diff --git a/src/ontology/mondo-edit.obo b/src/ontology/mondo-edit.obo index 0e01c3c2f8..ee7c794d5e 100644 --- a/src/ontology/mondo-edit.obo +++ b/src/ontology/mondo-edit.obo @@ -33383,7 +33383,7 @@ synonym: "recurrent major depression" EXACT [DOID:1470] synonym: "single major depressive episode" EXACT [DOID:1470] synonym: "unipolar depression" EXACT [MONDO:0005263] synonym: "unipolar depression, susceptibility to" EXACT [OMIM:608516, OMIM:genemap2] -xref: DOID:1470 {source="MONDO:equivalentTo", xref="EFO:0003761"} +xref: DOID:1470 {source="EFO:0003761", source="MONDO:equivalentTo"} xref: DOID:2848 {source="EFO:0003761", source="MONDO:directSiblingOf"} xref: EFO:0003761 {source="MONDO:equivalentTo", source="MONDO:EFO"} xref: ICD10CM:F32 {source="DOID:1470"} @@ -60315,7 +60315,7 @@ xref: MEDGEN:770969 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"} xref: NCIT:C40270 {source="MONDO:equivalentTo", source="DOID:5170"} xref: UMLS:C3642329 {source="MEDGEN:770969", source="MONDO:equivalentTo", source="MONDO:MEDGEN"} is_a: MONDO:0002140 {source="DOID:5170", source="MONDO:Redundant"} ! vagina sarcoma -is_a: MONDO:0003314 {comment="https://orcid.org/0000-0001-5208-3432"} ! endometrioid stromal and related neoplasms of the vagina +is_a: MONDO:0003314 {source="https://orcid.org/0000-0001-5208-3432"} ! endometrioid stromal and related neoplasms of the vagina is_a: MONDO:0005089 {source="DOID:5170/inferred"} ! sarcoma intersection_of: MONDO:0006745 ! endometrioid stromal sarcoma intersection_of: disease_has_location UBERON:0000996 ! vagina @@ -97161,7 +97161,7 @@ relationship: excluded_subClassOf MONDO:0005233 {source="DOID:3907", source="ONC id: MONDO:0005098 name: stroke disorder def: "A sudden loss of neurological function secondary to hemorrhage or ischemia in the brain parenchyma due to a vascular event." [NCIT:C3390] -comment: Stroke includes two main types, hemorrhagic and ischemic. Both types of stroke can cause acute seizures at the time of the acute event, as well as epilepsy as a long-term complication. In the elderly, cerebrovascular disease and stroke are the most common cause of acute seizures and epilepsy. {xref="https://orcid.org/0000-0001-5208-3432", xref="https://www.epilepsydiagnosis.org/etiology/stroke-overview.html"} +comment: Stroke includes two main types, hemorrhagic and ischemic. Both types of stroke can cause acute seizures at the time of the acute event, as well as epilepsy as a long-term complication. In the elderly, cerebrovascular disease and stroke are the most common cause of acute seizures and epilepsy. (https://www.epilepsydiagnosis.org/etiology/stroke-overview.html, https://orcid.org/0000-0001-5208-3432) subset: otar {source="MONDO:OTAR"} synonym: "cerebral infarction" RELATED [NCIT:C3390] synonym: "cerebrovascular accident" EXACT [NCIT:C3390] @@ -100856,7 +100856,7 @@ replaced_by: MONDO:0018912 id: MONDO:0005244 name: peripheral neuropathy def: "A disorder affecting the peripheral nervous system. It manifests with pain, tingling, numbness, and muscle weakness. It may be the result of physical injury, toxic substances, viral diseases, diabetes, renal failure, cancer, and drugs." [NCIT:C119734] -comment: Editor note: NCIT draws a distinction between neuropathy and peripheral neuropathy see https://github.com/NCI-Thesaurus/thesaurus-obo-edition/issues/20 +comment: Editor note: NCIT draws a distinction between neuropathy and peripheral neuropathy see https://github.com/NCI-Thesaurus/thesaurus-obo-edition/issues/20. Also, location of occurrence may also include optic nerve which is not PNS. subset: gard_rare {source="GARD:12192", source="MONDO:GARD"} subset: otar {source="MONDO:OTAR"} subset: rare @@ -100880,7 +100880,7 @@ xref: SCTID:42658009 {source="DOID:870"} xref: UMLS:C0031117 {source="MEDGEN:18386", source="MONDO:equivalentTo", source="MONDO:MEDGEN"} is_a: MONDO:0003620 {source="DOID:870", source="NCIT:C119734", source="NCIT:C119734/inferred", source="NCIT:C4731"} ! peripheral nervous system disorder is_a: MONDO:0019056 {source="ISBN-13:978-1-259-64403-0"} ! neuromuscular disease -relationship: disease_has_location UBERON:0000010 {comment="may also include optic nerve which is not PNS"} ! peripheral nervous system +relationship: disease_has_location UBERON:0000010 ! peripheral nervous system [Term] id: MONDO:0005245 @@ -101126,7 +101126,7 @@ relationship: curated_content_resource https://search.clinicalgenome.org/kb/cond id: MONDO:0005259 name: Asperger syndrome def: "A disorder most often diagnosed in the pediatric years in which the individual displays marked impairment in social interaction and a repetitive, stereotyped pattern of behavior. The individual, however, displays no delay in language or cognitive development, which differentiates Asperger Syndrome from autism." [NCIT:C97159] -comment: The name Aspergers is controversial, however, it seems to be the community accepted name. {xref="https://github.com/monarch-initiative/mondo/issues/705", xref="https://blogs.scientificamerican.com/observations/the-problem-with-aspergers/", xref="https://github.com/EBISPOT/efo/issues/275"} +comment: The name Aspergers is controversial, however, it seems to be the community accepted name. (https://blogs.scientificamerican.com/observations/the-problem-with-aspergers/, https://github.com/EBISPOT/efo/issues/275, https://github.com/monarch-initiative/mondo/issues/705) subset: inferred_rare subset: otar {source="MONDO:OTAR"} subset: rare @@ -101731,7 +101731,7 @@ xref: SCTID:39621005 {source="MONDO:equivalentTo", source="DOID:0060262"} xref: UMLS:C0016977 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:8947"} intersection_of: MONDO:0000001 ! disease intersection_of: disease_has_location UBERON:0002110 ! gallbladder -relationship: excluded_subClassOf MONDO:0003847 {source="https://orcid.org/0000-0001-5208-3432", comment="OMIMPS:600803"} ! hereditary disease +relationship: excluded_subClassOf MONDO:0003847 {source="OMIMPS:600803", source="https://orcid.org/0000-0001-5208-3432"} ! hereditary disease property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/6008" xsd:anyURI [Term] @@ -111488,7 +111488,7 @@ xref: MEDGEN:68625 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"} xref: MESH:C538080 {source="Orphanet:2140/e", source="Orphanet:2140"} xref: MESH:D006548 {source="DOID:3827"} xref: MESH:D006551 {source="EFO:0007216", source="MONDO:relatedTo"} -xref: MESH:D065630 {xref="https://github.com/monarch-initiative/mondo/issues/2212", xref="MONDO:equivaentTo"} +xref: MESH:D065630 {source="MONDO:equivalentTo", source="https://github.com/monarch-initiative/mondo/issues/2212"} xref: NANDO:1200911 {source="MONDO:NANDO", source="https://orcid.org/0000-0003-0011-764X", source="https://orcid.org/0000-0002-0170-9172"} xref: NANDO:2100040 {source="MONDO:NANDO", source="https://orcid.org/0000-0003-0011-764X", source="https://orcid.org/0000-0002-0170-9172"} xref: NANDO:2200210 {source="MONDO:NANDO", source="https://orcid.org/0000-0003-0011-764X", source="https://orcid.org/0000-0002-0170-9172"} @@ -128799,7 +128799,7 @@ xref: SCTID:300389006 {source="DOID:2861"} xref: SCTID:301317008 {source="DOID:2861", source="MONDO:equivalentTo"} xref: SCTID:82775009 {source="DOID:2861"} xref: UMLS:C0002882 {source="MEDGEN:284", source="MONDO:equivalentTo", source="MONDO:MEDGEN"} -is_a: MONDO:0003689 {xref="https://github.com/monarch-initiative/mondo/issues/1503", xref="https://orcid.org/0000-0001-6330-7526", source="DOID:2861"} ! familial hemolytic anemia +is_a: MONDO:0003689 {source="DOID:2861", source="https://github.com/monarch-initiative/mondo/issues/1503", source="https://orcid.org/0000-0001-6330-7526"} ! familial hemolytic anemia is_a: MONDO:0019050 {source="EFO:1000641"} ! inherited hemoglobinopathy relationship: has_characteristic MONDO:0021140 {source="https://orcid.org/0000-0002-4142-7153"} ! congenital property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/4069" xsd:anyURI @@ -160805,7 +160805,7 @@ xref: Orphanet:369999 {source="MONDO:relatedTo", source="OMIM:148700"} xref: Orphanet:370002 {source="MONDO:relatedTo", source="OMIM:148700"} xref: Orphanet:50942 {source="OMIM:148700"} xref: UMLS:C2931122 {source="MONDO:equivalentTo", source="MEDGEN:419717", source="MONDO:MEDGEN"} -is_a: MONDO:0019272 {xref="https://orcid.org/0000-0001-5208-3432", xref="https://orcid.org/0000-0001-5493-2602"} ! hereditary palmoplantar keratoderma +is_a: MONDO:0019272 {source="https://orcid.org/0000-0001-5208-3432", source="https://orcid.org/0000-0001-5493-2602"} ! hereditary palmoplantar keratoderma relationship: excluded_subClassOf MONDO:0018865 {source="DC-OMIM:148700", source="https://orcid.org/0000-0001-5208-3432"} ! striate palmoplantar keratoderma relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/3048 {source="MONDO:mim2gene_medgen"} ! DSG1 property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/3108" xsd:anyURI @@ -228511,7 +228511,7 @@ xref: SCTID:307343001 {source="MONDO:equivalentTo"} xref: UMLS:C0585216 {source="MEDGEN:108433", source="MONDO:equivalentTo", source="MONDO:MEDGEN"} is_a: MONDO:0002254 {source="DOID:0112125", source="https://orcid.org/0000-0002-5002-8648"} ! syndromic disease is_a: MONDO:0005570 {source="https://orcid.org/0000-0001-9310-0163"} ! hematologic disorder -relationship: excluded_subClassOf MONDO:0021141 {source="https://orcid.org/0000-0001-5208-3432", comment="acquired through somatic mutations"} ! acquired +relationship: excluded_subClassOf MONDO:0021141 {source="https://orcid.org/0000-0001-5208-3432"} ! acquired relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/886 {source="MONDO:mim2gene_medgen"} ! ATRX property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/4521" xsd:anyURI property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/6746" xsd:anyURI @@ -230088,7 +230088,7 @@ xref: Orphanet:319612 {source="MONDO:equivalentTo"} xref: UMLS:C1970879 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:370376"} is_a: MONDO:0003778 {source="DC-OMIM:300584", source="MESH:C536289"} ! inborn error of immunity is_a: MONDO:0003847 {source="https://orcid.org/0000-0001-5208-3432"} ! hereditary disease -is_a: MONDO:0021094 {xref="OMIM:300636"} ! immunodeficiency disease +is_a: MONDO:0021094 {source="OMIM:300636"} ! immunodeficiency disease is_a: MONDO:0100162 {source="https://orcid.org/0000-0002-7437-8060"} ! IKBKG-related immunodeficiency with or without ectodermal dysplasia relationship: excluded_subClassOf MONDO:0017905 {source="Orphanet:319612", source="https://orcid.org/0000-0001-5208-3432"} ! X-linked Mendelian susceptibility to mycobacterial diseases relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/5961 {source="MONDO:mim2gene_medgen"} ! IKBKG @@ -248250,7 +248250,7 @@ xref: GARD:4827 {source="MONDO:GARD"} xref: MEDGEN:330467 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"} xref: MESH:C537598 {source="MONDO:equivalentTo"} xref: OMIM:601356 {source="MONDO:equivalentTo"} -xref: Orphanet:646136 {xref="MONDO:equivalentTo"} +xref: Orphanet:646136 {source="MONDO:equivalentTo"} xref: UMLS:C1832435 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:330467"} is_a: MONDO:0003847 {source="MESH:C537598/inferred"} ! hereditary disease is_a: MONDO:0016357 {source="Orphanet:646136", source="https://orcid.org/0000-0001-5208-3432"} ! dysplastic cortical hyperostosis @@ -261822,7 +261822,7 @@ property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/ [Term] id: MONDO:0011597 name: dermatitis, atopic, 3 -def: "An inherited susceptibility or predisposition to developing atopic dermatitis that is associated with variation in the region 20p." [DOID:0110099, PMID:11279517] {comment="MONDO:patterns/inherited_susceptibility"} +def: "An inherited susceptibility or predisposition to developing atopic dermatitis that is associated with variation in the region 20p." [DOID:0110099, MONDO:patterns/inherited_susceptibility, PMID:11279517] synonym: "ATOD3" EXACT ABBREVIATION [DOID:0110099, MONDO:Lexical, OMIM:605804] synonym: "atopic dermatitis 3" EXACT [] synonym: "atopic dermatitis type 3" EXACT [DOID:0110099, MONDORULE:1] @@ -272721,7 +272721,7 @@ xref: Orphanet:247871 {source="OMIM:608391"} xref: UMLS:C1842113 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:331217"} is_a: MONDO:0020573 {source="OMIM:608391", source="https://orcid.org/0000-0001-5208-3432"} ! inherited disease susceptibility relationship: excluded_subClassOf MONDO:0007179 {source="OMIM:608391", source="https://orcid.org/0000-0001-5208-3432"} ! autoimmune disease -relationship: predisposes_towards MONDO:0007179 {comment="OMIM:608391"} ! autoimmune disease +relationship: predisposes_towards MONDO:0007179 {source="OMIM:608391"} ! autoimmune disease property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/4882" xsd:anyURI [Term] @@ -274791,7 +274791,7 @@ property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/ id: MONDO:0012114 name: Ehlers-Danlos syndrome, Beasley-Cohen type subset: gard_rare {source="GARD:10102", source="MONDO:GARD"} -subset: n_of_one {xref="PMID:477010"} +subset: n_of_one {source="PMID:477010"} subset: rare synonym: "Ehlers-Danlos syndrome with intellectual disability, deafness, and cataract" RELATED [OMIM:608763] synonym: "Ehlers-Danlos syndrome with mental retardation, deafness, and cataract" RELATED DEPRECATED [OMIM:608763] @@ -277877,7 +277877,7 @@ is_a: MONDO:0015736 {source="Orphanet:171433/btnt"} ! intermediate nemaline myop is_a: MONDO:0015738 {source="Orphanet:171439/btnt"} ! childhood-onset nemaline myopathy is_a: MONDO:0018958 {source="DOID:0110926", source="MESH:C538348", source="MONDO:Redundant", source="OMIM:609284"} ! nemaline myopathy is_a: MONDO:0019952 {source="OMIM:609284"} ! congenital myopathy -is_a: MONDO:0100108 {comment="https://clinicalgenome.org/docs/clingen-cmp-ep-acgs-collaboration/"} ! TPM3-related myopathy +is_a: MONDO:0100108 {source="https://clinicalgenome.org/docs/clingen-cmp-ep-acgs-collaboration/"} ! TPM3-related myopathy intersection_of: MONDO:0018958 ! nemaline myopathy intersection_of: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/12012 ! TPM3 relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/12012 {source="MONDO:mim2gene_medgen", source="OMIM:609284"} ! TPM3 @@ -349946,7 +349946,7 @@ synonym: "Streeter anomaly" RELATED [OMIM:217100] synonym: "Streeter dysplasia" EXACT [Orphanet:295000] synonym: "terminal transverse defects of arm" RELATED [OMIM:217100] xref: GARD:429 {source="MONDO:GARD"} -xref: ICD10CM:Q79.8 {source="Orphanet:295000/attributed", source="Orphanet:295000/ntbt", source="Orphanet:295000", xref="Orphanet:1034", xref="Orphanet:1034/attributed", xref="Orphanet:1034/ntbt"} +xref: ICD10CM:Q79.8 {source="Orphanet:295000/attributed", source="Orphanet:295000/ntbt", source="Orphanet:1034/attributed", source="Orphanet:1034/ntbt", source="Orphanet:1034", source="Orphanet:295000"} xref: icd11.foundation:1033549095 {source="Orphanet:295000", source="MONDO:equivalentTo", source="https://orcid.org/0000-0002-4142-7153"} xref: MEDGEN:66322 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"} xref: MESH:D000652 {source="Orphanet:1034", source="MONDO:equivalentTo", source="Orphanet:1034/e"} @@ -356419,7 +356419,7 @@ xref: ICD9:147.9 {source="DOID:9261"} xref: MedDRA:10028793 {source="Orphanet:150", source="Orphanet:150/e"} xref: MEDGEN:419909 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"} xref: MESH:C538339 {source="MONDO:equivalentObsolete", source="Orphanet:150", source="Orphanet:150/e"} -xref: MESH:D00007727 {xref="https://github.com/monarch-initiative/mondo/issues/2068", source="MONDO:equivalentTo"} +xref: MESH:D00007727 {source="MONDO:equivalentTo", source="https://github.com/monarch-initiative/mondo/issues/2068"} xref: MESH:D000077274 {source="https://orcid.org/0000-0003-1967-3726", source="MONDO:equivalentTo"} xref: MESH:D009303 {source="DOID:9261"} xref: NCIT:C3871 {source="MONDO:equivalentTo"} @@ -363198,7 +363198,7 @@ xref: NANDO:2200324 {source="MONDO:NANDO", source="https://orcid.org/0000-0003-0 xref: Orphanet:178029 {source="MONDO:equivalentTo"} xref: UMLS:C0687720 {source="MEDGEN:146919", source="MONDO:equivalentTo", source="MONDO:MEDGEN"} is_a: MONDO:0015127 {source="Orphanet:178029"} ! pituitary deficiency -is_a: MONDO:0100070 {xref="https://orcid.org/0000-0002-2825-0621"} ! neuroendocrine disorder +is_a: MONDO:0100070 {source="https://orcid.org/0000-0002-2825-0621"} ! neuroendocrine disorder [Term] id: MONDO:0015791 @@ -394064,12 +394064,13 @@ property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/ [Term] id: MONDO:0017297 -name: chronic lymphocytic inflammation with pontine perivascular enhancement responsive to steroids {xref="Orphanet:284448"} +name: chronic lymphocytic inflammation with pontine perivascular enhancement responsive to steroids subset: gard_rare {source="GARD:10779", source="MONDO:GARD"} subset: nord_rare {source="MONDO:NORD"} subset: ordo_disorder {source="Orphanet:284448"} subset: orphanet_rare {source="Orphanet:284448"} subset: rare +synonym: "chronic lymphocytic inflammation with pontine perivascular enhancement responsive to steroids" EXACT [Orphanet:284448] synonym: "CLIPPERS" EXACT [Orphanet:284448] xref: GARD:10779 {source="MONDO:GARD"} xref: icd11.foundation:913443626 {source="MONDO:equivalentTo"} @@ -409757,7 +409758,7 @@ xref: SCTID:19265001 {source="MONDO:equivalentTo"} xref: UMLS:C0041351 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:22520"} is_a: MONDO:0000314 {source="DOID:2123"} ! primary bacterial infectious disease is_a: MONDO:0005113 {source="DOID:2123/inferred", source="EFO:1001444", source="MESH:D014406/inferred", source="MONDO:Redundant", source="NCIT:C85208", source="Orphanet:3392"} ! bacterial infectious disease -is_a: MONDO:0100120 {comment="https://www.who.int/news-room/fact-sheets/detail/vector-borne-diseases"} ! vector-borne disease +is_a: MONDO:0100120 {source="https://www.who.int/news-room/fact-sheets/detail/vector-borne-diseases"} ! vector-borne disease intersection_of: MONDO:0005550 ! infectious disease intersection_of: disease_has_infectious_agent NCBITaxon:263 ! Francisella tularensis relationship: disease_has_infectious_agent NCBITaxon:263 {source="MONDO:Wikidata"} ! Francisella tularensis @@ -424871,7 +424872,7 @@ is_a: MONDO:0024237 {source="Orphanet:480864"} ! inherited neurodegenerative dis relationship: excluded_subClassOf MONDO:0000508 {source="Orphanet:480864", source="https://orcid.org/0000-0001-5208-3432"} ! syndromic intellectual disability relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/25439 {source="MONDO:mim2gene_medgen"} ! TANGO2 property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/5588" xsd:anyURI -property_value: seeAlso "https://rarediseases.info.nih.gov/diseases/13423/tango2-related-metabolic-encephalopathy-and-arrhythmias" xsd:anyURI {xref="GARD:0013423"} +property_value: seeAlso "https://rarediseases.info.nih.gov/diseases/13423/tango2-related-metabolic-encephalopathy-and-arrhythmias" xsd:anyURI {source="GARD:0013423"} [Term] id: MONDO:0018821 @@ -425212,7 +425213,7 @@ property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/ id: MONDO:0018838 name: lissencephaly spectrum disorders def: "The term lissencephaly covers a group of rare malformations sharing the common feature of anomalies in the appearance of brain convolutions (characterized by simplification or absence of folding) associated with abnormal organization of the cortical layers as a result of neuronal migration defects during embryogenesis." [Orphanet:48471] -comment: Lissencephaly is a spectrum of gyral abnormalities. Lissencephaly, pchygyria and subcortical band heterotopia are known to be caused by the same genes. The distinction between these radiographic terms is not clear cut. The clinical consequences for these radiographic abnormalities is also often overlapping. {xref="PMID:28440899", xref="PMID:20331703"} +comment: Lissencephaly is a spectrum of gyral abnormalities. Lissencephaly, pchygyria and subcortical band heterotopia are known to be caused by the same genes. The distinction between these radiographic terms is not clear cut. The clinical consequences for these radiographic abnormalities is also often overlapping. (PMID:20331703, PMID:28440899) subset: clingen {source="MONDO:CLINGEN"} subset: disease_grouping subset: gard_rare {source="GARD:12291", source="MONDO:GARD"} @@ -436476,7 +436477,7 @@ property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/ id: MONDO:0019269 name: ichthyosis def: "Disorders of cornification that are characterized by visible scaling and/or hyperkeratosis of most or all of the skin. Inherited ichthyoses, defined as the generalized form of Mendelian disorders of cornification, affect most or all of the skin. This etiologically and phenotypically heterogenous group of conditions is caused by mutations in various different genes important for keratinocyte differentiation and epidermal barrier function. Acquired forms of ichthyosis can be observed with certain autoimmune, inflammatory, metabolic, endocrine, or infectious diseases or with malignancies." [PMID:22739337] -comment: Epidermal keratinocytes undergo a unique form of terminal differentiation and programmed cell death known as cornification. Cornification leads to the formation of the outermost skin barrier, i.e. the cornified layer, as well as to the formation of hair and nails. {xref="PMID:23792051"} +comment: Epidermal keratinocytes undergo a unique form of terminal differentiation and programmed cell death known as cornification. Cornification leads to the formation of the outermost skin barrier, i.e. the cornified layer, as well as to the formation of hair and nails. (PMID:23792051) subset: disease_grouping subset: gard_rare {source="GARD:18985", source="MONDO:GARD"} subset: ordo_group_of_disorders {source="Orphanet:79354"} @@ -453703,8 +453704,8 @@ is_a: MONDO:0019755 {source="MONDO:0015332-obsoleted"} ! developmental defect du relationship: excluded_subClassOf MONDO:0019292 {source="Orphanet:98249", source="https://orcid.org/0000-0001-5208-3432"} ! obsolete dermis elastic tissue disorder relationship: excluded_subClassOf MONDO:0023603 {source="https://orcid.org/0000-0001-5208-3432", source="https://orcid.org/0000-0002-1780-5230"} ! hereditary disorder of connective tissue relationship: has_characteristic MONDO:0021152 {source="OMIMPS:130000"} ! inherited -property_value: excluded_synonym "Cutis hyperelastica" xsd:string {xref="DOID:13359", xref="SCTID:238848002", xref="SCTID:398114001", xref="UMLS:C0013720", xref="icd11.foundation:1122707206"} -property_value: excluded_synonym "India rubber skin" xsd:string {xref="SCTID:398114001"} +property_value: excluded_synonym "Cutis hyperelastica" xsd:string {source="DOID:13359", source="SCTID:238848002", source="SCTID:398114001", source="UMLS:C0013720", source="icd11.foundation:1122707206"} +property_value: excluded_synonym "India rubber skin" xsd:string {source="SCTID:398114001"} property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/5682" xsd:anyURI [Term] @@ -460010,7 +460011,7 @@ xref: ICD10CM:Q21.2 {source="Orphanet:99106/inclusion", source="Orphanet:99106", xref: icd11.foundation:1159570489 {source="Orphanet:99106", source="MONDO:equivalentTo", source="https://orcid.org/0000-0001-5208-3432"} xref: MEDGEN:1825952 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"} xref: MESH:C548006 {source="Orphanet:99106", source="MONDO:equivalentObsolete", source="Orphanet:99106/e"} -xref: MESH:D006344 {xref="MONDO:equivalentTo"} +xref: MESH:D006344 {source="MONDO:mondoIsNarrowerThanSource"} xref: Orphanet:99106 {source="MONDO:equivalentTo"} xref: SCTID:17718000 {source="MONDO:equivalentTo"} xref: UMLS:C5680294 {source="MEDGEN:1825952", source="MONDO:equivalentTo", source="MONDO:MEDGEN"} @@ -469233,7 +469234,7 @@ xref: DOID:0080690 {source="MONDO:equivalentTo"} xref: EFO:1001502 {source="MONDO:equivalentTo", source="MONDO:EFO"} xref: GARD:22213 {source="MONDO:GARD"} xref: MEDGEN:1792298 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"} -xref: NCIT:C179667 {xref="MONDO:equivalentTo"} +xref: NCIT:C179667 {source="MONDO:equivalentTo"} xref: Orphanet:536391 {source="MONDO:equivalentTo", source="https://github.com/monarch-initiative/mondo/issues/606"} xref: UMLS:C5555857 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:1792298"} is_a: MONDO:0003847 {source="https://orcid.org/0000-0001-5208-3432", source="https://orcid.org/0000-0002-0736-9199"} ! hereditary disease @@ -472143,7 +472144,7 @@ synonym: "tumour of trachea" EXACT OMO:0003005 [] xref: EFO:1001437 {source="MONDO:equivalentTo", source="MONDO:EFO"} xref: GTR:AN0481062 {source="UMLS:C0040582"} xref: GTR:AN0505660 {source="UMLS:C0040582"} -xref: HP:0100551 {xref="UMLS:C0040582", source="UMLS:C0040582"} +xref: HP:0100551 {source="UMLS:C0040582"} xref: MEDGEN:21602 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"} xref: MESH:D014134 {source="MONDO:equivalentTo", source="UMLS:C0040582"} xref: NCIT:C3419 {source="MONDO:equivalentTo", source="UMLS:C0040582"} @@ -481397,7 +481398,7 @@ xref: UMLS:C0263473 {source="MONDO:equivalentTo", source="MEDGEN:82667", source= is_a: MONDO:0005093 {source="MONDO:Redundant"} ! skin disorder is_a: MONDO:0006615 {source="MONDO:Redundant"} ! sweat gland disorder is_a: MONDO:0024467 {source="ICD10CM:L75.1", source="MONDO:Entailed", source="MONDO:Redundant"} ! apocrine sweat gland disorder -relationship: disease_has_location UBERON:0000382 {comment="typical"} ! apocrine sweat gland +relationship: disease_has_location UBERON:0000382 ! apocrine sweat gland property_value: seeAlso "https://rarediseases.info.nih.gov/diseases/10749/chromhidrosis" xsd:anyURI {source="GARD:0010749"} [Term] @@ -482332,7 +482333,7 @@ id: MONDO:0022462 name: anophthalmia esophageal atresia cryptorchidism def: "A syndrome characterized by bilateral anophthalmia, esophageal atresia, and cryptorchidism. This is an n-of-1 use case where only one patient or family has been described with this disorder." [https://orcid.org/0000-0001-5208-3432, PMID:1352427] comment: Reason of obsoletion: out of scope - MONDO:excludeHistoricalDisease. Term to consider: - -subset: n_of_one {xref="PMID:1352427"} +subset: n_of_one {source="PMID:1352427"} subset: obsoletion_candidate is_a: MONDO:0002254 {source="https://orcid.org/0000-0002-6601-2165"} ! syndromic disease property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/7700" xsd:anyURI @@ -499402,7 +499403,7 @@ xref: MESH:C562816 {source="MONDO:equivalentTo"} xref: OMIM:618892 {source="MONDO:equivalentTo"} xref: Orphanet:659672 {source="MONDO:equivalentTo"} xref: UMLS:C0342859 {source="MEDGEN:137981", source="MONDO:equivalentTo", source="MONDO:MEDGEN"} -is_a: MONDO:0003847 {comment="OMIM:618892"} ! hereditary disease +is_a: MONDO:0003847 {source="OMIM:618892"} ! hereditary disease is_a: MONDO:0800180 {source="https://clinicalgenome.org/affiliation/40097/", source="https://clinicalgenome.org/working-groups/clinical-domain/inborn-errors-of-metabolism/"} ! CPOX-related hereditary coproporphyria relationship: RO:0004001 http://identifiers.org/hgnc/2321 {source="OMIM:618892"} ! has material basis in gain of function germline mutation in CPOX @@ -535041,7 +535042,7 @@ property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/ id: MONDO:0100039 name: CDKL5 disorder def: "A monogenic disease that has material basis in mutation in the CDKL5 gene." [PMID:21154482, PMID:22872100, PMID:27080038, PMID:27528505] -comment: Subtypes of the heterogeneous, eponymously named Early Infantile Epileptic Encephalopathy, Atypical Rett Syndrome, West Syndrome are caused by mutations in the gene CDKL5. The common and most penetrant phenotype shared among these disease entities is early onset epilepsy, progressive microcephaly, dysmorphic facial features, and intellectual disability, with stereotypic hand movements, respiratory impairment with breath holding and hyperventilation having variable phenotypic expressivity. {xref="https://orcid.org/0000-0002-6733-369X"} +comment: Subtypes of the heterogeneous, eponymously named Early Infantile Epileptic Encephalopathy, Atypical Rett Syndrome, West Syndrome are caused by mutations in the gene CDKL5. The common and most penetrant phenotype shared among these disease entities is early onset epilepsy, progressive microcephaly, dysmorphic facial features, and intellectual disability, with stereotypic hand movements, respiratory impairment with breath holding and hyperventilation having variable phenotypic expressivity. (https://orcid.org/0000-0002-6733-369X) subset: clingen {source="MONDO:CLINGEN"} subset: gard_rare {source="MONDO:GARD"} subset: nord_rare {source="MONDO:NORD", source="NORD:904"} @@ -535072,7 +535073,7 @@ property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/ id: MONDO:0100040 name: FOXG1 disorder def: "A monogenic disease that has material basis in mutation in the FOXG1 gene." [] -comment: Subtypes of the heterogeneous, eponymously named Congenital variant of Rett Syndrome, and Atypical Rett Syndrome are caused by mutations in the gene FOXG1. The common and most penetrant phenotype shared among these disease entities is neurodevelopmental impairment present in early infancy, progressive microcephaly, and MRI of the brain showing reduced myelinization and/or abnormal corpus callosum. Stereotypic hand movements, epilepsy, and abnormal breathing can have variable phenotypic expressivity. {xref="https://orcid.org/0000-0002-6733-369X"} +comment: Subtypes of the heterogeneous, eponymously named Congenital variant of Rett Syndrome, and Atypical Rett Syndrome are caused by mutations in the gene FOXG1. The common and most penetrant phenotype shared among these disease entities is neurodevelopmental impairment present in early infancy, progressive microcephaly, and MRI of the brain showing reduced myelinization and/or abnormal corpus callosum. Stereotypic hand movements, epilepsy, and abnormal breathing can have variable phenotypic expressivity. (https://orcid.org/0000-0002-6733-369X) subset: clingen {source="MONDO:CLINGEN"} subset: gard_rare {source="MONDO:GARD"} subset: nord_rare {source="MONDO:NORD"} @@ -535123,7 +535124,7 @@ property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/ [Term] id: MONDO:0100043 name: epidermodysplasia verruciformis, susceptibility to -comment: An inherited susceptibility or predisposition to developing epidermodysplasia verruciformis. {xref="MONDO:patterns/inherited_susceptibility"} +def: "An inherited susceptibility or predisposition to developing epidermodysplasia verruciformis." [MONDO:patterns/inherited_susceptibility] xref: OMIMPS:226400 {source="MONDO:equivalentTo"} is_a: MONDO:0020573 {source="https://orcid.org/0000-0001-5208-3432"} ! inherited disease susceptibility relationship: has_characteristic MONDO:0021152 {source="OMIMPS:226400"} ! inherited @@ -535405,7 +535406,7 @@ property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0001-520 id: MONDO:0100062 name: developmental and epileptic encephalopathy def: "A complex neurodevelopmental disorder characterized by a range of developmental delays and epileptic encephalopathy phenotypes. Seizure onset is variable and intellectual disability is variable in presence and severity." [PMID:28276062] -comment: Individuals, both male and female, have been reported with variants in the GABRB3 gene. De novo and familial cases have been reported, with mostly missense and a few nonsense variants identified as causative. These patients have been described in the literature as having a range of phenotypes characterized as epileptic encephalopathy, Lennox-Gastaut syndrome, Dravet syndrome-like, and childhood absence epilepsy. Severity of intellectual disability is variable among reported probands, as is the age of onset of seizure phenotypes. In one case of epileptic encephalopathy, for example, the individual presented with severe intellectual disability while seizures onset at 12 years old. Additionally, individuals have been reported with the same de novo missense variants, and have been described with varying phenotypes. {xref="PMID:26544041", xref="PMID:26704558", xref="PMID:26645412", xref="PMID:26993267", xref="PMID:27476654"} +comment: Individuals, both male and female, have been reported with variants in the GABRB3 gene. De novo and familial cases have been reported, with mostly missense and a few nonsense variants identified as causative. These patients have been described in the literature as having a range of phenotypes characterized as epileptic encephalopathy, Lennox-Gastaut syndrome, Dravet syndrome-like, and childhood absence epilepsy. Severity of intellectual disability is variable among reported probands, as is the age of onset of seizure phenotypes. In one case of epileptic encephalopathy, for example, the individual presented with severe intellectual disability while seizures onset at 12 years old. Additionally, individuals have been reported with the same de novo missense variants, and have been described with varying phenotypes. (PMID:26544041, PMID:26704558, PMID:26645412, PMID:26993267, PMID:27476654) subset: clingen {source="MONDO:CLINGEN"} subset: gard_rare {source="GARD:9255", source="MONDO:GARD"} subset: nord_rare {source="MONDO:NORD"} @@ -536612,7 +536613,7 @@ is_a: MONDO:0000066 ! mitochondrial complex deficiency intersection_of: MONDO:0000001 ! disease intersection_of: disease_has_basis_in_dysfunction_of GO:0005747 ! obsolete mitochondrial respiratory chain complex I property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0001-5208-3432 -property_value: seeAlso "https://rarediseases.info.nih.gov/diseases/3908/mitochondrial-complex-i-deficiency" xsd:anyURI {xref="GARD:0003908"} +property_value: seeAlso "https://rarediseases.info.nih.gov/diseases/3908/mitochondrial-complex-i-deficiency" xsd:anyURI {source="GARD:0003908"} [Term] id: MONDO:0100134 @@ -537838,14 +537839,14 @@ xref: Orphanet:2273 {source="OMIM:308205"} xref: Orphanet:85284 {source="OMIM:308205"} xref: UMLS:C5399971 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:1746744"} is_a: MONDO:0020605 {source="DOID:0111821"} ! X-linked recessive disease -is_a: MONDO:0100212 {xref="OMIM:308205", source="OMIM:308205", source="https://orcid.org/0000-0001-5208-3432"} ! IFAP syndrome +is_a: MONDO:0100212 {source="OMIM:308205", source="https://orcid.org/0000-0001-5208-3432"} ! IFAP syndrome intersection_of: MONDO:0100212 ! IFAP syndrome intersection_of: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/15455 ! MBTPS2 relationship: curated_content_resource https://search.clinicalgenome.org/kb/conditions/MONDO:0100213 {source="MONDO:CLINGEN"} relationship: excluded_subClassOf MONDO:0015331 {source="Orphanet:2273", source="https://orcid.org/0000-0001-5208-3432"} ! obsolete malformation syndrome with skin/mucosae involvement relationship: excluded_subClassOf MONDO:0017269 {source="Orphanet:2273", source="https://orcid.org/0000-0001-5208-3432"} ! X-linked ichthyosis syndrome relationship: excluded_subClassOf MONDO:0021034 {source="Orphanet:2273", source="https://orcid.org/0000-0001-5208-3432"} ! obsolete hereditary alopecia -relationship: has_characteristic HP:0001419 {xref="OMIM:308205"} ! X-linked recessive inheritance +relationship: has_characteristic HP:0001419 {source="OMIM:308205"} ! X-linked recessive inheritance relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/15455 {source="MONDO:mim2gene_medgen"} ! MBTPS2 property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0001-5208-3432 property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/4521" xsd:anyURI @@ -538035,7 +538036,7 @@ subset: gard_rare {source="MONDO:GARD"} subset: rare xref: DOID:0112065 {source="MONDO:equivalentTo"} xref: OMIMPS:252010 {source="MONDO:equivalentTo"} -is_a: MONDO:0100133 {xref="https://orcid.org/0000-0001-5208-3432", source="DOID:0112065", source="OMIMPS:252010", source="https://github.com/monarch-initiative/mondo/issues/1042"} ! mitochondrial complex I deficiency +is_a: MONDO:0100133 {source="DOID:0112065", source="OMIMPS:252010", source="https://github.com/monarch-initiative/mondo/issues/1042", source="https://orcid.org/0000-0001-5208-3432"} ! mitochondrial complex I deficiency relationship: has_characteristic MONDO:0021152 {source="OMIMPS:252010"} ! inherited property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0001-5208-3432 @@ -544052,7 +544053,7 @@ subset: otar {source="MONDO:OTAR"} synonym: "ATP1A3 neurological disorder" EXACT [MONDO:patterns/disease_series_by_gene] synonym: "ATP1A3 related neurological disorder" EXACT CLINGEN_LABEL [MONDO:patterns/disease_series_by_gene] synonym: "neurological disorder caused by mutation in ATP1A3" EXACT [MONDO:patterns/disease_series_by_gene] -is_a: MONDO:0005071 {xref="PMID:20301295", xref="PMID:31178018", xref="PMID:33762331"} ! nervous system disorder +is_a: MONDO:0005071 {source="PMID:20301295", source="PMID:31178018", source="PMID:33762331"} ! nervous system disorder intersection_of: MONDO:0005071 ! nervous system disorder intersection_of: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/801 ! ATP1A3 relationship: curated_content_resource https://search.clinicalgenome.org/kb/conditions/MONDO:0700002 {source="MONDO:CLINGEN"} @@ -547719,7 +547720,7 @@ property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/ [Term] id: MONDO:0800042 name: restrictive dermopathy 1 -def: "A restrictive dermopathy that has material basis in homozygous or compound heterozygous mutation in the ZMPSTE24 gene on chromosome 1p34." [https://orcid.org/0000-0001-5208-3432] {comment="DOID:0070369"} +def: "A restrictive dermopathy that has material basis in homozygous or compound heterozygous mutation in the ZMPSTE24 gene on chromosome 1p34." [DOID:0070369, https://orcid.org/0000-0001-5208-3432] subset: gard_rare {source="MONDO:GARD"} subset: rare synonym: "fetal hypokinesia sequence due to restrictive dermopathy" EXACT [OMIM:275210] diff --git a/src/sparql/qc/general/qc-axiom-provenance-source.sparql b/src/sparql/qc/general/qc-axiom-provenance-source.sparql new file mode 100644 index 0000000000..bee9cab05c --- /dev/null +++ b/src/sparql/qc/general/qc-axiom-provenance-source.sparql @@ -0,0 +1,65 @@ +PREFIX rdf: +PREFIX skos: +prefix IAO: +prefix rdfs: +prefix oio: +prefix def: +prefix owl: +PREFIX xsd: +prefix oboInOwl: + +# description: Looks for axiom annotations which use faulty provenance properties + +SELECT DISTINCT ?entity ?property ?value + +WHERE +{ + ?entity ?property ?v . + + ?axiom owl:annotatedSource ?entity ; + owl:annotatedProperty ?property ; + owl:annotatedTarget ?v ; + ?provenance ?x . + + # The axiom provenance should typically use oio:source, so lets look for case where it does not + # (also, it should not correspond to the actual RDF-reified annotation properties) + FILTER( + ?provenance!=oio:source + && ?provenance!=owl:annotatedSource + && ?provenance!=owl:annotatedTarget + && ?provenance!=owl:annotatedProperty + && ?provenance!=rdf:type + ) + + # Ignore Synonym type annotations + FILTER( + !(?provenance = oio:hasSynonymType && + ( + ?property IN ( + oio:hasExactSynonym, + oio:hasRelatedSynonym, + oio:hasBroadSynonym, + oio:hasNarrowSynonym) + ) + ) + ) + + # Xrefs are allowed on definitions and synonyms + FILTER ( + !( + ?provenance = oio:hasDbXref && + ?property IN ( + IAO:0000115, + oio:hasExactSynonym, + oio:hasRelatedSynonym, + oio:hasBroadSynonym, + oio:hasNarrowSynonym + ) + ) + ) + + BIND(CONCAT(str(?v),CONCAT(": ",str(?provenance))) as ?value) + + FILTER( !isBlank(?entity) && STRSTARTS(str(?entity), "http://purl.obolibrary.org/obo/MONDO_")) +} ORDER BY ?entity +