diff --git a/src/ontology/mondo-edit.obo b/src/ontology/mondo-edit.obo index 3227b835af..596df40bae 100644 --- a/src/ontology/mondo-edit.obo +++ b/src/ontology/mondo-edit.obo @@ -243671,17 +243671,18 @@ property_value: confidence "3.666666666666667" xsd:double [Term] id: MONDO:0011399 -name: alpha thalassemia -def: "Alpha-thalassemia is an inherited hemoglobinopathy characterized by impaired synthesis of alpha-globin chains leading to a variable clinical picture depending on the number of affected alleles." [Orphanet:846] +name: alpha thalassemia spectrum +def: "An inherited hemoglobinopathy characterized by impaired synthesis of alpha-globin chains leading to a variable clinical picture depending on the number of affected alleles." [Orphanet:846] subset: gard_rare {source="GARD:621"} subset: nord_rare {source="NORD:1902", source="MONDO:NORD"} subset: ordo_disease {source="Orphanet:846"} subset: orphanet_rare {source="Orphanet:846"} subset: rare synonym: "A-thalassemia" RELATED [GARD:0000621] -synonym: "Alpha thalassaemia" EXACT [DOID:1099] -synonym: "alpha thalassemia" EXACT CLINGEN_LABEL [] +synonym: "alpha thalassaemia" EXACT [DOID:1099] +synonym: "alpha thalassemia spectrum" EXACT CLINGEN_LABEL [https://www.clinicalgenome.org/affiliation/40026/, https://www.clinicalgenome.org/affiliation/50052/, https://www.clinicalgenome.org/working-groups/disease-naming-advisory-committee/] synonym: "alpha-thalassemia" EXACT [DOID:1099] +synonym: "alpha-thalassemia trait" RELATED [https://www.clinicalgenome.org/affiliation/40026/, https://www.clinicalgenome.org/affiliation/50052/, https://www.clinicalgenome.org/working-groups/disease-naming-advisory-committee/] synonym: "thalassemia, alpha-" EXACT [OMIM:604131, OMIM:genemap2] synonym: "thalassemias, alpha-" EXACT [OMIM:604131, OMIM:genemap2] xref: DOID:1099 {source="MONDO:equivalentTo"} @@ -243704,6 +243705,7 @@ is_a: MONDO:0005570 ! hematologic disorder relationship: has_characteristic MONDO:0021136 ! rare property_value: confidence "0.5185185185185186" xsd:double 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/7561" xsd:anyURI [Term] id: MONDO:0011400 @@ -294644,7 +294646,7 @@ relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/ [Term] id: MONDO:0013512 name: hemoglobin H disease -def: "Hemoglobin H (HbH) disease is a moderate to severe form of alpha-thalassemia characterized by pronounced microcytic hypochromic hemolytic anemia." [Orphanet:93616] +def: "Alpha thalassemia caused by variation in three of the four copies of the alpha hemoglobin genes (e.g., large deletion in HBA1 and HBA2 genes in trans with a variant in either HBA1 or HBA2)." [https://www.clinicalgenome.org/affiliation/40026/, https://www.clinicalgenome.org/affiliation/50052/, https://www.clinicalgenome.org/working-groups/disease-naming-advisory-committee/] subset: gard_rare {source="GARD:16829"} subset: nord_rare {source="MONDO:NORD"} subset: ordo_clinical_subtype {source="Orphanet:93616"} @@ -294660,10 +294662,13 @@ synonym: "Haemoglobin H disease, Deletional" RELATED OMO:0003005 [] synonym: "haemoglobin H disease, deletional" EXACT OMO:0003005 [] synonym: "haemoglobin H disease, deletional and nondeletional" EXACT OMO:0003005 [] synonym: "Haemoglobin H disease, Nondeletional" RELATED OMO:0003005 [] +synonym: "HBA1;HBA2 digenic triallelic hemoglobin H disease" EXACT CLINGEN_LABEL [https://www.clinicalgenome.org/affiliation/40026/, https://www.clinicalgenome.org/affiliation/50052/, https://www.clinicalgenome.org/working-groups/disease-naming-advisory-committee/] synonym: "HbH" EXACT [DOID:0110031, MONDO:Lexical, OMIM:613978] synonym: "HbH disease" EXACT [Orphanet:93616] synonym: "HEMOGLOBIN H disease" RELATED [OMIM:613978] synonym: "hemoglobin H disease" EXACT [MONDO:Lexical, OMIM:613978] +synonym: "hemoglobin H disease caused by triallelic variation in HBA1;HBA2" EXACT [https://www.clinicalgenome.org/affiliation/40026/, https://www.clinicalgenome.org/affiliation/50052/, https://www.clinicalgenome.org/working-groups/disease-naming-advisory-committee/] +synonym: "hemoglobin H disease related to triallelic variation in HBA1 and HBA2" EXACT [https://www.clinicalgenome.org/affiliation/40026/, https://www.clinicalgenome.org/affiliation/50052/, https://www.clinicalgenome.org/working-groups/disease-naming-advisory-committee/] synonym: "Hemoglobin H disease, Deletional" RELATED [OMIM:613978] synonym: "hemoglobin H disease, deletional" EXACT [DOID:0110031] synonym: "hemoglobin H disease, deletional and nondeletional" EXACT [OMIM:613978, OMIM:genemap2] @@ -294681,9 +294686,11 @@ xref: UMLS:C0002312 {source="Orphanet:93616"} xref: UMLS:C1260396 {source="MONDO:notFoundInDiseaseSubset", source="Orphanet:93616"} xref: UMLS:C3161174 {source="NCIT:C95504", source="Orphanet:93616/e", source="MONDO:equivalentTo", source="MONDO:ncbi_mim2gene_medline", source="OMIM:613978", source="Orphanet:93616"} xref: UMLS:C3279561 {source="MONDO:notFoundInDiseaseSubset", source="OMIM:613978"} -is_a: MONDO:0011399 {source="DOID:0110031", source="NCIT:C95504", source="Orphanet:93616"} ! alpha thalassemia +is_a: MONDO:0011399 {source="DOID:0110031", source="NCIT:C95504", source="Orphanet:93616"} ! alpha thalassemia spectrum +is_a: MONDO:0100563 {source="https://www.clinicalgenome.org/affiliation/40026/", source="https://www.clinicalgenome.org/affiliation/50052/", source="https://www.clinicalgenome.org/working-groups/disease-naming-advisory-committee/"} ! digenic alpha thalassemia spectrum property_value: confidence "0.5185185185185186" xsd:double 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/7561" xsd:anyURI [Term] id: MONDO:0013513 @@ -342120,15 +342127,18 @@ replaced_by: MONDO:0002041 [Term] id: MONDO:0015579 name: Hb Bart's hydrops fetalis -def: "Hb Bart's hydrops fetalis is the most severe form of alpha-thalassemia and is almost always lethal. It is characterized by fetal onset of generalized edema, pleural and pericardial effusions, and severe hypochromic anemia." [Orphanet:163596] +def: "Alpha thalassemia caused by variation in all four copies of the alpha hemoglobin genes (e.g., homozygous deletion encompassing HBA1 and HBA2)." [https://www.clinicalgenome.org/affiliation/40026/, https://www.clinicalgenome.org/affiliation/50052/, https://www.clinicalgenome.org/working-groups/disease-naming-advisory-committee/] subset: gard_rare {source="GARD:16992"} subset: nord_rare {source="MONDO:NORD"} subset: ordo_clinical_subtype {source="Orphanet:163596"} subset: orphanet_rare {source="Orphanet:163596"} subset: rare -synonym: "Alpha-thalassemia hydrops fetalis" EXACT [Orphanet:163596] +synonym: "alpha-thalassemia hydrops fetalis" EXACT [Orphanet:163596] synonym: "Alpha-thalassemia major" EXACT [Orphanet:163596] synonym: "Haemoglobin Bart's hydrops fetalis" EXACT OMO:0003005 [] +synonym: "Hb Bart’s hydrops fetalis caused by quadallelic variation in HBA1;HBA2" EXACT [https://www.clinicalgenome.org/affiliation/40026/, https://www.clinicalgenome.org/affiliation/50052/, https://www.clinicalgenome.org/working-groups/disease-naming-advisory-committee/] +synonym: "Hb Bart’s hydrops fetalis related to quadallelic variation in HBA1 and HBA2" EXACT [https://www.clinicalgenome.org/affiliation/40026/, https://www.clinicalgenome.org/affiliation/50052/, https://www.clinicalgenome.org/working-groups/disease-naming-advisory-committee/] +synonym: "HBA1;HBA2 digenic quadallelic Hb Bart’s hydrops fetalis" EXACT CLINGEN_LABEL [https://www.clinicalgenome.org/affiliation/40026/, https://www.clinicalgenome.org/affiliation/50052/, https://www.clinicalgenome.org/working-groups/disease-naming-advisory-committee/] synonym: "Hemoglobin Bart's hydrops fetalis" EXACT [Orphanet:163596] synonym: "homozygous alpha0-thalassemia" EXACT [Orphanet:163596] xref: GARD:16992 {source="Orphanet:163596"} @@ -342136,9 +342146,10 @@ xref: ICD10CM:D56.0 {source="Orphanet:163596", source="Orphanet:163596/attribute xref: ICD9:282.49 {source="MONDO:relatedTo", source="MONDO:i2s"} xref: Orphanet:163596 {source="MONDO:equivalentTo"} xref: SCTID:5300004 {source="MONDO:equivalentTo"} -is_a: MONDO:0009369 ! non-immune hydrops fetalis -is_a: MONDO:0011399 {source="Orphanet:163596"} ! alpha thalassemia -property_value: confidence "6.312499999999999" xsd:double +is_a: MONDO:0009369 {source="https://orcid.org/0000-0001-5208-3432"} ! non-immune hydrops fetalis +is_a: MONDO:0011399 {source="Orphanet:163596"} ! alpha thalassemia spectrum +is_a: MONDO:0100563 {source="https://www.clinicalgenome.org/affiliation/40026/", source="https://www.clinicalgenome.org/affiliation/50052/", source="https://www.clinicalgenome.org/working-groups/disease-naming-advisory-committee/"} ! digenic alpha thalassemia spectrum +property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/7561" xsd:anyURI [Term] id: MONDO:0015580 @@ -513955,6 +513966,16 @@ relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/ 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/6461" xsd:anyURI +[Term] +id: MONDO:0100557 +name: RBFOX2-related congenital heart disorder +def: "Any congenital heart disease in which the cause of the disease is a mutation in the RBFOX2 gene." [https://clinicalgenome.org/affiliation/40130/, PMID:21925157, PMID:24151077, PMID:26785492, PMID:28991257, PMID:31241461, PMID:31778749, PMID:35137168, PMID:36198703] +is_a: MONDO:0005453 {source="https://clinicalgenome.org/affiliation/40130/"} ! congenital heart disease +intersection_of: MONDO:0005453 ! congenital heart disease +intersection_of: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/9906 ! RBFOX2 +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/7515" xsd:anyURI + [Term] id: MONDO:0100558 name: RNU4ATAC spectrum disorder @@ -513976,14 +513997,53 @@ property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0001-520 property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/7389" xsd:anyURI [Term] -id: MONDO:0100557 -name: RBFOX2-related congenital heart disorder -def: "Any congenital heart disease in which the cause of the disease is a mutation in the RBFOX2 gene." [https://clinicalgenome.org/affiliation/40130/, PMID:21925157, PMID:24151077, PMID:26785492, PMID:28991257, PMID:31241461, PMID:31778749, PMID:35137168, PMID:36198703] -is_a: MONDO:0005453 {source="https://clinicalgenome.org/affiliation/40130/"} ! congenital heart disease -intersection_of: MONDO:0005453 ! congenital heart disease -intersection_of: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/9906 ! RBFOX2 +id: MONDO:0100561 +name: HBA1-related alpha thalassemia spectrum +def: "Mild microcytic anemia caused by biallelic variation in the HBA1 gene." [https://www.clinicalgenome.org/affiliation/40026/, https://www.clinicalgenome.org/affiliation/50052/, https://www.clinicalgenome.org/working-groups/disease-naming-advisory-committee/] +synonym: "alpha-thalassemia trait" RELATED [https://www.clinicalgenome.org/affiliation/40026/, https://www.clinicalgenome.org/affiliation/50052/, https://www.clinicalgenome.org/working-groups/disease-naming-advisory-committee/] +is_a: MONDO:0100565 {source="https://www.clinicalgenome.org/affiliation/40026/", source="https://www.clinicalgenome.org/affiliation/50052/", source="https://www.clinicalgenome.org/working-groups/disease-naming-advisory-committee/"} ! monogenic alpha thalassemia spectrum +intersection_of: MONDO:0011399 ! alpha thalassemia spectrum +intersection_of: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/4823 ! HBA1 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/7515" xsd:anyURI +property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/7561" xsd:anyURI + +[Term] +id: MONDO:0100562 +name: HBA2-related alpha thalassemia spectrum +def: "Mild microcytic anemia caused by biallelic variation in the HBA2 gene." [https://www.clinicalgenome.org/affiliation/40026/, https://www.clinicalgenome.org/affiliation/50052/, https://www.clinicalgenome.org/working-groups/disease-naming-advisory-committee/] +synonym: "alpha-thalassemia trait" RELATED [https://www.clinicalgenome.org/affiliation/40026/, https://www.clinicalgenome.org/affiliation/50052/, https://www.clinicalgenome.org/working-groups/disease-naming-advisory-committee/] +is_a: MONDO:0100565 {source="https://www.clinicalgenome.org/affiliation/40026/", source="https://www.clinicalgenome.org/affiliation/50052/", source="https://www.clinicalgenome.org/working-groups/disease-naming-advisory-committee/"} ! monogenic alpha thalassemia spectrum +intersection_of: MONDO:0011399 ! alpha thalassemia spectrum +intersection_of: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/4824 ! HBA2 +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/7561" xsd:anyURI + +[Term] +id: MONDO:0100563 +name: digenic alpha thalassemia spectrum +def: "An instance of alpha thalessemia spectrum that is caused by an inherited multiallelic modification in an individual." [MONDO:patterns/hereditary] +is_a: MONDO:0011399 {source="https://www.clinicalgenome.org/affiliation/40026/", source="https://www.clinicalgenome.org/affiliation/50052/", source="https://www.clinicalgenome.org/working-groups/disease-naming-advisory-committee/"} ! alpha thalassemia spectrum +relationship: has_characteristic MONDO:0021152 {source="https://www.clinicalgenome.org/affiliation/40026/", source="https://www.clinicalgenome.org/affiliation/50052/", source="https://www.clinicalgenome.org/working-groups/disease-naming-advisory-committee/"} ! inherited +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/7561" xsd:anyURI + +[Term] +id: MONDO:0100564 +name: HBA1; HBA2-related digenic alpha thalassemia spectrum +def: "Mild microcytic anemia caused by variation in two of the four copies of the alpha hemoglobin genes, which can be in cis (e.g., large deletion of HBA1 and HBA2 genes) or in trans (e.g., HBA1 variant on one chromosome and HBA2 variant on the other chromosome)." [https://www.clinicalgenome.org/affiliation/40026/, https://www.clinicalgenome.org/affiliation/50052/, https://www.clinicalgenome.org/working-groups/disease-naming-advisory-committee/] +synonym: "alpha-thalassemia trait" RELATED [https://www.clinicalgenome.org/affiliation/40026/, https://www.clinicalgenome.org/affiliation/50052/, https://www.clinicalgenome.org/working-groups/disease-naming-advisory-committee/] +is_a: MONDO:0100563 {source="https://www.clinicalgenome.org/affiliation/40026/", source="https://www.clinicalgenome.org/affiliation/50052/", source="https://www.clinicalgenome.org/working-groups/disease-naming-advisory-committee/"} ! digenic alpha thalassemia spectrum +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/7561" xsd:anyURI + +[Term] +id: MONDO:0100565 +name: monogenic alpha thalassemia spectrum +def: "An instance of alpha thalessemia spectrum that is caused by an inherited monogenomic modification in an individual." [MONDO:patterns/hereditary] +is_a: MONDO:0011399 {source="https://www.clinicalgenome.org/affiliation/40026/", source="https://www.clinicalgenome.org/affiliation/50052/", source="https://www.clinicalgenome.org/working-groups/disease-naming-advisory-committee/"} ! alpha thalassemia spectrum +relationship: has_characteristic MONDO:0021152 {source="https://www.clinicalgenome.org/affiliation/40026/", source="https://www.clinicalgenome.org/affiliation/50052/", source="https://www.clinicalgenome.org/working-groups/disease-naming-advisory-committee/"} ! inherited +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/7561" xsd:anyURI [Term] id: MONDO:0100560