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obsolete Li-Fraumeni syndrome 1 (#6483)
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* obsolete Li-Fraumeni syndrome 1

and obsolete Li-Fraumeni syndrome 2
merge into Li-Fraumeni syndrome

close #6269

* revise UMLS xref

* revise syns

* add source

* remove HPOA annotation
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@nicolevasilevsky
nicolevasilevsky authored Jul 26, 2023
1 parent 02b968e commit 150628e
Showing 1 changed file with 39 additions and 53 deletions.
92 changes: 39 additions & 53 deletions src/ontology/mondo-edit.obo
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Original file line number Diff line number Diff line change
Expand Up @@ -142565,39 +142565,11 @@ intersection_of: has_characteristic MONDO:0021152 ! inherited

[Term]
id: MONDO:0007903
name: Li-Fraumeni syndrome 1
def: "Any Li-Fraumeni syndrome in which the cause of the disease is a mutation in the TP53 gene." [MONDO:patterns/disease_series_by_gene]
comment: Reason of obsoletion: MONDO:excludeHistoricalDisease. Term to consider: Li-Fraumeni syndrome'-MONDO:0018875
subset: clingen
subset: obsoletion_candidate
synonym: "LFS" RELATED ABBREVIATION [OMIM:151623]
synonym: "LFS1" RELATED ABBREVIATION [MONDO:Lexical, OMIM:151623]
synonym: "LFS3" EXACT ABBREVIATION [MONDO:0012234, MONDO:Lexical, OMIM:609266]
synonym: "Li-Fraumeni syndrome" RELATED [OMIM:151623]
synonym: "Li-Fraumeni syndrome 1" EXACT CLINGEN_PREFERRED [MONDO:Lexical, OMIM:151623]
synonym: "Li-Fraumeni syndrome 3" RELATED [MONDO:Lexical, OMIM:609266]
synonym: "Li-Fraumeni syndrome caused by mutation in TP53" EXACT [MONDO:design_pattern]
synonym: "Li-Fraumeni syndrome type 1" EXACT [MONDORULE:1, OMIM:151623]
synonym: "Li-Fraumeni-like syndrome" RELATED [OMIM:151623]
synonym: "sarcoma family syndrome of 51 and Fraumeni" RELATED [OMIM:151623]
synonym: "Sbla syndrome" RELATED [OMIM:151623]
synonym: "TP53 Li-Fraumeni syndrome" EXACT [MONDO:design_pattern, MONDO:patterns/disease_series_by_gene]
xref: DOID:0111503 {source="MONDO:equivalentTo"}
xref: MESH:C563754 {source="MONDO:equivalentTo"}
xref: OMIM:151623 {source="MONDO:equivalentTo", source="MONDO:preferredExternal"}
xref: OMIM:609266 {source="MONDO:equivalentObsolete"}
xref: Orphanet:524 {source="OMIM:151623", source="OMIM:609266"}
xref: UMLS:C1835398 {source="OMIM:151623", source="MONDO:equivalentTo", source="MONDO:ncbi_mim2gene_medline"}
xref: UMLS:C1836481 {source="MONDO:equivalentTo", source="MONDO:ncbi_mim2gene_medline", source="OMIM:609266"}
xref: UMLS:C2675080 {source="OMIM:151623", source="MONDO:notFoundInDiseaseSubset"}
is_a: MONDO:0018875 {source="DC-OMIM:151623", source="DC-OMIM:609266", source="MESH:C563754", source="MONDO:Redundant", source="OMIM:151623", source="OMIM:609266"} ! Li-Fraumeni syndrome
intersection_of: MONDO:0018875 ! Li-Fraumeni syndrome
intersection_of: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/11998 ! TP53
relationship: has_characteristic HP:0000006 {source="MONDO:HPOA", source="OMIM:151623"} ! Autosomal dominant inheritance
relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/11998 {source="MONDO:mim2gene_medgen"} ! TP53
property_value: confidence "1.9982363315696645" xsd:double
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/6260" xsd:anyURI
property_value: IAO:0006012 "2023-08-01" xsd:string
name: obsolete Li-Fraumeni syndrome 1
property_value: IAO:0000231 "terms merged" xsd:string
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/6269" xsd:anyURI
is_obsolete: true
replaced_by: MONDO:0018875

[Term]
id: MONDO:0007904
Expand Down Expand Up @@ -242280,29 +242252,24 @@ is_a: MONDO:0003847 ! hereditary disease

[Term]
id: MONDO:0012233
name: Li-Fraumeni syndrome 2
def: "Any Li-Fraumeni syndrome in which the cause of the disease is a mutation in the CHEK2 gene." [MONDO:patterns/disease_series_by_gene]
comment: Reason of obsoletion: out of scope - MONDO:excludeHistoricalDisease. Term to consider: Li-Fraumeni syndrome'-MONDO:0018875
name: obsolete Li-Fraumeni syndrome 2
def: "OBSOLETE. Any Li-Fraumeni syndrome in which the cause of the disease is a mutation in the CHEK2 gene." [MONDO:patterns/disease_series_by_gene]
subset: clingen
subset: obsoletion_candidate
synonym: "CHEK2 Li-Fraumeni syndrome" EXACT [MONDO:design_pattern, MONDO:patterns/disease_series_by_gene]
synonym: "LFS2" RELATED ABBREVIATION [MONDO:Lexical, OMIM:609265]
synonym: "Li-Fraumeni syndrome 2" EXACT [MONDO:Lexical, OMIM:609265]
synonym: "Li-Fraumeni syndrome caused by mutation in CHEK2" EXACT [MONDO:design_pattern]
synonym: "Li-Fraumeni syndrome type 2" EXACT [MONDORULE:1, OMIM:609265]
xref: DOID:0111504 {source="MONDO:equivalentTo"}
xref: MESH:C563755 {source="MONDO:equivalentTo"}
xref: OMIM:609265 {source="MONDO:equivalentTo"}
xref: DOID:0111504 {source="MONDO:obsoleteEquivalent"}
xref: MESH:C563755 {source="MONDO:obsoleteEquivalent"}
xref: OMIM:609265 {source="MONDO:obsoleteEquivalent"}
xref: Orphanet:524 {source="OMIM:609265"}
xref: UMLS:C1836482 {source="MONDO:equivalentTo", source="MONDO:ncbi_mim2gene_medline", source="OMIM:609265"}
is_a: MONDO:0018875 {source="DC-OMIM:609265", source="MESH:C563755", source="MONDO:Redundant", source="OMIM:609265"} ! Li-Fraumeni syndrome
intersection_of: MONDO:0018875 ! Li-Fraumeni syndrome
intersection_of: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/16627 ! CHEK2
relationship: has_characteristic HP:0000006 {source="MONDO:HPOA", source="OMIM:609265"} ! Autosomal dominant inheritance
relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/16627 {source="MONDO:mim2gene_medgen"} ! CHEK2
property_value: confidence "1.9982363315696645" xsd:double
xref: UMLS:C1836482 {source="MONDO:obsoleteEquivalent", source="MONDO:ncbi_mim2gene_medline", source="OMIM:609265"}
property_value: IAO:0000231 "out of scope" xsd:string {source="MONDO:excludeHistoricalDisease"}
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/6260" xsd:anyURI
property_value: IAO:0006012 "2023-08-01" xsd:string
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/6269" xsd:anyURI
is_obsolete: true
consider: MONDO:0018875

[Term]
id: MONDO:0012234
Expand Down Expand Up @@ -361089,32 +361056,51 @@ property_value: seeAlso "https://rarediseases.info.nih.gov/diseases/537/acute-no
[Term]
id: MONDO:0018875
name: Li-Fraumeni syndrome
def: "Li-Fraumeni syndrome (LFS) is a rare cancer predisposition syndrome characterized by the early-onset of multiple primary cancers such as breast cancer, soft tissue and bone sarcomas, brain tumors and adrenal cortical carcinoma (ACC)." [Orphanet:524]
def: "A rare cancer predisposition syndrome characterized by the early-onset of multiple primary cancers such as breast cancer, soft tissue and bone sarcomas, brain tumors and adrenal cortical carcinoma (ACC)." [Orphanet:524]
subset: clingen
subset: ordo_disease {source="Orphanet:524"}
synonym: "Li Fraumeni syndrome" RELATED [GARD:0006902]
synonym: "LFS" EXACT ABBREVIATION [OMIM:151623]
synonym: "LFS1" RELATED ABBREVIATION [MONDO:Lexical, OMIM:151623]
synonym: "LFS3" RELATED ABBREVIATION [MONDO:0012234, MONDO:Lexical, OMIM:609266]
synonym: "Li Fraumeni syndrome" EXACT [GARD:0006902]
synonym: "Li-Fraumeni familial cancer susceptibility syndrome" EXACT [NCIT:C3476]
synonym: "Li-Fraumeni familiar cancer susceptibility syndrome" EXACT [DOID:3012, NCIT:C3476]
synonym: "Li-Fraumeni syndrome" EXACT CLINGEN_PREFERRED [NCIT:C3476]
synonym: "Li-Fraumeni syndrome" EXACT [OMIM:151623]
synonym: "Li-Fraumeni syndrome caused by mutation in TP53" EXACT [MONDO:design_pattern]
synonym: "Li-Fraumeni-like syndrome" RELATED [OMIM:151623]
synonym: "sarcoma family syndrome of 51 and Fraumeni" RELATED [OMIM:151623]
synonym: "sarcoma family syndrome of Li and Fraumeni" RELATED [GARD:0006902]
synonym: "sarcoma, breast, leukaemia and adrenal gland syndrome" EXACT [DOID:3012]
synonym: "SBLA syndrome" EXACT [DOID:3012]
synonym: "SBLA syndrome" EXACT [DOID:3012, OMIM:151623]
synonym: "SBLA syndrome (sarcoma, breast, leukemia, and adrenal gland)" RELATED [GARD:0006902]
synonym: "TP53 Li-Fraumeni syndrome" EXACT [MONDO:design_pattern, MONDO:patterns/disease_series_by_gene]
xref: DOID:0111503
xref: DOID:3012 {source="MONDO:equivalentTo"}
xref: GARD:0006902 {source="MONDO:equivalentTo"}
xref: ICD10CM:D48.9 {source="Orphanet:524", source="Orphanet:524/attributed", source="Orphanet:524/ntbt"}
xref: ICD9:V84.01 {source="MONDO:relatedTo", source="MONDO:i2s"}
xref: MedDRA:10066795 {source="Orphanet:524", source="Orphanet:524/e"}
xref: MESH:C563754
xref: MESH:D016864 {source="DOID:3012", source="Orphanet:524", source="MONDO:equivalentTo", source="Orphanet:524/e"}
xref: NCIT:C3476 {source="DOID:3012", source="MONDO:equivalentTo", source="MONDO:exact-label-match"}
xref: OMIMPS:151623 {source="MONDO:cjm", source="MONDO:equivalentTo"}
xref: OMIM:151623 {source="MONDO:equivalentTo"}
xref: OMIM:609266 {source="MONDO:equivalentObsolete"}
xref: OMIMPS:151623 {source="MONDO:cjm", source="MONDO:relatedTo"}
xref: Orphanet:524 {source="OMIM:151623", source="OMIM:609266"}
xref: Orphanet:524 {source="DOID:3012", source="MONDO:equivalentTo"}
xref: SCTID:428850001 {source="DOID:3012", source="MONDO:equivalentTo"}
xref: UMLS:C0085390 {source="DOID:3012", source="Orphanet:524", source="MONDO:equivalentTo", source="Orphanet:524/e", source="NCIT:C3476"}
xref: UMLS:C1835398 {source="OMIM:151623", source="MONDO:ncbi_mim2gene_medline"}
xref: UMLS:C1836481 {source="MONDO:ncbi_mim2gene_medline", source="OMIM:609266"}
xref: UMLS:C2675080 {source="OMIM:151623", source="MONDO:notFoundInDiseaseSubset"}
is_a: MONDO:0000426 {source="DOID:3012", source="MONDO:Redundant"} ! autosomal dominant disease
is_a: MONDO:0015356 {source="MESH:D016864", source="NCIT:C3476", source="Orphanet:524"} ! hereditary neoplastic syndrome
is_a: MONDO:0016756 {source="Orphanet:524"} ! inherited nervous system cancer-predisposing syndrome
relationship: has_characteristic HP:0000006 {source="Orphanet:524"} ! Autosomal dominant inheritance
relationship: has_characteristic HP:0000006 {source="OMIM:151623", source="Orphanet:524"} ! Autosomal dominant inheritance
relationship: has_characteristic MONDO:0021152 {source="OMIMPS:151623"} ! inherited
relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/11998 {source="MONDO:mim2gene_medgen"} ! TP53
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/6260" xsd:anyURI

[Term]
id: MONDO:0018876
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