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Mondo Disease Ontology
http://obofoundry.org/ontology/mondo
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disentangle germline vs somatic molecular abnormalities #3473

Open cmungall opened 3 years ago

cmungall commented 3 years ago

See also #3452.

compare:

id: MONDO:0043452
name: chromosome 8, trisomy
def: "A chromosomal abnormality consisting of the presence of a third copy of chromosome 8 in somatic cells." [NCIT:C36396]
synonym: "chromosome 8 duplication" RELATED [MESH:C537942]
synonym: "trisomy 8" EXACT [MESH:C537942, NCIT:C36396]
xref: MESH:C537942 {source="MONDO:equivalentTo"}
xref: NCIT:C36396 {source="MONDO:equivalentTo"}
xref: SCTID:205649008 {source="MONDO:equivalentTo"}
xref: UMLS:C0432412 {source="NCIT:C36396", source="MONDO:notFoundInDiseaseSubset"}
is_a: MONDO:0020050 {source="NCIT:C36396"} ! autosomal trisomy
id: MONDO:0016526
name: trisomy 9p
def: "Trisomy 9p is a rare chromosomal anomaly syndrome, resulting from a partial or complete trisomy of the short arm of chromosome 9, with a wide phenotypic variablility, typically characterized by intellectual disability, craniofacial dysmorphism (e.g. microcephaly, large anterior fontanel, hypertelorism, strabismus, downslanting palpebral fissures, malformed, low-set, protruding ears, bulbous nose, macrostomia, down-turned corners of mouth, micrognathia), digital anomalies (brachydactyly and clinodactyly), and short stature. Less frequently patients present with cardiopathy and renal, skeletal, and central nervous system malformations." [Orphanet:236]
subset: ordo_malformation_syndrome {source="Orphanet:236"}
synonym: "Duplication 9p" EXACT [Orphanet:236]
synonym: "Duplication of the short arm of chromosome 9" EXACT [Orphanet:236]
synonym: "trisomy of the short arm of chromosome 9" EXACT [Orphanet:236]
synonym: "trisomy type 9p" EXACT [MONDORULE:4, Orphanet:236]
xref: ICD10:Q92.2 {source="Orphanet:236", source="ORDO:236/attributed", source="ORDO:236/ntbt"}
xref: Orphanet:236 {source="MONDO:equivalentTo"}
xref: UMLS:C0265428 {source="Orphanet:236", source="MONDO:equivalentTo"}
is_a: MONDO:0016946 {source="Orphanet:236"} ! partial trisomy of the short arm of chromosome 9

(yes I know 8 != 9 just picked random two examples to illustrate a point)

the label for the former doesn't say anything about it being somatic, but by the definition it is

The latter is pretty well implicitly germline or at least early somatic

to further confse, the NCIT xref is not to a disease but to a shadow branch:

image

we need to disentangle germline vs somatic, disease vs chromosomal feature

maglott commented 3 years ago

FYI, the definition of MESH:C537942 {source="MONDO:equivalentTo"} does not include somatic. A condition caused by an extra copy of chromosome 8. The effects can vary from normal development in some individuals, to facial, growth, and limb abnromalities, as well as delayed speech and intellectual disability. Trisomy 8 may also cause kidney, heart, and bone abnormalities.

Date introduced: August 25, 2010

nicolevasilevsky commented 3 years ago

@sabrinatoro will work on this after finishing chromosomal anomaly remodeling

cmungall commented 3 years ago

We should also look to importing the NCIT molecular abnormality branch to axiomatize cancer subtypes