From 608a94694c13ab40975e962ac4f31c669084ccc4 Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Wed, 30 Oct 2024 14:32:09 +0200 Subject: [PATCH 1/3] Adds a QC check that looks for cases where excluded subclassof axioms are asserted This tests a case where we said, deliberately: This subclass axiom should not exist, but it turns out, it does! --- .../mondo/qc-excluded-subclass-is-asserted.sparql | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 src/sparql/qc/mondo/qc-excluded-subclass-is-asserted.sparql diff --git a/src/sparql/qc/mondo/qc-excluded-subclass-is-asserted.sparql b/src/sparql/qc/mondo/qc-excluded-subclass-is-asserted.sparql new file mode 100644 index 0000000000..ea6b1e881b --- /dev/null +++ b/src/sparql/qc/mondo/qc-excluded-subclass-is-asserted.sparql @@ -0,0 +1,15 @@ +prefix owl: +prefix oboInOwl: +prefix rdfs: + +# Tests if an excluded-subclass-of axiom is asserted + +SELECT DISTINCT ?entity ?property ?value +WHERE +{ + VALUES ?property { } + ?entity ?property ?value . + + ?entity rdfs:subClassOf ?value . +} +ORDER BY ?entity \ No newline at end of file From 8b116f353a3ffee412ade3d17b664feb67b1d19f Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Wed, 30 Oct 2024 14:32:25 +0200 Subject: [PATCH 2/3] Update a few descriptions of excluded-subclass-of related checks --- src/sparql/qc/general/qc-excluded-subclass.sparql | 3 ++- src/sparql/qc/general/qc-provenance-missing.sparql | 3 ++- src/sparql/qc/mondo/qc-excluded-subsumption-is-inferred.sparql | 2 ++ 3 files changed, 6 insertions(+), 2 deletions(-) diff --git a/src/sparql/qc/general/qc-excluded-subclass.sparql b/src/sparql/qc/general/qc-excluded-subclass.sparql index 0bfa6c2e48..494ffaaef4 100644 --- a/src/sparql/qc/general/qc-excluded-subclass.sparql +++ b/src/sparql/qc/general/qc-excluded-subclass.sparql @@ -8,7 +8,8 @@ PREFIX xsd: prefix oboInOwl: -# Tests if an animal disease made it into the rare disease subset +# Tests if an excluded subclass of axiom is asserted between a Mondo class +# and a non-Mondo class, or between a Mondo class and a class expression SELECT DISTINCT ?entity ?property ?value WHERE { diff --git a/src/sparql/qc/general/qc-provenance-missing.sparql b/src/sparql/qc/general/qc-provenance-missing.sparql index c7eeb6a66e..bd371ae868 100644 --- a/src/sparql/qc/general/qc-provenance-missing.sparql +++ b/src/sparql/qc/general/qc-provenance-missing.sparql @@ -8,7 +8,8 @@ PREFIX xsd: prefix oboInOwl: -# Tests if an animal disease made it into the rare disease subset +# Tests if an excluded subclass of axiom exists which does not have +# at least 1 ORCID as provenance SELECT DISTINCT ?entity ?property ?value WHERE { diff --git a/src/sparql/qc/mondo/qc-excluded-subsumption-is-inferred.sparql b/src/sparql/qc/mondo/qc-excluded-subsumption-is-inferred.sparql index 15de95510e..0007ef98ab 100644 --- a/src/sparql/qc/mondo/qc-excluded-subsumption-is-inferred.sparql +++ b/src/sparql/qc/mondo/qc-excluded-subsumption-is-inferred.sparql @@ -5,6 +5,8 @@ prefix mondo: prefix mondoSparqlQcGeneral: prefix mondoSparqlQcMondo: +# Tests if an excluded-subclass-of axiom can be inferred + SELECT DISTINCT ?entity ?property ?value WHERE { From e1526f4f1b130e8fb77bf12e5d6a763831a7fa4a Mon Sep 17 00:00:00 2001 From: Trish Whetzel Date: Tue, 5 Nov 2024 23:29:33 -0800 Subject: [PATCH 3/3] remove directly asserted parents that should be excluded --- src/ontology/mondo-edit.obo | 66 ------------------------------------- 1 file changed, 66 deletions(-) diff --git a/src/ontology/mondo-edit.obo b/src/ontology/mondo-edit.obo index a963d1e0d0..aed47fe6fc 100644 --- a/src/ontology/mondo-edit.obo +++ b/src/ontology/mondo-edit.obo @@ -2515,7 +2515,6 @@ name: oropharyngeal anthrax def: "A anthrax infection that involves the oropharynx." [MONDO:patterns/location] synonym: "oropharynx anthrax infection" EXACT [MONDO:patterns/location] xref: DOID:0050059 {source="MONDO:equivalentTo"} -is_a: MONDO:0001701 {source="DOID:0050059"} ! gastrointestinal anthrax intersection_of: MONDO:0005119 ! anthrax infection intersection_of: disease_has_location UBERON:0001729 ! oropharynx relationship: disease_has_infectious_agent NCBITaxon:1392 ! Bacillus anthracis @@ -10370,7 +10369,6 @@ xref: DOID:0040087 {source="MONDO:equivalentTo"} xref: DOID:0060499 {source="MONDO:equivalentTo", source="MONDO:preferredExternal"} xref: MEDGEN:1843469 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"} xref: UMLS:C2748363 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:1843469"} -is_a: MONDO:0000590 {source="DOID:0040087"} ! autoimmune disorder of peripheral nervous system intersection_of: MONDO:0005244 ! peripheral neuropathy intersection_of: disease_arises_from_feature HP:0002960 ! Autoimmunity relationship: excluded_subClassOf MONDO:0000568 {source="DOID:0060499", source="https://orcid.org/0000-0001-5208-3432"} ! autoimmune disorder of central nervous system @@ -26836,7 +26834,6 @@ xref: SCTID:266628008 {source="DOID:13148"} xref: SCTID:68226007 {source="MONDO:equivalentTo", source="DOID:13148"} xref: UMLS:C0149523 {source="MEDGEN:57429", source="MONDO:equivalentTo", source="MONDO:MEDGEN"} is_a: MONDO:0005247 {source="https://github.com/monarch-initiative/mondo/issues/841"} ! bacterial urinary tract infection -is_a: MONDO:0006032 {source="DOID:13148"} ! cystitis intersection_of: MONDO:0006032 ! cystitis intersection_of: has_characteristic PATO:0000389 ! acute relationship: disease_has_feature HP:0002027 {source="MONDO:Wikidata"} ! Abdominal pain @@ -27793,7 +27790,6 @@ xref: SCTID:193683001 {source="MONDO:equivalentTo", source="DOID:13399"} xref: SCTID:193685008 {source="DOID:13399"} xref: SCTID:53481002 {source="DOID:13399"} xref: UMLS:C5681659 {source="MEDGEN:1826147", source="MONDO:equivalentTo", source="MONDO:MEDGEN"} -is_a: MONDO:0001941 {source="DOID:13399", source="NCIT:C3891"} ! blindness (disorder) is_a: MONDO:0021084 {source="MONDO:Redundant", source="NCIT:C3891/inferred", source="https://orcid.org/0000-0002-6601-2165"} ! vision disorder relationship: disease_has_basis_in_dysfunction_of CL:0000573 ! retinal cone cell relationship: excluded_subClassOf MONDO:0001941 {source="NCIT:C3891", source="https://orcid.org/0000-0001-5208-3432"} ! blindness (disorder) @@ -42650,7 +42646,6 @@ xref: SCTID:373905003 {source="DOID:2842", source="MONDO:equivalentTo"} xref: SCTID:49518001 {source="DOID:2842"} xref: UMLS:C0022387 {source="MEDGEN:5929", source="MONDO:equivalentTo", source="MONDO:MEDGEN"} is_a: MONDO:0002442 {source="DOID:2842", source="MESH:D029593", source="NCIT:C84793"} ! long QT syndrome -is_a: MONDO:0019171 {source="Orphanet:90647"} ! familial long QT syndrome relationship: curated_content_resource https://search.clinicalgenome.org/kb/conditions/MONDO:0002441 {source="MONDO:CLINGEN"} relationship: excluded_subClassOf MONDO:0019171 {source="MONDO:Redundant", source="Orphanet:90647", source="https://orcid.org/0000-0001-5208-3432"} ! familial long QT syndrome relationship: has_characteristic MONDO:0021152 {source="OMIMPS:220400"} ! inherited @@ -43053,7 +43048,6 @@ xref: NCIT:C5102 {source="MONDO:equivalentTo", source="DOID:292"} xref: SCTID:416510003 {source="MONDO:equivalentTo", source="DOID:292"} xref: UMLS:C1334361 {source="MONDO:equivalentTo", source="MEDGEN:272790", source="MONDO:MEDGEN"} is_a: MONDO:0001854 {source="DOID:292", source="NCIT:C5102"} ! lacrimal apparatus disorder -is_a: MONDO:0002236 {source="DOID:292"} ! ocular cancer intersection_of: MONDO:0004992 ! cancer intersection_of: disease_has_location UBERON:0001750 ! lacrimal apparatus relationship: excluded_subClassOf MONDO:0002236 {source="DOID:292", source="https://orcid.org/0000-0001-5208-3432"} ! ocular cancer @@ -80565,7 +80559,6 @@ xref: MEDGEN:107849 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"} xref: NCIT:C27183 {source="MONDO:equivalentTo", source="DOID:7806"} xref: SCTID:276829003 {source="MONDO:equivalentTo", source="DOID:7806"} xref: UMLS:C0559185 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:107849"} -is_a: MONDO:0002542 {source="DOID:7806"} ! spinal cord glioma is_a: MONDO:0020690 {source="NCIT:C27183"} ! adult glioblastoma intersection_of: MONDO:0018177 ! glioblastoma intersection_of: disease_has_location UBERON:0002240 ! spinal cord @@ -86279,7 +86272,6 @@ xref: SCTID:188342008 {source="DOID:8731"} xref: SCTID:447883002 {source="DOID:8731", source="MONDO:equivalentTo"} xref: SCTID:93740003 {source="DOID:8731"} xref: UMLS:C0153656 {source="MEDGEN:56318", source="MONDO:equivalentTo", source="MONDO:MEDGEN"} -is_a: MONDO:0002095 {source="DOID:8731"} ! vascular cancer is_a: MONDO:0005627 {source="MONDO:Redundant", source="NCIT:C3574"} ! head and neck cancer is_a: MONDO:0021053 {source="MONDO:Redundant", source="NCIT:C3574"} ! carotid body paraganglioma is_a: MONDO:0021069 {source="MONDO:Redundant", source="NCIT:C3574/inferred"} ! malignant endocrine neoplasm @@ -153533,7 +153525,6 @@ xref: OMIM:132090 {source="Orphanet:25968", source="MONDO:equivalentTo", source= xref: Orphanet:25968 {source="MONDO:equivalentTo", source="OMIM:132090"} xref: UMLS:C1851549 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:377052"} is_a: MONDO:0015650 {source="https://orcid.org/0000-0001-5208-3432"} ! epilepsy syndrome -is_a: MONDO:0020072 {source="https://orcid.org/0000-0001-5208-3432", source="https://www.epilepsydiagnosis.org/syndrome/epilepsy-syndrome-groupoverview.html"} ! childhood-onset epilepsy syndrome relationship: excluded_subClassOf MONDO:0020072 {source="Orphanet:25968", source="https://orcid.org/0000-0001-5208-3432"} ! childhood-onset epilepsy syndrome property_value: seeAlso "https://rarediseases.info.nih.gov/diseases/2170/epilepsy-benign-occipital" xsd:anyURI {source="GARD:0002170"} @@ -159598,7 +159589,6 @@ xref: OMIM:146590 {source="Orphanet:79503", source="MONDO:equivalentTo", source= xref: Orphanet:79503 {source="OMIM:146590", source="MONDO:equivalentTo"} xref: SCTID:254170001 {source="MONDO:equivalentTo"} xref: UMLS:C1840296 {source="MEDGEN:326700", source="MONDO:equivalentTo", source="MONDO:MEDGEN"} -is_a: MONDO:0017266 {source="Orphanet:79503"} ! keratinopathic ichthyosis is_a: MONDO:0859383 {source="OMIM:146590"} ! ichthyosis hystrix intersection_of: MONDO:0859383 ! ichthyosis hystrix intersection_of: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/6412 ! KRT1 @@ -163639,7 +163629,6 @@ xref: Orphanet:404560 {source="OMIM:155600"} xref: Orphanet:618 {source="OMIM:155600"} xref: SCTID:254819008 {source="MONDO:equivalentTo"} xref: UMLS:C1835047 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:320506"} -is_a: MONDO:0024462 {source="OMIM:155600"} ! susceptibility to familial cutaneous melanoma intersection_of: MONDO:0020573 ! inherited disease susceptibility intersection_of: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/9588 ! PTEN intersection_of: predisposes_towards MONDO:0005012 ! cutaneous melanoma @@ -163673,9 +163662,7 @@ xref: NCIT:C7584 {source="MONDO:equivalentTo"} xref: OMIM:155601 {source="MONDO:equivalentTo", source="DOID:10041"} xref: Orphanet:618 {source="OMIM:155601"} xref: UMLS:C1835044 {source="MEDGEN:331891", source="MONDO:equivalentTo", source="MONDO:MEDGEN"} -is_a: MONDO:0000426 {source="DOID:10041"} ! autosomal dominant disease is_a: MONDO:0020573 {source="OMIM:155601"} ! inherited disease susceptibility -is_a: MONDO:0024462 {source="OMIM:155601"} ! susceptibility to familial cutaneous melanoma intersection_of: MONDO:0020573 ! inherited disease susceptibility intersection_of: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/1787 ! CDKN2A intersection_of: predisposes_towards MONDO:0005012 ! cutaneous melanoma @@ -166437,7 +166424,6 @@ xref: SCTID:445503007 {source="MONDO:equivalentTo"} xref: UMLS:C4551496 {source="MEDGEN:1645893", source="MONDO:equivalentTo", source="MONDO:MEDGEN"} is_a: MONDO:0000608 {source="DC-OMIM:162000", source="MONDO:Redundant", source="OMIM:162000"} ! familial juvenile hyperuricemic nephropathy is_a: MONDO:0002473 {source="MONDO:Redundant", source="NCIT:C123172"} ! cystic kidney disease -is_a: MONDO:0008264 {source="Orphanet:88950"} ! autosomal dominant medullary cystic kidney disease with or without hyperuricemia is_a: MONDO:0019236 {source="Orphanet:209886"} ! inborn disorder of purine metabolism is_a: MONDO:0019741 {source="Orphanet:209886"} ! familial cystic renal disease intersection_of: MONDO:0000608 ! familial juvenile hyperuricemic nephropathy @@ -171402,7 +171388,6 @@ xref: OMIM:174700 {source="Orphanet:93338/e", source="MONDO:equivalentTo", sourc xref: Orphanet:93338 {source="OMIM:174700", source="MONDO:equivalentTo"} xref: SCTID:84598000 xref: UMLS:C1868111 {source="MEDGEN:357420", source="MONDO:equivalentTo", source="MONDO:MEDGEN"} -is_a: MONDO:0005066 {source="MONDO:Redundant", source="NCIT:C125597"} ! metabolic disease is_a: MONDO:0017425 {source="DC-OMIM:174700", source="OMIM:174700", source="Orphanet:93338", source="icd11.foundation:973656080"} ! preaxial polydactyly of fingers is_a: MONDO:0021651 {source="https://github.com/monarch-initiative/mondo/issues/3919", source="https://orcid.org/0000-0002-4142-7153"} ! synpolydactyly is_a: MONDO:0800066 {source="PMID:31633310"} ! polydactyly-syndactyly-triphalangism @@ -177741,7 +177726,6 @@ xref: Orphanet:90341 {source="MONDO:equivalentObsolete", source="OMIM:609464"} xref: SCTID:699861000 {source="DOID:0050678", source="MONDO:equivalentTo"} xref: UMLS:C5201146 {source="MEDGEN:1684759", source="MONDO:equivalentTo", source="MONDO:MEDGEN"} is_a: MONDO:0002254 {source="NCIT:C116794"} ! syndromic disease -is_a: MONDO:0007179 {source="NCIT:C116794"} ! autoimmune disease is_a: MONDO:0019338 {source="DC-OMIM:609464"} ! sarcoidosis is_a: MONDO:0019751 ! autoinflammatory syndrome relationship: curated_content_resource https://search.clinicalgenome.org/kb/conditions/MONDO:0008523 {source="MONDO:CLINGEN"} @@ -219353,7 +219337,6 @@ xref: OMIM:268900 {source="MONDO:equivalentTo", source="Orphanet:3129", source=" xref: Orphanet:3129 {source="MONDO:equivalentTo", source="OMIM:268900"} xref: SCTID:64852002 {source="MONDO:equivalentTo"} xref: UMLS:C0268563 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:120651"} -is_a: MONDO:0019239 {source="Orphanet:3129"} ! inborn disorder of serine family metabolism is_a: MONDO:0100477 {source="PMID:33340416"} ! disorder of methylamine metabolism relationship: curated_content_resource https://search.clinicalgenome.org/kb/conditions/MONDO:0010008 {source="MONDO:CLINGEN"} relationship: disease_has_basis_in_disruption_of GO:0006544 {source="https://en.wikipedia.org/wiki/Sarcosine_dehydrogenase", source="https://orcid.org/0000-0001-5208-3432"} ! glycine metabolic process @@ -226421,7 +226404,6 @@ xref: Orphanet:85282 {source="MONDO:equivalentTo", source="OMIM:300148", source= xref: SCTID:722037004 {source="MONDO:equivalentTo"} xref: UMLS:C1846278 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:375855"} is_a: MONDO:0002254 {source="https://orcid.org/0000-0001-5208-3432"} ! syndromic disease -is_a: MONDO:0020119 {source="DOID:0060801", source="OMIM:300148", source="https://clinicalgenome.org/affiliation/40060/"} ! X-linked syndromic intellectual disability relationship: curated_content_resource https://search.clinicalgenome.org/kb/conditions/MONDO:0010258 {source="MONDO:CLINGEN"} relationship: excluded_subClassOf MONDO:0016402 {source="Orphanet:85282", source="https://orcid.org/0000-0001-5208-3432"} ! obsolete mitochondrial disease with epilepsy relationship: excluded_subClassOf MONDO:0016403 {source="Orphanet:85282", source="https://orcid.org/0000-0001-5208-3432"} ! obsolete mitochondrial disease with peripheral neuropathy @@ -228622,7 +228604,6 @@ xref: OMIM:300472 {source="Orphanet:52055/e", source="MONDO:equivalentTo", sourc xref: Orphanet:52055 {source="OMIM:300472", source="MONDO:equivalentTo", source="DOID:0060816"} xref: SCTID:722282008 {source="MONDO:equivalentTo"} xref: UMLS:C1845446 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:335185"} -is_a: MONDO:0020119 {source="DOID:0060816", source="OMIM:300472", source="https://clinicalgenome.org/affiliation/40060/"} ! X-linked syndromic intellectual disability is_a: MONDO:0021147 {source="MONDO:0017122-obsoleted"} ! disorder of development or morphogenesis relationship: curated_content_resource https://search.clinicalgenome.org/kb/conditions/MONDO:0010333 {source="MONDO:CLINGEN"} relationship: excluded_subClassOf MONDO:0015159 {source="Orphanet:52055", source="https://orcid.org/0000-0001-5208-3432"} ! multiple congenital anomalies/dysmorphic syndrome-intellectual disability @@ -228848,7 +228829,6 @@ xref: MESH:C564505 {source="MONDO:equivalentTo"} xref: OMIM:300491 {source="Orphanet:85294/e", source="MONDO:equivalentTo", source="Orphanet:85294"} xref: Orphanet:85294 {source="OMIM:300491", source="MONDO:equivalentTo"} xref: UMLS:C5774177 {source="MONDO:equivalentTo", source="MEDGEN:1823951", source="MONDO:MEDGEN"} -is_a: MONDO:0020119 {source="https://clinicalgenome.org/affiliation/40060/"} ! X-linked syndromic intellectual disability is_a: MONDO:0859390 {source="OMIM:300491"} ! epilepsy, X-linked, with or without impaired intellectual development and dysmorphic features relationship: excluded_from_qc_check http://purl.obolibrary.org/obo/mondo/sparql/qc/general/qc-single-child.sparql relationship: excluded_subClassOf MONDO:0002254 {source="https://orcid.org/0000-0001-5208-3432"} ! syndromic disease @@ -229210,7 +229190,6 @@ xref: Orphanet:59 {source="MONDO:equivalentTo", source="OMIM:300523"} xref: SCTID:702327009 {source="MONDO:equivalentTo"} xref: UMLS:C0795889 {source="MEDGEN:208645", source="MONDO:equivalentTo", source="MONDO:MEDGEN"} is_a: MONDO:0002254 {source="MONDO:Redundant", source="NCIT:C118843"} ! syndromic disease -is_a: MONDO:0020119 {source="https://clinicalgenome.org/affiliation/40060/"} ! X-linked syndromic intellectual disability relationship: curated_content_resource https://search.clinicalgenome.org/kb/conditions/MONDO:0010354 {source="MONDO:CLINGEN"} relationship: excluded_subClassOf MONDO:0016412 {source="Orphanet:59", source="https://orcid.org/0000-0001-5208-3432"} ! peripheral hypothyroidism relationship: excluded_subClassOf MONDO:0017226 {source="Orphanet:59", source="https://orcid.org/0000-0001-5208-3432"} ! Pelizaeus-Merzbacher-like disease @@ -234227,7 +234206,6 @@ xref: Orphanet:127 {source="MONDO:equivalentTo", source="OMIM:301900", source="D xref: SCTID:21634003 {source="MONDO:equivalentTo", source="DOID:0050681"} xref: UMLS:C0265339 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:78557"} is_a: MONDO:0002254 {source="https://orcid.org/0000-0001-5208-3432"} ! syndromic disease -is_a: MONDO:0020119 {source="DOID:0050681", source="OMIM:301900", source="https://clinicalgenome.org/affiliation/40060/"} ! X-linked syndromic intellectual disability relationship: curated_content_resource https://search.clinicalgenome.org/kb/conditions/MONDO:0010537 {source="MONDO:CLINGEN"} relationship: excluded_subClassOf MONDO:0015159 {source="Orphanet:127", source="https://orcid.org/0000-0001-5208-3432"} ! multiple congenital anomalies/dysmorphic syndrome-intellectual disability relationship: excluded_subClassOf MONDO:0015653 {source="Orphanet:127", source="https://orcid.org/0000-0001-5208-3432"} ! monogenic epilepsy @@ -235021,9 +234999,7 @@ xref: OMIM:303600 {source="DOID:3783", source="MONDO:equivalentTo", source="Orph xref: Orphanet:192 {source="MONDO:equivalentTo", source="OMIM:303600"} xref: SCTID:15182000 {source="DOID:3783", source="MONDO:equivalentTo"} xref: UMLS:C0265252 {source="MEDGEN:75556", source="MONDO:equivalentTo", source="MONDO:MEDGEN"} -is_a: MONDO:0000508 {source="https://clinicalgenome.org/affiliation/40060/"} ! syndromic intellectual disability is_a: MONDO:0002254 {source="MONDO:Redundant", source="NCIT:C84643"} ! syndromic disease -is_a: MONDO:0020119 {source="https://clinicalgenome.org/affiliation/40060/"} ! X-linked syndromic intellectual disability relationship: curated_content_resource https://search.clinicalgenome.org/kb/conditions/MONDO:0010561 {source="MONDO:CLINGEN"} relationship: excluded_subClassOf MONDO:0000508 {source="https://github.com/monarch-initiative/mondo/issues/926", source="https://orcid.org/0000-0001-5208-3432"} ! syndromic intellectual disability relationship: excluded_subClassOf MONDO:0001071 {source="MESH:C536435", source="MESH:D038921/inferred", source="MONDO:Redundant", source="MONDO:indirect", source="https://orcid.org/0000-0001-5208-3432"} ! intellectual disability @@ -236065,7 +236041,6 @@ xref: Orphanet:323 {source="OMIM:305450"} xref: Orphanet:93932 {source="MONDO:equivalentTo", source="https://orcid.org/0000-0002-6601-2165"} xref: UMLS:C5399762 {source="MEDGEN:1768809", source="MONDO:equivalentTo", source="MONDO:MEDGEN"} is_a: MONDO:0002010 {source="DC-OMIM:305450", source="MONDO:Redundant", source="OMIM:305450"} ! FG syndrome -is_a: MONDO:0020119 {source="https://clinicalgenome.org/affiliation/40060/"} ! X-linked syndromic intellectual disability is_a: MONDO:0100000 {source="MONDO:Redundant"} ! MED12-related intellectual disability syndrome intersection_of: MONDO:0002010 ! FG syndrome intersection_of: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/11957 ! MED12 @@ -236133,7 +236108,6 @@ xref: SCTID:205573006 {source="DOID:2120", source="MONDO:equivalentTo"} xref: SCTID:2298005 {source="DOID:2120"} xref: UMLS:C0016395 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:42055"} is_a: MONDO:0019755 ! developmental defect during embryogenesis -is_a: MONDO:0020119 {source="https://clinicalgenome.org/affiliation/40060/"} ! X-linked syndromic intellectual disability relationship: curated_content_resource https://search.clinicalgenome.org/kb/conditions/MONDO:0010592 {source="MONDO:CLINGEN"} relationship: excluded_subClassOf MONDO:0003900 {source="https://orcid.org/0000-0001-5208-3432"} ! connective tissue disorder relationship: excluded_subClassOf MONDO:0005328 {source="https://orcid.org/0000-0001-5208-3432"} ! eye disorder @@ -236983,7 +236957,6 @@ xref: SCTID:402771003 {source="DOID:1700"} xref: SCTID:72523005 {source="DOID:1700"} xref: UMLS:C0079588 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:86937"} is_a: MONDO:0000425 {source="DOID:1700", source="MONDO:Redundant"} ! X-linked disease -is_a: MONDO:0015947 {source="PMID:20643494"} ! inherited ichthyosis is_a: MONDO:0020605 {source="DOID:1700"} ! X-linked recessive disease relationship: disease_has_basis_in_disruption_of GO:0004773 ! steryl-sulfatase activity relationship: disease_has_basis_in_disruption_of GO:0016125 ! sterol metabolic process @@ -237690,7 +237663,6 @@ xref: Orphanet:2484 {source="MONDO:equivalentTo", source="OMIM:309350"} xref: SCTID:13449007 {source="MONDO:equivalentTo"} xref: UMLS:C0025237 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:6292"} is_a: MONDO:0018233 {source="DOID:0111788", source="Orphanet:2484"} ! otopalatodigital syndrome spectrum disorder -is_a: MONDO:0020119 {source="https://clinicalgenome.org/affiliation/40060/"} ! X-linked syndromic intellectual disability relationship: excluded_subClassOf MONDO:0005328 {source="MONDO:0020222-obsoleted", source="https://orcid.org/0000-0001-5208-3432"} ! eye disorder relationship: excluded_subClassOf MONDO:0015161 {source="Orphanet:2484", source="https://orcid.org/0000-0001-5208-3432"} ! multiple congenital anomalies/dysmorphic syndrome without intellectual disability relationship: excluded_subClassOf MONDO:0019690 {source="PMID:31633310", source="https://orcid.org/0000-0001-5208-3432"} ! filamin-related bone disorder @@ -237844,7 +237816,6 @@ xref: Orphanet:3242 {source="OMIM:309500", source="DOID:0060179", source="MONDO: xref: SCTID:699669001 {source="MONDO:equivalentTo"} xref: UMLS:C0796135 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:208670"} is_a: MONDO:0002254 {source="https://orcid.org/0000-0001-5208-3432"} ! syndromic disease -is_a: MONDO:0020119 {source="DOID:0060179", source="OMIM:309500", source="https://clinicalgenome.org/affiliation/40060/"} ! X-linked syndromic intellectual disability relationship: curated_content_resource https://search.clinicalgenome.org/kb/conditions/MONDO:0010653 {source="MONDO:CLINGEN"} relationship: disease_has_feature HP:0000252 ! Microcephaly relationship: disease_has_feature HP:0000275 ! Narrow face @@ -237892,7 +237863,6 @@ xref: OMIM:309510 {source="Orphanet:94083/e", source="MONDO:equivalentTo", sourc xref: Orphanet:94083 {source="MONDO:equivalentTo", source="DOID:14744", source="OMIM:309510"} xref: UMLS:C0796250 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:163237"} is_a: MONDO:0005071 {source="https://orcid.org/0000-0001-5208-3432"} ! nervous system disorder -is_a: MONDO:0020119 {source="DOID:14744", source="OMIM:309510", source="https://clinicalgenome.org/affiliation/40060/"} ! X-linked syndromic intellectual disability relationship: excluded_subClassOf MONDO:0015921 {source="Orphanet:94083", source="https://orcid.org/0000-0001-5208-3432"} ! obsolete ARX-related epileptic encephalopathy relationship: excluded_subClassOf MONDO:0020119 {source="DC-OMIM:309510", source="DOID:14744", source="OMIM:309510", source="Orphanet:94083", source="https://orcid.org/0000-0001-5208-3432"} ! X-linked syndromic intellectual disability relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/18060 {source="MONDO:mim2gene_medgen"} ! ARX @@ -238299,7 +238269,6 @@ xref: Orphanet:3459 {source="MONDO:equivalentTo", source="OMIM:309585", source=" xref: SCTID:719834005 {source="MONDO:equivalentTo"} xref: UMLS:C1839736 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:333393"} is_a: MONDO:0002254 {source="https://orcid.org/0000-0001-5208-3432"} ! syndromic disease -is_a: MONDO:0020119 {source="DOID:0060814", source="OMIM:309585", source="https://clinicalgenome.org/affiliation/40060/"} ! X-linked syndromic intellectual disability relationship: excluded_subClassOf MONDO:0016565 {source="Orphanet:3459", source="https://orcid.org/0000-0001-5208-3432"} ! obsolete syndromic genetic obesity relationship: excluded_subClassOf MONDO:0020119 {source="DC-OMIM:309585", source="DOID:0060814", source="OMIM:309585", source="Orphanet:3459", source="https://orcid.org/0000-0001-5208-3432"} ! X-linked syndromic intellectual disability relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/25726 {source="MONDO:mim2gene_medgen"} ! LAS1L @@ -238346,7 +238315,6 @@ xref: Orphanet:2958 {source="OMIM:309610", source="MONDO:equivalentTo", source=" xref: SCTID:719140001 {source="MONDO:equivalentTo"} xref: UMLS:C1839730 {source="MEDGEN:374294", source="MONDO:equivalentTo", source="MONDO:MEDGEN"} is_a: MONDO:0002254 {source="https://orcid.org/0000-0001-5208-3432"} ! syndromic disease -is_a: MONDO:0020119 {source="DOID:0060805", source="OMIM:309610", source="https://clinicalgenome.org/affiliation/40060/"} ! X-linked syndromic intellectual disability relationship: excluded_subClassOf MONDO:0020119 {source="DC-OMIM:309610", source="DOID:0060805", source="OMIM:309610", source="Orphanet:2958", source="https://orcid.org/0000-0001-5208-3432"} ! X-linked syndromic intellectual disability 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/5588" xsd:anyURI @@ -238379,7 +238347,6 @@ xref: Orphanet:1436 {source="GARD:0003520", source="MONDO:equivalentTo", source= xref: SCTID:722478008 {source="MONDO:equivalentTo"} xref: UMLS:C1839729 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:326949"} is_a: MONDO:0019694 {source="Orphanet:1436"} ! spondylodysplastic dysplasia -is_a: MONDO:0020119 {source="https://clinicalgenome.org/affiliation/40060/"} ! X-linked syndromic intellectual disability relationship: excluded_subClassOf MONDO:0020119 {source="Orphanet:1436", source="https://orcid.org/0000-0001-5208-3432"} ! X-linked syndromic intellectual disability 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/5588" xsd:anyURI @@ -239483,7 +239450,6 @@ xref: OMIM:311510 {source="Orphanet:2379", source="MONDO:equivalentTo", source=" xref: Orphanet:2379 {source="MONDO:equivalentTo", source="OMIM:311510"} xref: SCTID:716107009 {source="MONDO:equivalentTo"} xref: UMLS:C0796195 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:208674"} -is_a: MONDO:0020119 {source="https://clinicalgenome.org/affiliation/40060/"} ! X-linked syndromic intellectual disability is_a: MONDO:0021095 {source="MONDO:0017661-obsoleted"} ! parkinsonian disorder relationship: curated_content_resource https://search.clinicalgenome.org/kb/conditions/MONDO:0010709 {source="MONDO:CLINGEN"} relationship: excluded_subClassOf MONDO:0020119 {source="Orphanet:2379", source="https://orcid.org/0000-0001-5208-3432"} ! X-linked syndromic intellectual disability @@ -246400,7 +246366,6 @@ xref: Orphanet:768 {source="OMIM:601005", source="DOID:0060173"} xref: UMLS:C1832916 {source="MEDGEN:331395", source="MONDO:equivalentTo", source="MONDO:MEDGEN"} is_a: MONDO:0000426 {source="DOID:0060173", source="MONDO:Redundant"} ! autosomal dominant disease is_a: MONDO:0002442 {source="MESH:C536962", source="MONDO:Redundant", source="NCIT:C142894", source="OMIM:601005"} ! long QT syndrome -is_a: MONDO:0019171 {source="Orphanet:65283"} ! familial long QT syndrome relationship: disease_has_feature HP:0001279 {source="MONDO:Wikidata"} ! Syncope relationship: disease_has_feature HP:0001649 {source="MONDO:Wikidata"} ! Tachycardia relationship: disease_has_feature HP:0001663 {source="MONDO:Wikidata"} ! Ventricular fibrillation @@ -248954,7 +248919,6 @@ xref: OMIM:615325 {source="MONDO:equivalentObsolete", source="Orphanet:363543", xref: Orphanet:363543 {source="OMIM:615325", source="MONDO:equivalentObsolete", source="DOID:0110286"} xref: Orphanet:98909 {source="MONDO:equivalentTo", source="MONDO:preferredExternal", source="OMIM:601419"} xref: UMLS:C1832370 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:330449"} -is_a: MONDO:0016187 {source="Orphanet:98909"} ! qualitative or quantitative defects of desmin is_a: MONDO:0016333 ! familial dilated cardiomyopathy is_a: MONDO:0018943 {source="DOID:0080092", source="MONDO:Redundant", source="OMIM:601419", source="Orphanet:98909"} ! myofibrillar myopathy is_a: MONDO:0019056 ! neuromuscular disease @@ -270907,7 +270871,6 @@ xref: OMIM:608035 {source="MONDO:equivalentTo"} xref: Orphanet:618 {source="OMIM:608035"} xref: UMLS:C1842643 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:334129"} is_a: MONDO:0020573 {source="https://orcid.org/0000-0002-4142-7153"} ! inherited disease susceptibility -is_a: MONDO:0024462 {source="OMIM:608035"} ! susceptibility to familial cutaneous melanoma relationship: excluded_subClassOf MONDO:0018961 {source="Orphanet:618/btnt", source="https://orcid.org/0000-0001-5208-3432"} ! familial melanoma relationship: excluded_subClassOf MONDO:0024462 {source="OMIM:608035", source="https://orcid.org/0000-0001-5208-3432"} ! susceptibility to familial cutaneous melanoma relationship: predisposes_towards MONDO:0005012 {source="https://orcid.org/0000-0002-4142-7153"} ! cutaneous melanoma @@ -276106,7 +276069,6 @@ xref: MEDGEN:332346 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"} xref: OMIM:608984 {source="DOID:0111170", source="MONDO:equivalentTo"} xref: UMLS:C1837015 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:332346"} is_a: MONDO:0003847 {source="OMIM:608984"} ! hereditary disease -is_a: MONDO:0100309 {source="DOID:0111170"} ! hereditary ataxia is_a: MONDO:0100311 {source="https://orcid.org/0000-0001-5208-3432"} ! sensory ataxia intersection_of: MONDO:0100311 ! sensory ataxia intersection_of: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/25358 ! RNF170 @@ -276486,7 +276448,6 @@ xref: OMIM:609048 {source="MONDO:equivalentTo"} xref: Orphanet:618 {source="OMIM:609048"} xref: UMLS:C1836892 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:373202"} is_a: MONDO:0020573 {source="OMIM:609048"} ! inherited disease susceptibility -is_a: MONDO:0024462 {source="OMIM:609048"} ! susceptibility to familial cutaneous melanoma intersection_of: MONDO:0020573 ! inherited disease susceptibility intersection_of: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/1773 ! CDK4 intersection_of: predisposes_towards MONDO:0005012 ! cutaneous melanoma @@ -281346,7 +281307,6 @@ xref: UMLS:C1864923 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source= is_a: MONDO:0002254 {source="https://orcid.org/0000-0002-6601-2165"} ! syndromic disease is_a: MONDO:0015653 {source="Orphanet:1947"} ! monogenic epilepsy is_a: MONDO:0016295 {source="DC-OMIM:610003", source="DOID:0110724", source="OMIM:610003", source="Orphanet:1947"} ! neuronal ceroid lipofuscinosis -is_a: MONDO:0020074 {source="Orphanet:1947", source="https://orcid.org/0000-0001-5208-3432", source="https://orcid.org/0000-0002-4142-7153"} ! progressive myoclonus epilepsy relationship: excluded_subClassOf MONDO:0020074 {source="Orphanet:1947", source="https://orcid.org/0000-0001-5208-3432"} ! progressive myoclonus epilepsy relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/2079 {source="MONDO:mim2gene_medgen"} ! CLN8 property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/6406" xsd:anyURI @@ -292633,7 +292593,6 @@ xref: MEDGEN:394200 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"} xref: OMIM:612263 {source="MONDO:equivalentTo"} xref: UMLS:C2677089 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:394200"} is_a: MONDO:0020573 {source="https://orcid.org/0000-0002-4142-7153"} ! inherited disease susceptibility -is_a: MONDO:0024462 {source="OMIM:612263"} ! susceptibility to familial cutaneous melanoma relationship: excluded_subClassOf MONDO:0003847 {source="https://orcid.org/0000-0001-5208-3432"} ! hereditary disease relationship: excluded_subClassOf MONDO:0018961 {source="https://orcid.org/0000-0001-5208-3432", source="https://orcid.org/0000-0002-6601-2165"} ! familial melanoma relationship: excluded_subClassOf MONDO:0024462 {source="OMIM:612263", source="https://orcid.org/0000-0001-5208-3432"} ! susceptibility to familial cutaneous melanoma @@ -297030,7 +296989,6 @@ xref: OMIM:612841 {source="DOID:0110702", source="MONDO:equivalentTo"} xref: Orphanet:444 {source="OMIM:612841"} xref: UMLS:C2748535 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:440568"} is_a: MONDO:0003037 {source="DOID:0110702", source="MESH:C567554", source="MONDO:Redundant", source="OMIM:612841"} ! hypotrichosis -is_a: MONDO:0018631 {source="https://orcid.org/0000-0001-5493-2602"} ! Marie Unna hereditary hypotrichosis relationship: excluded_subClassOf MONDO:0018631 {source="Orphanet:444/btnt", source="https://orcid.org/0000-0001-5208-3432"} ! Marie Unna hereditary hypotrichosis property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/6357" xsd:anyURI @@ -299021,7 +298979,6 @@ xref: MESH:D006317 {source="MONDO:equivalentTo"} xref: NCIT:C34664 {source="MONDO:equivalentTo"} xref: SCTID:73415002 {source="MONDO:equivalentTo"} xref: UMLS:C0018781 {source="MEDGEN:5455", source="MONDO:equivalentTo", source="MONDO:MEDGEN"} -is_a: MONDO:0003847 {source="https://orcid.org/0000-0001-5208-3432"} ! hereditary disease is_a: MONDO:0005365 {source="EFO:1001254", source="MESH:D006317/inferred", source="NCIT:C34664"} ! hearing loss disorder relationship: excluded_subClassOf MONDO:0003847 {source="https://orcid.org/0000-0001-5208-3432"} ! hereditary disease @@ -299896,7 +299853,6 @@ xref: OMIM:613099 {source="MONDO:equivalentTo"} xref: Orphanet:618 {source="OMIM:613099"} xref: UMLS:C2751295 {source="MONDO:equivalentTo", source="MEDGEN:416516", source="MONDO:MEDGEN"} is_a: MONDO:0020573 {source="OMIM:613099"} ! inherited disease susceptibility -is_a: MONDO:0024462 {source="OMIM:613099"} ! susceptibility to familial cutaneous melanoma intersection_of: MONDO:0020573 ! inherited disease susceptibility intersection_of: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/6929 ! MC1R intersection_of: predisposes_towards MONDO:0005012 ! cutaneous melanoma @@ -309581,7 +309537,6 @@ xref: MEDGEN:462767 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"} xref: OMIM:613972 {source="MONDO:equivalentTo"} xref: Orphanet:618 {source="OMIM:613972"} xref: UMLS:C3151417 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:462767"} -is_a: MONDO:0024462 {source="OMIM:613972"} ! susceptibility to familial cutaneous melanoma intersection_of: MONDO:0020573 ! inherited disease susceptibility intersection_of: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/12830 ! XRCC3 intersection_of: predisposes_towards MONDO:0005012 ! cutaneous melanoma @@ -314276,8 +314231,6 @@ xref: Orphanet:309108 {source="OMIM:614338"} xref: Orphanet:309111 {source="OMIM:614338"} xref: SCTID:78960005 {source="MONDO:equivalentTo"} xref: UMLS:C3280527 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:482157"} -is_a: MONDO:0002356 {source="https://orcid.org/0000-0002-3458-4839", source="https://orcid.org/0000-0002-5002-8648"} ! pancreas disorder -is_a: MONDO:0002525 {source="https://orcid.org/0000-0001-5208-3432"} ! inherited lipid metabolism disorder is_a: MONDO:0003847 {source="https://orcid.org/0000-0002-5002-8648"} ! hereditary disease is_a: MONDO:0005066 {source="https://orcid.org/0000-0001-9310-0163"} ! metabolic disease relationship: excluded_subClassOf MONDO:0002356 {source="https://orcid.org/0000-0001-5208-3432", source="https://orcid.org/0000-0002-3458-4839", source="https://orcid.org/0000-0002-5002-8648"} ! pancreas disorder @@ -315670,7 +315623,6 @@ xref: OMIM:614456 {source="Orphanet:293822/e", source="MONDO:equivalentTo", sour xref: Orphanet:293822 {source="OMIM:614456", source="MONDO:equivalentTo"} xref: UMLS:C3152204 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:463554"} is_a: MONDO:0020573 {source="OMIM:614456"} ! inherited disease susceptibility -is_a: MONDO:0024462 {source="OMIM:614456"} ! susceptibility to familial cutaneous melanoma intersection_of: MONDO:0020573 ! inherited disease susceptibility intersection_of: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/7105 ! MITF intersection_of: predisposes_towards MONDO:0005012 ! cutaneous melanoma @@ -331167,7 +331119,6 @@ xref: Orphanet:251630 {source="OMIM:616568", source="MONDO:relatedTo"} xref: Orphanet:618 {source="OMIM:615848"} xref: UMLS:C4014476 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:862913"} is_a: MONDO:0020573 {source="OMIM:615848"} ! inherited disease susceptibility -is_a: MONDO:0024462 {source="OMIM:615848"} ! susceptibility to familial cutaneous melanoma relationship: excluded_subClassOf MONDO:0018961 {source="Orphanet:618/btnt", source="https://orcid.org/0000-0001-5208-3432"} ! familial melanoma relationship: excluded_subClassOf MONDO:0024462 {source="OMIM:615848", source="https://orcid.org/0000-0001-5208-3432"} ! susceptibility to familial cutaneous melanoma relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/17284 {source="MONDO:mim2gene_medgen"} ! POT1 @@ -367106,7 +367057,6 @@ xref: Orphanet:90324 {source="DOID:2962"} xref: SCTID:205832003 {source="DOID:2962"} xref: SCTID:21086008 {source="MONDO:equivalentTo", source="DOID:2962"} xref: UMLS:C0009207 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:40363"} -is_a: MONDO:0006025 {source="DOID:2962"} ! autosomal recessive disease is_a: MONDO:0015333 {source="Orphanet:191", source="https://orcid.org/0000-0002-0736-9199", source="https://orcid.org/0000-0002-1780-5230"} ! progeroid syndrome relationship: disease_has_basis_in_disruption_of GO:0006289 {source="https://orcid.org/0000-0002-6601-2165"} ! nucleotide-excision repair relationship: disease_has_feature HP:0000992 ! Cutaneous photosensitivity @@ -372965,7 +372915,6 @@ xref: SCTID:721146009 {source="MONDO:equivalentTo"} xref: UMLS:C2931736 {source="MONDO:equivalentTo", source="MEDGEN:419481", source="MONDO:MEDGEN"} is_a: MONDO:0002254 {source="MONDO:0022314/inferred", source="MONDO:Redundant", source="https://orcid.org/0000-0002-6601-2165"} ! syndromic disease is_a: MONDO:0015159 {source="Orphanet:2139"} ! multiple congenital anomalies/dysmorphic syndrome-intellectual disability -is_a: MONDO:0020066 {source="MESH:C538112"} ! Ehlers-Danlos syndrome relationship: excluded_subClassOf MONDO:0000508 {source="MONDO:Redundant", source="Orphanet:2139", source="https://orcid.org/0000-0001-5208-3432"} ! syndromic intellectual disability relationship: excluded_subClassOf MONDO:0020066 {source="MESH:C538112", source="https://orcid.org/0000-0001-5208-3432"} ! Ehlers-Danlos syndrome property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/3597" xsd:anyURI @@ -403698,7 +403647,6 @@ xref: NCIT:C6620 {source="MONDO:equivalentTo", source="DOID:6759"} xref: Orphanet:314684 {source="MONDO:equivalentTo"} xref: SCTID:766935007 {source="MONDO:equivalentTo"} xref: UMLS:C1332582 {source="MEDGEN:231451", source="MONDO:equivalentTo", source="MONDO:MEDGEN"} -is_a: MONDO:0002129 {source="DOID:6759", source="NCIT:C6620"} ! bone cancer is_a: MONDO:0017207 {source="NCIT:C6620", source="Orphanet:314684"} ! primary organ-specific lymphoma intersection_of: MONDO:0005062 ! lymphoma intersection_of: disease_has_location UBERON:0002481 ! bone tissue @@ -407492,7 +407440,6 @@ xref: GARD:12567 {source="MONDO:GARD"} xref: ICD10CM:G23.0 {source="Orphanet:329303/attributed", source="Orphanet:329303/ntbt", source="Orphanet:329303"} xref: NORD:1302 {source="MONDO:NORD"} xref: Orphanet:329303 {source="MONDO:equivalentTo"} -is_a: MONDO:0018307 {source="Orphanet:329303"} ! neurodegeneration with brain iron accumulation intersection_of: MONDO:0018307 ! neurodegeneration with brain iron accumulation intersection_of: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/9039 ! PLA2G6 relationship: excluded_subClassOf MONDO:0018118 {source="Orphanet:329303", source="https://orcid.org/0000-0001-5208-3432"} ! obsolete disorder of phospholipids, sphingolipids and fatty acids biosynthesis with central nervous system predominant involvement @@ -428898,7 +428845,6 @@ xref: NCIT:C84792 {source="MONDO:equivalentTo"} xref: Orphanet:64734 {source="MONDO:equivalentTo", source="GARD:0000060"} xref: SCTID:129623003 {source="MONDO:equivalentTo"} xref: UMLS:C1096100 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:242751"} -is_a: MONDO:0002254 {source="https://orcid.org/0000-0001-5208-3432"} ! syndromic disease relationship: disease_has_feature MONDO:0005041 {source="GARD:0000060-text", source="Orphanet:64734", source="https://orcid.org/0000-0002-6601-2165"} ! glaucoma relationship: excluded_subClassOf MONDO:0002254 {source="NCIT:C84792", source="https://orcid.org/0000-0001-5208-3432"} ! syndromic disease relationship: excluded_subClassOf MONDO:0015120 {source="Orphanet:64734", source="https://orcid.org/0000-0001-5208-3432"} ! obsolete rare acquired eye disease @@ -432398,7 +432344,6 @@ xref: Orphanet:73256 {source="MONDO:equivalentTo"} xref: SCTID:128858006 {source="DOID:14174"} xref: SCTID:302832007 {source="DOID:14174"} xref: UMLS:C0206719 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:104924"} -is_a: MONDO:0002682 {source="DOID:14174", source="EFO:1000856", source="NCIT:C3791"} ! cerebral ventricle cancer is_a: MONDO:0016729 {source="NCIT:C3791"} ! mixed neuronal-glial tumor relationship: excluded_subClassOf MONDO:0002682 {source="DOID:14174", source="https://orcid.org/0000-0001-5208-3432"} ! cerebral ventricle cancer relationship: has_characteristic MONDO:0024492 {source="NCIT:C3791"} ! tumor grade 2, general grading system @@ -434931,7 +434876,6 @@ xref: SCTID:44176004 {source="MONDO:equivalentTo", source="DOID:9265"} xref: UMLS:C0268512 {source="MEDGEN:541342", source="MONDO:equivalentTo", source="MONDO:MEDGEN"} is_a: MONDO:0004736 {source="DOID:9265", source="MONDO:Entailed", source="MONDO:Redundant"} ! inborn disorder of amino acid metabolism is_a: MONDO:0005066 {source="https://orcid.org/0000-0001-5208-3432"} ! metabolic disease -is_a: MONDO:0019189 {source="Orphanet:79181"} ! inborn disorder of amino acid and other organic acid metabolism intersection_of: MONDO:0000001 ! disease intersection_of: MONDO:0019052 ! inborn errors of metabolism intersection_of: disease_has_basis_in_disruption_of GO:0006547 ! L-histidine metabolic process @@ -435251,7 +435195,6 @@ xref: Orphanet:79197 {source="MONDO:equivalentTo"} xref: SCTID:116020001 {source="MONDO:equivalentTo"} xref: UMLS:C0342712 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:87452"} is_a: MONDO:0004736 {source="PMID:33340416"} ! inborn disorder of amino acid metabolism -is_a: MONDO:0019189 {source="Orphanet:79197"} ! inborn disorder of amino acid and other organic acid metabolism intersection_of: MONDO:0019052 ! inborn errors of metabolism intersection_of: disease_has_basis_in_disruption_of GO:0009081 ! branched-chain amino acid metabolic process relationship: excluded_subClassOf MONDO:0019189 {source="Orphanet:79197", source="https://orcid.org/0000-0001-5208-3432"} ! inborn disorder of amino acid and other organic acid metabolism @@ -439535,7 +439478,6 @@ xref: Orphanet:85335 {source="MONDO:equivalentTo"} xref: SCTID:718848000 {source="MONDO:equivalentTo"} xref: UMLS:C4305134 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:930803"} is_a: MONDO:0002254 {source="https://orcid.org/0000-0001-5208-3432"} ! syndromic disease -is_a: MONDO:0020119 {source="https://clinicalgenome.org/affiliation/40060/"} ! X-linked syndromic intellectual disability relationship: excluded_subClassOf MONDO:0015159 {source="Orphanet:85335", source="https://orcid.org/0000-0001-5208-3432"} ! multiple congenital anomalies/dysmorphic syndrome-intellectual disability relationship: excluded_subClassOf MONDO:0020119 {source="Orphanet:85335", source="https://orcid.org/0000-0001-5208-3432"} ! X-linked syndromic intellectual disability property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/5588" xsd:anyURI @@ -453931,7 +453873,6 @@ synonym: "X-linked syndromic intellectual disability" EXACT CLINGEN_LABEL [] xref: DOID:0060309 {source="MONDO:equivalentTo"} xref: OMIMPS:309510 {source="MONDO:equivalentTo", source="DOID:0060309"} xref: Orphanet:98464 {source="MONDO:equivalentObsolete"} -is_a: MONDO:0000508 {source="DOID:0060309"} ! syndromic intellectual disability is_a: MONDO:0100284 {source="https://clinicalgenome.org/affiliation/40006/", source="https://github.com/monarch-initiative/mondo/issues/2670"} ! X-linked intellectual disability intersection_of: MONDO:0000508 ! syndromic intellectual disability intersection_of: has_characteristic HP:0001417 ! X-linked inheritance @@ -493858,7 +493799,6 @@ xref: SCTID:95411002 {source="DOID:9898"} xref: SCTID:95412009 {source="MONDO:equivalentTo", source="DOID:2702", source="EFO:1001106"} xref: UMLS:C0039106 {source="MEDGEN:11691", source="MONDO:equivalentTo", source="MONDO:MEDGEN"} is_a: MONDO:0002400 {source="DOID:2702", source="MESH:D013586"} ! synovitis -is_a: MONDO:0002522 {source="NCIT:C3401"} ! tenosynovial giant cell tumor is_a: MONDO:0005554 {source="Orphanet:66627"} ! rheumatic disorder is_a: MONDO:0024715 {source="NCIT:C3401"} ! benign synovial neoplasm relationship: excluded_subClassOf MONDO:0002522 {source="EFO:1001106", source="https://orcid.org/0000-0001-5208-3432"} ! tenosynovial giant cell tumor @@ -494238,7 +494178,6 @@ synonym: "secondary carcinoma" EXACT [NCIT:C36310] xref: MEDGEN:88450 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"} xref: NCIT:C36310 {source="MONDO:equivalentTo"} xref: UMLS:C0085668 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:88450"} -is_a: MONDO:0004993 {source="NCIT:C36310"} ! carcinoma is_a: MONDO:0024881 {source="NCIT:C36310"} ! secondary malignant neoplasm intersection_of: MONDO:0024882 ! secondary neoplasm intersection_of: disease_arises_from_feature MONDO:0004993 ! carcinoma @@ -496759,7 +496698,6 @@ xref: MEDGEN:1683361 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"} xref: OMIM:301025 {source="MONDO:equivalentTo"} xref: UMLS:C5193010 {source="MEDGEN:1683361", source="MONDO:equivalentTo", source="MONDO:MEDGEN"} is_a: MONDO:0002254 {source="https://orcid.org/0000-0001-5208-3432"} ! syndromic disease -is_a: MONDO:0020119 {source="DOID:0111843", source="OMIM:301025", source="https://clinicalgenome.org/affiliation/40060/"} ! X-linked syndromic intellectual disability relationship: excluded_subClassOf MONDO:0020119 {source="OMIM:301025", source="https://orcid.org/0000-0001-5208-3432"} ! X-linked syndromic intellectual disability 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/5588" xsd:anyURI @@ -520632,7 +520570,6 @@ xref: UMLS:C0265962 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source= is_a: MONDO:0002051 {source="https://orcid.org/0000-0001-9310-0163", source="https://orcid.org/0000-0003-4830-7530"} ! integumentary system disorder is_a: MONDO:0002254 {source="PMID:25710899", source="https://orcid.org/0000-0002-5002-8648"} ! syndromic disease is_a: MONDO:0006025 ! autosomal recessive disease -is_a: MONDO:0015947 {source="https://orcid.org/0000-0001-5208-3432"} ! inherited ichthyosis relationship: excluded_subClassOf MONDO:0015947 {source="https://orcid.org/0000-0001-5208-3432"} ! inherited ichthyosis property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/2114" xsd:anyURI property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/6749" xsd:anyURI @@ -521384,7 +521321,6 @@ xref: MESH:D008309 {source="MONDO:equivalentTo"} xref: NCIT:C84881 {source="MONDO:equivalentTo"} xref: SCTID:35265002 {source="MONDO:equivalentTo"} xref: UMLS:C0024633 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:44265"} -is_a: MONDO:0002254 {source="NCIT:C84881"} ! syndromic disease relationship: disease_has_location UBERON:0007650 ! esophagogastric junction relationship: excluded_subClassOf MONDO:0002243 {source="https://orcid.org/0000-0001-5208-3432"} ! hemorrhagic disease relationship: excluded_subClassOf MONDO:0002254 {source="NCIT:C84881", source="https://orcid.org/0000-0001-5208-3432"} ! syndromic disease @@ -534157,7 +534093,6 @@ synonym: "FOXG1 disorder" EXACT CLINGEN_LABEL [] synonym: "FOXG1 inherited genetic disease" EXACT [MONDO:patterns/disease_series_by_gene] synonym: "inherited genetic disease caused by mutation in FOXG1" EXACT [] is_a: MONDO:0000594 {source="https://clinicalgenome.org/affiliation/50022/", source="https://orcid.org/0000-0001-5208-3432"} ! pervasive developmental disorder -is_a: MONDO:0015653 {source="https://clinicalgenome.org/affiliation/50022/", source="https://orcid.org/0000-0001-5208-3432"} ! monogenic epilepsy intersection_of: MONDO:0003847 ! hereditary disease intersection_of: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/3811 ! FOXG1 relationship: curated_content_resource https://search.clinicalgenome.org/kb/conditions/MONDO:0100040 {source="MONDO:CLINGEN"} @@ -540963,7 +540898,6 @@ xref: UMLS:C4721549 {source="MEDGEN:1648542", source="MONDO:equivalentTo", sourc is_a: MONDO:0004860 {source="DOID:9719"} ! vitreous disorder is_a: MONDO:0005283 {source="DOID:9719", source="MESH:D018630", source="MONDO:indirect"} ! retinal disorder is_a: MONDO:0020246 {source="EFO:1001129", source="https://clinicalgenome.org/affiliation/40072/"} ! inherited vitreoretinopathy -is_a: MONDO:0020248 {source="Orphanet:329211"} ! vitreoretinal degeneration is_a: MONDO:0700115 {source="https://clinicalgenome.org/affiliation/40072/"} ! proliferative vitreoretinopathy relationship: curated_content_resource https://search.clinicalgenome.org/kb/conditions/MONDO:0100450 {source="MONDO:CLINGEN"} relationship: excluded_from_qc_check http://purl.obolibrary.org/obo/mondo/sparql/qc/general/qc-single-child.sparql