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ready to merge: split Birt-Hogg-Dube syndrome #6895

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merged 7 commits into from
Nov 27, 2023
Merged

ready to merge: split Birt-Hogg-Dube syndrome #6895

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bb08b06
split Birt-Hogg-Dube syndrome
nicolevasilevsky Nov 21, 2023
5e677d3
exclude qc
nicolevasilevsky Nov 21, 2023
cf24868
fix syn
nicolevasilevsky Nov 21, 2023
32fcdf6
add MONDO:0800455 Birt-Hogg-Dube syndrome 2
nicolevasilevsky Nov 21, 2023
f0d0204
remove exclude from qc
nicolevasilevsky Nov 21, 2023
1d96577
revise consider annotation
nicolevasilevsky Nov 21, 2023
988ba4c
Merge branch 'master' into issue-6518
nicolevasilevsky Nov 27, 2023
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78 changes: 48 additions & 30 deletions src/ontology/mondo-edit.obo
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Expand Up @@ -138269,38 +138269,13 @@ property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/

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@nicolevasilevsky this should not be "replaced_by" should be "considered" with both new terms

[Term]
id: MONDO:0007607
name: Birt-Hogg-Dube syndrome
def: "Birt-Hogg-Dube (BHD) syndrome is characterized by skin lesions, kidney tumors, and pulmonary cysts that may be associated with pneumothorax. It is a rare clinicopathologic condition named after the three Canadian physicians who reported the syndrome in 1977." [Orphanet:122]
comment: This will be obsoleted in the 2023-10-01 release. The term will be split and the new ID for this term will be MONDO:0800444 (Birt-Hogg-Dube syndrome), and MONDO:0800445 (Birt-Hogg-Dube syndrome 1).
subset: obsoletion_candidate
subset: ordo_malformation_syndrome {source="Orphanet:122"}
synonym: "BHD" RELATED ABBREVIATION [MONDO:Lexical, OMIM:135150]
synonym: "BHD syndrome" RELATED [GARD:0002322]
synonym: "Birt Hogg Dube syndrome" RELATED [GARD:0002322]
synonym: "Birt-Hogg-Dube syndrome" EXACT CLINGEN_PREFERRED [MONDO:Lexical, NCIT:C28244, OMIM:135150]
synonym: "Birt-Hogg-Dubé syndrome" RELATED [Orphanet:122]
synonym: "fibrofolliculomas with trichodiscomas and acrochordons" EXACT [OMIM:135150, Orphanet:122]
synonym: "Hornstein-Knickenberg syndrome" RELATED [OMIM:135150]
xref: DOID:0050676 {source="MONDO:equivalentTo"}
xref: EFO:1001273 {source="MONDO:equivalentTo"}
xref: ICD9:704.8 {source="MONDO:relatedTo", source="MONDO:i2s"}
xref: MedDRA:10067736 {source="Orphanet:122/e", source="Orphanet:122"}
xref: MESH:D058249 {source="Orphanet:122/e", source="MONDO:equivalentTo", source="Orphanet:122"}
xref: NCIT:C28244 {source="MONDO:equivalentTo", source="MONDO:exact-label-match"}
xref: OMIM:135150 {source="Orphanet:122/e", source="DOID:0050676", source="MONDO:equivalentTo", source="Orphanet:122"}
xref: Orphanet:122 {source="OMIM:135150", source="MONDO:equivalentTo"}
xref: SCTID:110985001 {source="MONDO:equivalentTo"}
xref: UMLS:C0346010 {source="OMIM:135150", source="Orphanet:122/e", source="NCIT:C28244", source="MONDO:equivalentTo", source="MONDO:ncbi_mim2gene_medline", source="Orphanet:122"}
is_a: MONDO:0000426 {source="DOID:0050676", source="MONDO:Redundant"} ! autosomal dominant disease
is_a: MONDO:0002254 {source="https://orcid.org/0000-0001-5208-3432"} ! syndromic disease
is_a: MONDO:0015356 {source="MESH:D058249", source="MONDO:Redundant", source="NCIT:C28244", source="Orphanet:122/inferred"} ! hereditary neoplastic syndrome
relationship: excluded_subClassOf MONDO:0019300 {source="Orphanet:122"} ! obsolete rare skin tumor or hamartoma
relationship: has_characteristic HP:0000006 {source="MONDO:HPOA", source="OMIM:135150", source="Orphanet:122"} ! Autosomal dominant inheritance
relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/27310 {source="MONDO:mim2gene_medgen"} ! FLCN
property_value: confidence "4.7142857142857135" xsd:double
name: obsolete Birt-Hogg-Dube syndrome
property_value: IAO:0000231 IAO:0000229
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/6518" xsd:anyURI
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/6749" xsd:anyURI
property_value: IAO:0006012 "2023-10-01" xsd:string
is_obsolete: true
consider: MONDO:0800444
consider: MONDO:0800445

[Term]
id: MONDO:0007608
Expand Down Expand Up @@ -460918,6 +460893,39 @@ is_a: MONDO:0100038 {source="https://clinicalgenome.org/affiliation/40006/"} ! c
relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/14677 {source="https://clinicalgenome.org/affiliation/40006/"} ! DEAF1
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/6228" xsd:anyURI

[Term]
id: MONDO:0800444
name: Birt-Hogg-Dube syndrome
synonym: "BHD" EXACT ABBREVIATION [OMIMPS:135150]
xref: OMIMPS:135150 {source="MONDO:equivalentTo"}
is_a: MONDO:0000426 {source="OMIMPS:135150"} ! autosomal dominant disease
is_a: MONDO:0002254 {source="https://orcid.org/0000-0001-5208-3432"} ! syndromic disease
relationship: has_characteristic MONDO:0021152 {source="OMIMPS:135150"} ! inherited
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/6518" xsd:anyURI

[Term]
id: MONDO:0800445
name: Birt-Hogg-Dube syndrome 1
def: "Any Birt-Hogg-Dube (BHD) syndrome in which the cause of the disease is a variation in the FLCN gene." [MONDO:patterns/disease_series_by_gene]
subset: ordo_malformation_syndrome {source="Orphanet:122"}
synonym: "fibrofolliculomas with trichodiscomas and acrochordons" EXACT [OMIM:135150, Orphanet:122]
synonym: "Hornstein-Knickenberg syndrome" EXACT [OMIM:135150]
xref: DOID:0050676 {source="MONDO:equivalentTo"}
xref: EFO:1001273 {source="MONDO:equivalentTo"}
xref: ICD9:704.8 {source="MONDO:relatedTo", source="MONDO:i2s"}
xref: MedDRA:10067736 {source="Orphanet:122/e", source="Orphanet:122"}
xref: MESH:D058249 {source="Orphanet:122/e", source="MONDO:equivalentTo", source="Orphanet:122"}
xref: NCIT:C28244 {source="MONDO:equivalentTo", source="MONDO:exact-label-match"}
xref: OMIM:135150 {source="Orphanet:122/e", source="DOID:0050676", source="MONDO:equivalentTo", source="Orphanet:122"}
xref: Orphanet:122 {source="OMIM:135150", source="MONDO:equivalentTo"}
xref: SCTID:110985001 {source="MONDO:equivalentTo"}
xref: UMLS:C0346010 {source="OMIM:135150", source="Orphanet:122/e", source="NCIT:C28244", source="MONDO:equivalentTo", source="MONDO:ncbi_mim2gene_medline", source="Orphanet:122"}
is_a: MONDO:0800444 {source="OMIM:135150"} ! Birt-Hogg-Dube syndrome
intersection_of: MONDO:0800444 ! Birt-Hogg-Dube syndrome
intersection_of: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/27310 ! FLCN
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/6518" xsd:anyURI
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/6749" xsd:anyURI

[Term]
id: MONDO:0800446
name: bleeding diathesis due to thromboxane synthesis deficiency
Expand Down Expand Up @@ -461010,6 +461018,16 @@ is_a: MONDO:0003847 {source="https://orcid.org/0000-0001-5208-3432"} ! hereditar
relationship: has_characteristic MONDO:0021152 {source="OMIMPS:616033"} ! inherited
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/6777" xsd:anyURI

[Term]
id: MONDO:0800455
name: Birt-Hogg-Dube syndrome 2
def: "Birt-Hogg-Dube syndrome caused by the mutations in PRDM10." [MONDO:patterns/disease_series_by_gene]
synonym: "BHD2" EXACT ABBREVIATION [OMIM:620459]
xref: OMIM:620459 {source="MONDO:equivalentTo"}
is_a: MONDO:0800444 {source="OMIM:620459"} ! Birt-Hogg-Dube syndrome
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/6546" xsd:anyURI

[Term]
id: MONDO:0810000
name: choroidal neovascularization
Expand Down
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