From b1c09514890cb18e5f9cc4b1f2d0db2ec18697a4 Mon Sep 17 00:00:00 2001 From: Trish Whetzel Date: Sun, 5 Jan 2025 13:47:03 -0800 Subject: [PATCH] Obsoletion status of xref update (#8508) * [create-pull-request] automated change * updated xref equivalent status to match term obsoletion status in source * fix qc check errors * revert Orphanet xref for MONDO:0015238 to equivalentObsolete * revert Orphanet xref for MONDO:0009971 to MONDO:equivalentObsolete * revert Orphanet xref for MONDO:0011054 to equivalentObsolete * revert DOID xref on MONDO:0013209 to equivalentObsolete * revert Orphanet xref on MONDO:0015637 to equivalentObsolete * revert Orphanet xref on MONDO:0015638 to equivalentObsolete * revert Orphanet xref on MONDO:0015639 to equivalentObsolete * revert Orphanet xref for MONDO:0016022 to equivalentObsolete * revert Orphanet xref on MONDO:0018932 to equivalentObsolete * reverted Orphanet xref on MONDO:0018981 to equivalentObsolete * revert Orphanet xref on MONDO:0033672 to equivalentObsolete --------- Co-authored-by: twhetzel --- src/ontology/mondo-edit.obo | 52 ++++++++++++++++++------------------- 1 file changed, 26 insertions(+), 26 deletions(-) diff --git a/src/ontology/mondo-edit.obo b/src/ontology/mondo-edit.obo index 37b68a0c48..b184cd81c1 100644 --- a/src/ontology/mondo-edit.obo +++ b/src/ontology/mondo-edit.obo @@ -32678,7 +32678,7 @@ xref: MedDRA:10016221 {source="Orphanet:99906/e", source="Orphanet:99906"} xref: MEDGEN:8785 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"} xref: MESH:D005203 {source="Orphanet:99906/e", source="Orphanet:99906", source="DOID:14453"} xref: NCIT:C34605 {source="MONDO:equivalentTo", source="DOID:14453"} -xref: Orphanet:99906 {source="MONDO:equivalentTo"} +xref: Orphanet:99906 {source="MONDO:equivalentObsolete"} xref: SCTID:155581001 {source="DOID:14453"} xref: SCTID:18690003 {source="MONDO:equivalentTo", source="DOID:14453"} xref: SCTID:266399001 {source="DOID:14453"} @@ -110423,7 +110423,7 @@ xref: MedDRA:10004941 {source="Orphanet:99908/e", source="Orphanet:99908"} xref: MEDGEN:586 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"} xref: MESH:D001716 {source="Orphanet:99908/e", source="MONDO:equivalentTo", source="EFO:0007170", source="DOID:13891", source="Orphanet:99908"} xref: NCIT:C34425 {source="MONDO:equivalentTo", source="DOID:13891"} -xref: Orphanet:99908 {source="MONDO:equivalentTo"} +xref: Orphanet:99908 {source="MONDO:equivalentObsolete"} xref: SCTID:195987000 {source="DOID:13891"} xref: SCTID:69339004 {source="MONDO:equivalentTo", source="DOID:13891"} xref: UMLS:C0005592 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:586"} @@ -140991,7 +140991,7 @@ synonym: "anemia due to adenosine triphosphatase deficiency" RELATED [GARD:00005 xref: GARD:548 {source="MONDO:GARD"} xref: MEDGEN:350115 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"} xref: MESH:C566311 {source="MONDO:equivalentTo"} -xref: OMIM:102800 {source="MONDO:equivalentTo"} +xref: OMIM:102800 {source="MONDO:equivalentObsolete"} xref: Orphanet:1044 {source="MONDO:equivalentObsolete", source="OMIM:102800"} xref: SCTID:725057008 {source="MONDO:equivalentTo"} xref: UMLS:C1863225 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:350115"} @@ -158045,7 +158045,7 @@ xref: GARD:16724 {source="MONDO:GARD"} xref: ICD10CM:E78.4 {source="Orphanet:79506/attributed", source="Orphanet:79506/ntbt", source="Orphanet:79506"} xref: MEDGEN:840020 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"} xref: OMIM:143470 {source="Orphanet:79506", source="MONDO:equivalentTo", source="Orphanet:79506/e"} -xref: Orphanet:79506 {source="OMIM:143470", source="MONDO:equivalentTo"} +xref: Orphanet:79506 {source="MONDO:equivalentObsolete", source="OMIM:143470"} xref: SCTID:15771000119109 {source="MONDO:equivalentTo"} xref: UMLS:C3875011 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:840020"} is_a: MONDO:0015903 {source="Orphanet:79506"} ! hyperalphalipoproteinemia @@ -174638,7 +174638,7 @@ xref: MESH:D008949 {source="MONDO:equivalentTo", source="DOID:452"} xref: NCIT:C35691 {source="DOID:452"} xref: NCIT:C8602 {source="MONDO:equivalentTo", source="DOID:452"} xref: OMIM:181030 {source="MONDO:equivalentTo", source="Orphanet:454821", source="DOID:452", source="Orphanet:454821/e"} -xref: Orphanet:454821 {source="MONDO:equivalentTo"} +xref: Orphanet:454821 {source="MONDO:equivalentObsolete"} xref: SCTID:447888006 {source="MONDO:equivalentTo"} xref: SCTID:8360001 {source="DOID:452"} xref: UMLS:C1519176 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:275400"} @@ -218560,7 +218560,7 @@ xref: MESH:C566881 {source="MONDO:equivalentTo"} xref: MESH:D006819 {source="DOID:12716", source="EFO:1000644"} xref: NORD:1659 {source="MONDO:NORD"} xref: OMIM:267450 {source="MONDO:equivalentTo", source="Orphanet:70587", source="DOID:12716", source="EFO:1000644", source="Orphanet:70587/e"} -xref: Orphanet:70587 {source="OMIM:267450", source="MONDO:equivalentTo"} +xref: Orphanet:70587 {source="OMIM:267450", source="MONDO:equivalentObsolete"} xref: UMLS:C1968593 {source="MEDGEN:368840", source="MONDO:equivalentTo", source="MONDO:MEDGEN"} is_a: MONDO:0002254 {source="NCIT:C27560"} ! syndromic disease is_a: MONDO:0017015 {source="Orphanet:70587"} ! primary interstitial lung disease specific to childhood @@ -241038,7 +241038,7 @@ subset: obsoletion_candidate synonym: "XH antigen" EXACT [] xref: MEDGEN:854528 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"} xref: MESH:C009691 {source="MONDO:equivalentTo"} -xref: OMIM:314800 {source="MONDO:equivalentTo"} +xref: OMIM:314800 {source="MONDO:equivalentObsolete"} xref: UMLS:C3887689 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:854528"} is_a: MONDO:0003847 {source="https://orcid.org/0000-0001-5208-3432"} ! hereditary disease property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/8409" xsd:anyURI @@ -246991,7 +246991,7 @@ synonym: "telangiectasia, hereditary hemorrhagic, type 3" RELATED [MONDO:Lexical xref: GARD:9902 {source="MONDO:GARD"} xref: MEDGEN:371403 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"} xref: MESH:C537140 {source="MONDO:equivalentTo"} -xref: OMIM:601101 {source="GARD:0009902", source="MONDO:equivalentTo"} +xref: OMIM:601101 {source="GARD:0009902", source="MONDO:equivalentObsolete"} xref: Orphanet:774 {source="GARD:0009902", source="OMIM:601101"} xref: UMLS:C1832774 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:371403"} is_a: MONDO:0019180 {source="DC-OMIM:601101", source="MESH:C537140", source="OMIM:601101"} ! hereditary hemorrhagic telangiectasia @@ -248498,7 +248498,7 @@ xref: ICD10CM:Q73.0 {source="Orphanet:1027", source="Orphanet:1027/attributed", xref: MEDGEN:321955 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"} xref: MESH:C563338 {source="MONDO:equivalentTo"} xref: OMIM:601360 {source="MONDO:equivalentTo", source="Orphanet:1027", source="Orphanet:1027/e"} -xref: Orphanet:1027 {source="MONDO:equivalentTo", source="OMIM:601360"} +xref: Orphanet:1027 {source="MONDO:equivalentObsolete", source="OMIM:601360"} xref: SCTID:726735000 {source="MONDO:equivalentTo"} xref: UMLS:C1832432 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:321955"} is_a: MONDO:0006025 {source="MONDO:Redundant"} ! autosomal recessive disease @@ -292796,7 +292796,7 @@ xref: MESH:C567379 {source="MONDO:equivalentTo"} xref: NANDO:1200362 {source="MONDO:NANDO", source="https://orcid.org/0000-0003-0011-764X", source="https://orcid.org/0000-0002-0170-9172"} xref: NANDO:2200763 {source="MONDO:NANDO", source="https://orcid.org/0000-0003-0011-764X", source="https://orcid.org/0000-0002-0170-9172"} xref: OMIM:612260 {source="Orphanet:183713/e", source="MONDO:equivalentTo", source="Orphanet:183713"} -xref: Orphanet:183713 {source="MONDO:equivalentTo", source="OMIM:612260"} +xref: Orphanet:183713 {source="MONDO:equivalentObsolete", source="OMIM:612260"} xref: UMLS:C2677092 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:383023"} is_a: MONDO:0021094 {source="OMIM:612260", source="https://orcid.org/0000-0001-5208-3432"} ! immunodeficiency disease relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/7562 {source="MONDO:mim2gene_medgen", source="OMIM:612260"} ! MYD88 @@ -302116,7 +302116,7 @@ synonym: "non-alcoholic fatty liver" EXACT [DOID:0080546, MONDO:0007026] synonym: "non-alcoholic fatty liver disease" EXACT [DOID:0080208, NCIT:C84444] synonym: "nonalcoholic fatty liver disease" EXACT [DOID:0080208, NCIT:C84444] xref: DOID:0080208 {source="MONDO:equivalentTo", source="MONDO:preferredExternal"} -xref: DOID:0080546 {source="MONDO:equivalentTo"} +xref: DOID:0080546 {source="MONDO:equivalentObsolete"} xref: EFO:0003095 {source="MONDO:equivalentTo", source="MONDO:EFO"} xref: ICD9:571.8 {source="MONDO:relatedTo", source="MONDO:i2s"} xref: MedDRA:10029530 {source="EFO:1001248"} @@ -351654,7 +351654,7 @@ synonym: "congenital absence of nose and anterior nasopharynx" RELATED [GARD:000 xref: GARD:8755 {source="MONDO:GARD"} xref: ICD10CM:Q87.0 {source="Orphanet:1135/attributed", source="Orphanet:1135/ntbt", source="Orphanet:1135"} xref: NORD:1909 {source="MONDO:NORD"} -xref: Orphanet:1135 {source="GARD:0008755", source="MONDO:equivalentTo"} +xref: Orphanet:1135 {source="GARD:0008755", source="MONDO:equivalentObsolete"} is_a: MONDO:0015161 {source="Orphanet:1135"} ! multiple congenital anomalies/dysmorphic syndrome without intellectual disability property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/7813" xsd:anyURI property_value: IAO:0006012 "2025-02-01" xsd:string @@ -360269,7 +360269,7 @@ subset: rare xref: GARD:20071 {source="MONDO:GARD"} xref: ICD10CM:G40.4 {source="Orphanet:166295/attributed", source="Orphanet:166295/ntbt", source="Orphanet:166295"} xref: MEDGEN:1843116 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"} -xref: Orphanet:166295 {source="MONDO:equivalentTo"} +xref: Orphanet:166295 {source="MONDO:equivalentObsolete"} xref: UMLS:C5680425 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:1843116"} is_a: MONDO:0015642 {source="Orphanet:166295"} ! benign partial infantile seizures @@ -360284,7 +360284,7 @@ xref: GARD:20072 {source="MONDO:GARD"} xref: ICD10CM:G40.2 {source="Orphanet:166299", source="Orphanet:166299/attributed", source="Orphanet:166299/ntbt"} xref: icd11.foundation:147618459 {source="MONDO:equivalentTo"} xref: MEDGEN:1654146 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"} -xref: Orphanet:166299 {source="MONDO:equivalentTo"} +xref: Orphanet:166299 {source="MONDO:equivalentObsolete"} xref: UMLS:C4749347 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:1654146"} is_a: MONDO:0015637 {source="Orphanet:166299"} ! benign non-familial infantile seizures @@ -360299,7 +360299,7 @@ xref: GARD:20073 {source="MONDO:GARD"} xref: ICD10CM:G40.1 {source="Orphanet:166302", source="Orphanet:166302/attributed", source="Orphanet:166302/ntbt"} xref: icd11.foundation:413225821 {source="MONDO:equivalentTo"} xref: MEDGEN:1656339 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"} -xref: Orphanet:166302 {source="MONDO:equivalentTo"} +xref: Orphanet:166302 {source="MONDO:equivalentObsolete"} xref: UMLS:C4749728 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:1656339"} is_a: MONDO:0015637 {source="Orphanet:166302"} ! benign non-familial infantile seizures @@ -366858,7 +366858,7 @@ xref: GARD:920 {source="MONDO:obsoleteEquivalent", source="MONDO:GARD"} xref: ICD10CM:Q78.4 {source="Orphanet:1844/inclusion", source="Orphanet:1844", source="Orphanet:1844/ntbt"} xref: icd11.foundation:2054115498 {source="MONDO:obsoleteEquivalent"} xref: MEDGEN:929662 {source="MONDO:obsoleteEquivalent", source="MONDO:MEDGEN"} -xref: Orphanet:1844 {source="MONDO:obsoleteEquivalent"} +xref: Orphanet:1844 {source="MONDO:obsoleteEquivalentObsolete"} xref: SCTID:720566004 {source="MONDO:obsoleteEquivalent"} xref: UMLS:C4303993 {source="MONDO:obsoleteEquivalent", source="MEDGEN:929662", source="MONDO:MEDGEN"} property_value: IAO:0000231 OMO:0001000 {source="MONDO:excludeHistoricalDisease"} @@ -367834,7 +367834,7 @@ xref: MEDGEN:124373 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"} xref: MESH:D004831 {source="DOID:308"} xref: NANDO:1200594 {source="MONDO:NANDO", source="https://orcid.org/0000-0003-0011-764X", source="https://orcid.org/0000-0002-0170-9172"} xref: NCIT:C116593 {source="MONDO:equivalentTo"} -xref: Orphanet:1935 {source="MONDO:equivalentTo"} +xref: Orphanet:1935 {source="MONDO:equivalentObsolete"} xref: SCTID:192847001 {source="DOID:308"} xref: SCTID:192992007 {source="DOID:308"} xref: SCTID:37356005 {source="DOID:308"} @@ -392075,7 +392075,7 @@ subset: rare synonym: "Heide syndrome" EXACT [Orphanet:2787] xref: GARD:18778 {source="MONDO:GARD"} xref: MEDGEN:899606 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"} -xref: Orphanet:2787 {source="MONDO:equivalentTo"} +xref: Orphanet:2787 {source="MONDO:equivalentObsolete"} xref: SCTID:716189005 {source="MONDO:equivalentTo"} xref: UMLS:C4274786 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:899606"} is_a: MONDO:0002254 {source="https://orcid.org/0000-0001-5208-3432"} ! syndromic disease @@ -412668,7 +412668,7 @@ xref: GARD:18823 {source="MONDO:GARD"} xref: ICD10CM:I72.0 {source="Orphanet:36382", source="Orphanet:36382/attributed", source="Orphanet:36382/ntbt"} xref: ICD10CM:I72.5 {source="Orphanet:36382", source="Orphanet:36382/attributed", source="Orphanet:36382/ntbt"} xref: MEDGEN:1659372 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"} -xref: Orphanet:36382 {source="MONDO:equivalentTo"} +xref: Orphanet:36382 {source="MONDO:equivalentObsolete"} xref: UMLS:C4755308 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:1659372"} is_a: MONDO:0006061 {source="https://orcid.org/0000-0001-5208-3432"} ! cervical artery dissection intersection_of: MONDO:0006061 ! cervical artery dissection @@ -419873,7 +419873,7 @@ name: obsolete intellectual disability-expressive aphasia-facial dysmorphism syn subset: otar {source="MONDO:OTAR"} synonym: "intellectual disability-loss of expressive language-facial dysmorphism syndrome" EXACT [] xref: ICD10CM:Q87.0 {source="Orphanet:436151", source="Orphanet:436151/attributed", source="Orphanet:436151/ntbt"} -xref: Orphanet:436151 {source="MONDO:obsoleteEquivalent"} +xref: Orphanet:436151 {source="MONDO:obsoleteEquivalentObsolete"} relationship: excluded_subClassOf MONDO:0000508 {source="Orphanet:436151", source="https://orcid.org/0000-0001-5208-3432"} ! syndromic intellectual disability property_value: IAO:0000231 OMO:0001000 {source="MONDO:excludeGrouping"} property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/5114" xsd:anyURI @@ -427592,7 +427592,7 @@ xref: GARD:18852 {source="MONDO:GARD"} xref: ICD10CM:I42.8 {source="Orphanet:57777", source="Orphanet:57777/ntbt"} xref: icd11.foundation:1268082489 {source="MONDO:equivalentTo"} xref: MEDGEN:1391593 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"} -xref: Orphanet:57777 {source="MONDO:equivalentTo"} +xref: Orphanet:57777 {source="MONDO:equivalentObsolete"} xref: SCTID:725416005 {source="MONDO:equivalentTo"} xref: UMLS:C4511053 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:1391593"} is_a: MONDO:0016330 {source="Orphanet:57777"} ! non-familial hypertrophic cardiomyopathy @@ -429053,7 +429053,7 @@ xref: GARD:18860 {source="MONDO:GARD"} xref: ICD10CM:G40.4 {source="Orphanet:64545/ntbt", source="Orphanet:64545"} xref: icd11.foundation:1131336245 {source="MONDO:equivalentTo"} xref: MEDGEN:140738 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"} -xref: Orphanet:64545 {source="MONDO:equivalentTo"} +xref: Orphanet:64545 {source="MONDO:equivalentObsolete"} xref: UMLS:C0393693 {source="MEDGEN:140738", source="MONDO:equivalentTo", source="MONDO:MEDGEN"} is_a: MONDO:0020070 {source="Orphanet:64545"} ! neonatal epilepsy syndrome relationship: has_characteristic HP:0003623 {source="Orphanet:64545"} ! Neonatal onset @@ -461600,7 +461600,7 @@ xref: GARD:19703 {source="MONDO:GARD"} xref: ICD10CM:J67.8 {source="Orphanet:99907/ntbt", source="Orphanet:99907"} xref: icd11.foundation:1985023223 {source="MONDO:equivalentTo"} xref: MEDGEN:1387737 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"} -xref: Orphanet:99907 {source="MONDO:equivalentTo"} +xref: Orphanet:99907 {source="MONDO:equivalentObsolete"} xref: SCTID:725415009 {source="MONDO:equivalentTo"} xref: UMLS:C4511048 {source="MEDGEN:1387737", source="MONDO:equivalentTo", source="MONDO:MEDGEN"} is_a: MONDO:0017853 {source="Orphanet:99907"} ! hypersensitivity pneumonitis @@ -461617,7 +461617,7 @@ replaced_by: MONDO:0005668 id: MONDO:0020537 name: obsolete occupational allergic alveolitis def: "OBSOLETE. Occupational allergic alveolitis designates a hypersensitivity pneumonitis resulting from the inhalation of an antigen to which an individual has been previously sensitized in his/her occupational environment. Symptoms vary depending on the antigen and the form (acute, subacute, chronic) of the disease. They may be cough, dyspnea, chills, fever, weight loss, loss of appetite and general malaise" [Orphanet:99909] -xref: Orphanet:99909 {source="MONDO:obsoleteEquivalent"} +xref: Orphanet:99909 {source="MONDO:obsoleteEquivalentObsolete"} property_value: IAO:0000231 OMO:0001000 {source="MONDO:excludeGrouping"} property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/5114" xsd:anyURI property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/6693" xsd:anyURI @@ -513710,7 +513710,7 @@ subset: gard_rare {source="GARD:18842", source="MONDO:GARD"} subset: rare xref: GARD:18842 {source="MONDO:GARD"} xref: MEDGEN:928219 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"} -xref: Orphanet:50817 {source="MONDO:equivalentTo"} +xref: Orphanet:50817 {source="MONDO:equivalentObsolete"} xref: UMLS:C4302550 {source="MEDGEN:928219", source="MONDO:equivalentTo", source="MONDO:MEDGEN"} is_a: MONDO:0000001 {source="Orphanet:50817"} ! disease is_a: MONDO:0002254 {source="https://orcid.org/0000-0002-4142-7153"} ! syndromic disease @@ -528508,7 +528508,7 @@ xref: EFO:1001967 {source="MONDO:equivalentTo", source="MONDO:EFO"} xref: GARD:17929 {source="MONDO:GARD"} xref: MEDGEN:83545 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"} xref: NCIT:C7991 {source="MONDO:equivalentTo"} -xref: Orphanet:500481 {source="MONDO:equivalentTo"} +xref: Orphanet:500481 {source="MONDO:equivalentObsolete"} xref: UMLS:C0279697 {source="MEDGEN:83545", source="MONDO:equivalentTo", source="MONDO:MEDGEN"} is_a: MONDO:0000521 {source="MONDO:Redundant", source="NCIT:C7991"} ! salivary gland carcinoma is_a: MONDO:0010150 {source="NCIT:C7991"} ! head and neck squamous cell carcinoma