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rename Alpha thalassemia spectrum (#7567)
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* rename Alpha thalassemia spectrum

- add new terms:
    - HBA1-related alpha thalassemia spectrum
    - HBA2-related alpha thalassemia spectrum
    - digenic alpha thalassemia spectrum
    - monogenic alpha thalassemia spectrum
and reclassify children

close #7561

* add new term HBA1; HBA2-related digenic alpha thalassemia spectrum

* add xrefs

* fix synonym scope

* fix def

* add issue link

* fix ID for monogenic alpha thalassemia spectrum

duplicate ID, uggghhhh

---------

Co-authored-by: Sabrina Toro <[email protected]>
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@nicolevasilevsky @sabrinatoro
nicolevasilevsky and sabrinatoro authored Apr 10, 2024
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Showing 1 changed file with 78 additions and 18 deletions.
96 changes: 78 additions & 18 deletions src/ontology/mondo-edit.obo
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Original file line number Diff line number Diff line change
Expand Up @@ -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"}
Expand All @@ -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
Expand Down Expand Up @@ -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"}
Expand All @@ -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]
Expand All @@ -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
Expand Down Expand Up @@ -342120,25 +342127,29 @@ 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"}
xref: ICD10CM:D56.0 {source="Orphanet:163596", source="Orphanet:163596/attributed", source="Orphanet:163596/ntbt"}
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
Expand Down Expand Up @@ -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
Expand All @@ -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
Expand Down

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