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add new terms (#7651)
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* add new terms

close #7643
close #7605
close #7599
close #7572

* add genes

* add term CTNNB1-related neurodevelopmental disorder and/or vitreoretinopathy

* add superclass

* fix whitespace

* update def

* fix typo

* revise xrefs

* revise  parent for CTNNB1-related neurodevelopmental disorder and/or vitreoretinopathy
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@nicolevasilevsky
nicolevasilevsky committed May 3, 2024
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Expand Up @@ -309100,12 +309100,14 @@ xref: Orphanet:404473 {source="MONDO:equivalentTo", source="OMIM:615075"}
xref: UMLS:C3554449 {source="MONDO:equivalentTo", source="MONDO:ncbi_mim2gene_medline", source="OMIM:615075"}
is_a: MONDO:0000508 {source="MONDO:Redundant", source="Orphanet:404473", source="https://clinicalgenome.org/affiliation/40060/"} ! syndromic intellectual disability
is_a: MONDO:0015159 {source="Orphanet:404473"} ! multiple congenital anomalies/dysmorphic syndrome-intellectual disability
is_a: MONDO:0100571 {source="https://clinicalgenome.org/affiliation/40006/"} ! CTNNB1-related neurodevelopmental disorder and/or vitreoretinopathy
relationship: excluded_subClassOf MONDO:0015802 {source="DOID:0070049", source="https://orcid.org/0000-0001-5208-3432"} ! autosomal dominant non-syndromic intellectual disability
relationship: has_characteristic HP:0000006 ! Autosomal dominant inheritance
relationship: has_characteristic MONDO:0021136 {source="MONDO:0015162", source="MONDO:0015983"} ! rare
relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/2514 {source="MONDO:mim2gene_medgen"} ! CTNNB1
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
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/7572" xsd:anyURI
property_value: seeAlso "https://rarediseases.info.nih.gov/diseases/3505/severe-intellectual-disability-progressive-spastic-diplegia-syndrome" xsd:anyURI {source="GARD:0003505"}

[Term]
Expand Down Expand Up @@ -318150,8 +318152,10 @@ xref: OMIM:615937 {source="MONDO:equivalentTo"}
xref: Orphanet:83473 {source="OMIM:615937"}
xref: UMLS:C4014738 {source="MONDO:equivalentTo", source="MONDO:ncbi_mim2gene_medline"}
is_a: MONDO:0019375 {source="DC-OMIM:615937", source="MONDO:Redundant", source="OMIM:615937"} ! megalencephaly-polymicrogyria-postaxial polydactyly-hydrocephalus syndrome
is_a: MONDO:0800485 {source="https://clinicalgenome.org/affiliation/50020/"} ! AKT3-related overgrowth spectrum
intersection_of: MONDO:0019375 ! megalencephaly-polymicrogyria-postaxial polydactyly-hydrocephalus syndrome
intersection_of: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/393 ! AKT3
relationship: excluded_from_qc_check http://purl.obolibrary.org/obo/mondo/sparql/qc/general/qc-single-child.sparql
relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/393 {source="MONDO:mim2gene_medgen"} ! AKT3

[Term]
Expand Down Expand Up @@ -325031,11 +325035,13 @@ xref: Orphanet:397692 {source="OMIM:616553"}
xref: UMLS:C4225284 {source="MONDO:equivalentTo", source="MONDO:ncbi_mim2gene_medline"}
is_a: MONDO:0005570 {source="https://orcid.org/0000-0001-9310-0163"} ! hematologic disorder
is_a: MONDO:0015780 {source="DOID:0070023", source="MONDO:Redundant", source="OMIM:616553"} ! dyskeratosis congenita
is_a: MONDO:0100569 {source="https://orcid.org/0009-0007-0138-2054"} ! ACD-related short telomere syndrome
intersection_of: MONDO:0015780 ! dyskeratosis congenita
intersection_of: has_characteristic HP:0000006 ! Autosomal dominant inheritance
intersection_of: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/25070 ! ACD
relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/25070 {source="MONDO:mim2gene_medgen"} ! ACD
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/6746" xsd:anyURI
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/7605" xsd:anyURI

[Term]
id: MONDO:0014691
Expand Down Expand Up @@ -489444,6 +489450,8 @@ xref: OMIM:617572 {source="DOID:0080264", source="MONDO:equivalentTo"}
xref: Orphanet:891 {source="OMIM:617572"}
xref: UMLS:C4539767 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MONDO:notFoundInDiseaseSubset", source="OMIM:617572"}
is_a: MONDO:0019516 {source="DOID:0080264", source="OMIM:617572"} ! exudative vitreoretinopathy
is_a: MONDO:0100571 {source="https://clinicalgenome.org/affiliation/40006/"} ! CTNNB1-related neurodevelopmental disorder and/or vitreoretinopathy
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/7572" xsd:anyURI

[Term]
id: MONDO:0033135
Expand Down Expand Up @@ -519289,6 +519297,33 @@ property_value: IAO:0000231 OMO:0001000 {source="MONDO:excludeTrait"}
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/7616" xsd:anyURI
is_obsolete: true

[Term]
id: MONDO:0100569
name: ACD-related short telomere syndrome
def: "A spectrum of conditions, including dyskeratosis congenita, Hoyeraal-Hreidarsson syndrome, hereditary aplastic anemia, and pulmonary fibrosis, typically characterized by shortened telomeres due to a pathogenic variant(s) in ACD that results in impaired telomere maintenance." [https://orcid.org/0009-0007-0138-2054]
is_a: MONDO:0800469 {source="https://orcid.org/0009-0007-0138-2054"} ! ACD-related telomere biology disorder
relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/25070 {source="https://orcid.org/0009-0007-0138-2054"} ! ACD
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/7605" xsd:anyURI

[Term]
id: MONDO:0100570
name: ACD-related long telomere syndrome
def: "A telomere biology disorder typically characterized by increased telomere length due to a pathogenic variant in the ACD gene that may cause familial melanoma." [https://orcid.org/0009-0007-0138-2054]
is_a: MONDO:0800469 {source="https://orcid.org/0009-0007-0138-2054"} ! ACD-related telomere biology disorder
relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/25070 {source="https://orcid.org/0009-0007-0138-2054"} ! ACD
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/7605" xsd:anyURI

[Term]
id: MONDO:0100571
name: CTNNB1-related neurodevelopmental disorder and/or vitreoretinopathy
def: "Any neurodevelopmental disorder and/or exudative vitreoretinopathy caused by a monoallelic variant in the CTNNB1 gene. Variants in CTNNB1 are related to a neurodevelopmental condition with a broad spectrum of presentations ranging from isolated vitreoretinopathy to a complex neurodevelopmental disorder with mild to severe intellectual disability, microcephaly, spasticity, autism spectrum disorder, and visual defects, including retinal detachment, and abnormal retinal vascularization." [https://clinicalgenome.org/affiliation/40006/]
is_a: MONDO:0003847 {source="https://orcid.org/0000-0001-5208-3432"} ! hereditary disease
relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/2514 {source="https://clinicalgenome.org/affiliation/40006/"} ! CTNNB1
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/7572" xsd:anyURI

[Term]
id: MONDO:0200000
name: uterine ligament adenosarcoma
Expand Down Expand Up @@ -525210,7 +525245,9 @@ subset: rare
synonym: "DKCB7" EXACT ABBREVIATION [OMIM:616553]
xref: OMIM:616553 {source="MONDO:includedEntryInOMIM"}
is_a: MONDO:0015780 {source="https://orcid.org/0000-0001-5208-3432"} ! dyskeratosis congenita
is_a: MONDO:0100569 {source="https://orcid.org/0009-0007-0138-2054"} ! ACD-related short telomere syndrome
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/5507" xsd:anyURI
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/7605" xsd:anyURI

[Term]
id: MONDO:0800371
Expand Down Expand Up @@ -526173,6 +526210,18 @@ is_a: MONDO:0019042 {source="https://clinicalgenome.org/affiliation/40130/"} ! m
relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/7976 {source="https://clinicalgenome.org/affiliation/40130/"} ! NR2F2
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/6666" xsd:anyURI

[Term]
id: MONDO:0800459
name: noxacusis
def: "Noxacusis/pain hyperacusis is characterized by individuals who experience otalgia or pain (e.g., dull ache, burning, sharp, stabbing pain and throbbing pain) in response to everyday sounds. This differs clinically from those whose primary symptom is the perception of everyday sounds as excessively loud (termed loudness hyperacusis)." [PMID:25104073, PMID:26553995]
synonym: "auditory nociception" EXACT [PMID:25104073, PMID:26553995]
synonym: "noise-induced pain" EXACT [PMID:25104073, PMID:26553995]
synonym: "noxacusis" EXACT [PMID:25104073, PMID:26553995]
synonym: "pain hyperacusis" EXACT [PMID:25104073, PMID:26553995]
is_a: MONDO:0043303 {source="PMID:25104073", source="PMID:26553995"} ! hyperacusis
relationship: excluded_from_qc_check http://purl.obolibrary.org/obo/mondo/sparql/qc/general/qc-single-child.sparql
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/7643" xsd:anyURI

[Term]
id: MONDO:0800460
name: ASAH1-related disorders
Expand Down Expand Up @@ -526263,6 +526312,15 @@ intersection_of: MONDO:0019119 ! muscular channelopathy
intersection_of: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/10591 ! SCN4A
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/6882" xsd:anyURI

[Term]
id: MONDO:0800469
name: ACD-related telomere biology disorder
def: "A complex set of inherited conditions caused by a pathogenic variant(s) in the ACD gene that results in aberrant telomere biology." [https://orcid.org/0009-0007-0138-2054, PMID:20301779]
synonym: "ACD-related telomeropathy" EXACT [https://orcid.org/0009-0007-0138-2054]
is_a: MONDO:0100137 {source="https://orcid.org/0009-0007-0138-2054"} ! telomere syndrome
relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/25070 {source="https://orcid.org/0009-0007-0138-2054"} ! ACD
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/7605" xsd:anyURI

[Term]
id: MONDO:0800470
name: TUBB4A-related neurologic disorder
Expand Down Expand Up @@ -526383,6 +526441,14 @@ is_a: MONDO:0005217 {source="PMID:29298659", source="https://orcid.org/0009-0007
relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/9386 {source="PMID:29298659", source="https://orcid.org/0009-0007-0138-2054", source="https://www.clinicalgenome.org/affiliation/40104/"} ! PRKAG2
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/6446" xsd:anyURI

[Term]
id: MONDO:0800485
name: AKT3-related overgrowth spectrum
def: "Any overgrowth syndrome where the cause of the disease is a gain-of-function variant in the AKT3 gene." [PMID:28969385]
is_a: MONDO:0019716 {source="https://clinicalgenome.org/affiliation/50020/"} ! overgrowth syndrome
relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/393 {source="https://clinicalgenome.org/affiliation/50020/"} ! AKT3
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/7599" xsd:anyURI

[Term]
id: MONDO:0800486
name: metabolic bone disorder
Expand Down

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