OMIA:001232-9860 {source="MONDO:equivalentTo"} is_a: MONDO:1011768 {source="OMIA:001232", source="https://orcid.org/0000-0002-5002-8648"} ! bone spavin, non-human animal -relationship: in_taxon NCBITaxon:9860 {source="OMIA:001232-9860", source="https://orcid.org/0000-0002-5002-8648"} ! Cervus elaphus +relationship: in_taxon NCBITaxon:9860 {source="OMIA:001232-9860", source="https://orcid.org/0000-0002-5002-8648"} property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/7225" xsd:anyURI [Term] @@ -581509,7 +581504,7 @@ name: unilateral subcortical heterotopia, California sea lion xref: OMIA:001463-9704 {source="MONDO:equivalentTo"} is_a: MONDO:1011876 {source="OMIA:001463", source="https://orcid.org/0000-0002-5002-8648"} ! unilateral subcortical heterotopia, non-human animal relationship: excluded_from_qc_check http://purl.obolibrary.org/obo/mondo/sparql/qc/general/qc-single-child.sparql -relationship: in_taxon NCBITaxon:9704 {source="OMIA:001463-9704", source="https://orcid.org/0000-0002-5002-8648"} ! Zalophus californianus +relationship: in_taxon NCBITaxon:9704 {source="OMIA:001463-9704", source="https://orcid.org/0000-0002-5002-8648"} property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/7225" xsd:anyURI [Term] @@ -581561,7 +581556,7 @@ id: MONDO:1012394 name: growth-hormone deficiency dwarfism, zebu cattle xref: OMIA:001473-9915 {source="MONDO:equivalentTo"} is_a: MONDO:1011959 {source="OMIA:001473", source="https://orcid.org/0000-0002-5002-8648"} ! growth-hormone deficiency dwarfism,, non-human animal -relationship: in_taxon NCBITaxon:9915 {source="OMIA:001473-9915", source="https://orcid.org/0000-0002-5002-8648"} ! Bos indicus +relationship: in_taxon NCBITaxon:9915 {source="OMIA:001473-9915", source="https://orcid.org/0000-0002-5002-8648"} property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/7225" xsd:anyURI [Term] @@ -582115,7 +582110,7 @@ id: MONDO:1012457 name: hemangiosarcoma, cockatiel xref: OMIA:001813-13180 {source="MONDO:equivalentTo"} is_a: MONDO:1011823 {source="OMIA:001813", source="https://orcid.org/0000-0002-5002-8648"} ! hemangiosarcoma, non-human animal -relationship: in_taxon NCBITaxon:13180 {source="OMIA:001813-13180", source="https://orcid.org/0000-0002-5002-8648"} ! Nymphicus hollandicus +relationship: in_taxon NCBITaxon:13180 {source="OMIA:001813-13180", source="https://orcid.org/0000-0002-5002-8648"} property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/7225" xsd:anyURI [Term] @@ -582131,7 +582126,7 @@ id: MONDO:1012459 name: hemangiosarcoma, African hunting dog xref: OMIA:001813-9622 {source="MONDO:equivalentTo"} is_a: MONDO:1011823 {source="OMIA:001813", source="https://orcid.org/0000-0002-5002-8648"} ! hemangiosarcoma, non-human animal -relationship: in_taxon NCBITaxon:9622 {source="OMIA:001813-9622", source="https://orcid.org/0000-0002-5002-8648"} ! Lycaon pictus +relationship: in_taxon NCBITaxon:9622 {source="OMIA:001813-9622", source="https://orcid.org/0000-0002-5002-8648"} property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/7225" xsd:anyURI [Term] @@ -582206,7 +582201,7 @@ id: MONDO:1012468 name: pentalogy of Fallot, Amur tiger xref: OMIA:001857-74533 {source="MONDO:equivalentTo"} is_a: MONDO:1011650 {source="OMIA:001857", source="https://orcid.org/0000-0002-5002-8648"} ! pentalogy of Fallot, non-human animal -relationship: in_taxon NCBITaxon:74533 {source="OMIA:001857-74533", source="https://orcid.org/0000-0002-5002-8648"} ! Panthera tigris altaica +relationship: in_taxon NCBITaxon:74533 {source="OMIA:001857-74533", source="https://orcid.org/0000-0002-5002-8648"} property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/7225" xsd:anyURI [Term] @@ -582239,7 +582234,7 @@ name: horn cancer, zebu cattle xref: OMIA:001859-9915 {source="MONDO:equivalentTo"} is_a: MONDO:1011824 {source="OMIA:001859", source="https://orcid.org/0000-0002-5002-8648"} ! horn cancer, non-human animal relationship: excluded_from_qc_check http://purl.obolibrary.org/obo/mondo/sparql/qc/general/qc-single-child.sparql -relationship: in_taxon NCBITaxon:9915 {source="OMIA:001859-9915", source="https://orcid.org/0000-0002-5002-8648"} ! Bos indicus +relationship: in_taxon NCBITaxon:9915 {source="OMIA:001859-9915", source="https://orcid.org/0000-0002-5002-8648"} property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/7225" xsd:anyURI [Term] @@ -582834,7 +582829,7 @@ name: white skin color and iridophoroma, leopard gecko xref: OMIA:002363-481883 {source="MONDO:equivalentTo"} is_a: MONDO:1011901 {source="OMIA:002363", source="https://orcid.org/0000-0002-5002-8648"} ! white skin color and iridophoroma, non-human animal relationship: excluded_from_qc_check http://purl.obolibrary.org/obo/mondo/sparql/qc/general/qc-single-child.sparql -relationship: in_taxon NCBITaxon:481883 {source="OMIA:002363-481883", source="https://orcid.org/0000-0002-5002-8648"} ! Eublepharis macularius +relationship: in_taxon NCBITaxon:481883 {source="OMIA:002363-481883", source="https://orcid.org/0000-0002-5002-8648"} property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/7225" xsd:anyURI [Term] @@ -582870,7 +582865,7 @@ name: neuropathy and feather color dilution, Northern goshawk xref: OMIA:002398-8957 {source="MONDO:equivalentTo"} is_a: MONDO:1011902 {source="OMIA:002398", source="https://orcid.org/0000-0002-5002-8648"} ! neuropathy and feather color dilution, non-human animal relationship: excluded_from_qc_check http://purl.obolibrary.org/obo/mondo/sparql/qc/general/qc-single-child.sparql -relationship: in_taxon NCBITaxon:8957 {source="OMIA:002398-8957", source="https://orcid.org/0000-0002-5002-8648"} ! Accipiter gentilis +relationship: in_taxon NCBITaxon:8957 {source="OMIA:002398-8957", source="https://orcid.org/0000-0002-5002-8648"} property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/7225" xsd:anyURI [Term] @@ -583331,7 +583326,7 @@ def: "An autoinflammatory disease in which the cause of the disease is a variati synonym: "sharpenia" EXACT [https://orcid.org/0000-0002-0146-1162, PMID:38609546] is_a: MONDO:0019751 {source="PMID:38609546", source="https://orcid.org/0000-0002-0146-1162"} ! autoinflammatory syndrome intersection_of: MONDO:0019751 ! autoinflammatory syndrome -intersection_of: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/25321 ! SHARPIN +intersection_of: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/25321 property_value: http://purl.org/dc/elements/1.1/date "2024-07-02T15:47:35Z" xsd:dateTime property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-0587-4693 property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/7706" xsd:anyURI diff --git a/src/sparql/qc/general/qc-xref-without-source.sparql b/src/sparql/qc/general/qc-xref-without-source.sparql index c625fbd96a..bb1b38e23a 100644 --- a/src/sparql/qc/general/qc-xref-without-source.sparql +++ b/src/sparql/qc/general/qc-xref-without-source.sparql @@ -16,7 +16,7 @@ SELECT DISTINCT ?entity ?xref WHERE { } # 20.06.2024: had to remove Orphanet and NCIT as they actually had too many errors # strstarts(str(?xref), "Orphanet:") || strstarts(str(?xref), "ORDO:") || strstarts(str(?xref), "NCIT:") - FILTER (strstarts(str(?xref), "OMIM:") || strstarts(str(?xref), "OMIMPS:") || strstarts(str(?xref), "DOID:")) + FILTER (strstarts(str(?xref), "OMIM:") || strstarts(str(?xref), "OMIMPS:") || strstarts(str(?xref), "DOID:") || strstarts(str(?xref), "OMIA:")) FILTER (isIRI(?entity) && STRSTARTS(str(?entity), "http://purl.obolibrary.org/obo/MONDO_")) } ORDER BY ?entity \ No newline at end of file diff --git a/src/sparql/qc/mondo/qc-preferred-external-no-equivalent.sparql b/src/sparql/qc/mondo/qc-preferred-external-no-equivalent.sparql new file mode 100644 index 0000000000..b0ee330179 --- /dev/null +++ b/src/sparql/qc/mondo/qc-preferred-external-no-equivalent.sparql @@ -0,0 +1,46 @@ +PREFIX skos: +PREFIX rdf: +PREFIX rdfs: +PREFIX IAO: +PREFIX OMO: +PREFIX MONDO: +PREFIX owl: +prefix oboInOwl: + +# description: Ensure that preferredExternal annotations are used correctly + +SELECT ?entity ?property ?value WHERE { + VALUES ?property { oboInOwl:hasDbXref } + { + # Check for cases where there is a preferredExternal annotation + # but no MONDO:equivalentTo + [] owl:annotatedSource ?entity ; + owl:annotatedProperty ?property ; + owl:annotatedTarget ?value ; + oboInOwl:source "MONDO:preferredExternal" . + FILTER NOT EXISTS { + [] owl:annotatedSource ?entity ; + owl:annotatedProperty ?property ; + owl:annotatedTarget ?value ; + oboInOwl:source "MONDO:equivalentTo" . + } + } UNION { + # Check for cases where there is a preferredExternal annotation + # but no MONDO:equivalentTo to a different class + # This indicates that there is no point to saying "preferredExternal" + # as there is nothing this can be preferred to. + [] owl:annotatedSource ?entity ; + owl:annotatedProperty ?property ; + owl:annotatedTarget ?value ; + oboInOwl:source "MONDO:preferredExternal" . + FILTER NOT EXISTS { + [] owl:annotatedSource ?entity2 ; + owl:annotatedProperty ?property ; + owl:annotatedTarget ?value ; + oboInOwl:source "MONDO:equivalentTo" . + } + FILTER(?entity!=?entity2) + FILTER (isIRI(?entity2) && STRSTARTS(str(?entity2), "http://purl.obolibrary.org/obo/MONDO_")) + } + FILTER (isIRI(?entity) && STRSTARTS(str(?entity), "http://purl.obolibrary.org/obo/MONDO_")) +} \ No newline at end of file