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missing MONDO:0021145 in mondo API #128

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newgene opened this issue Jun 28, 2023 · 2 comments
Open

missing MONDO:0021145 in mondo API #128

newgene opened this issue Jun 28, 2023 · 2 comments
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@newgene
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newgene commented Jun 28, 2023

Somehow this particular MONDO ID does not exists in our mondo API:

https://biothings.ncats.io/mondo/disease/MONDO:0021145

(updated to MONDO version 2023-06-01)

Check the original mondo.obo file of that version, it does contains a record of MONDO:0021145:

[Term]
id: MONDO:0021145
name: obsolete disorder of genitourinary system
def: "OBSOLETE. A disease that involves the genitourinary system." [MONDO:patterns/location]
comment: Reason: out of scope - grouping term. Terms to consider: 'reproductive system disorder' (MONDO:0005039), 'urinary system disorder' (MONDO:0002118).
synonym: "disease of genitourinary system" EXACT [MONDO:patterns/location_top]
synonym: "disease or disorder of genitourinary system" EXACT []
synonym: "disorder of genitourinary system" EXACT [MONDO:patterns/location_top]
synonym: "disorder of the genitourinary system" EXACT []
synonym: "genitourinary system disease" EXACT [MONDO:patterns/location]
synonym: "genitourinary system disease or disorder" EXACT [MONDO:design_pattern, MONDO:patterns/location]
synonym: "syndrome of the genitourinary system" RELATED []
synonym: "urogenital disease" RELATED []
synonym: "urogenital disorder" RELATED []
xref: ICD10CM:N00-N99 {source="https://github.com/monarch-initiative/mondo/issues/4536", source="MONDO:obsoleteEquivalent", source="https://orcid.org/0000-0001-5208-3432", source="https://orcid.org/0000-0002-4142-7153"}
xref: SCTID:42030000 {source="MONDO:obsoleteEquivalent"}
xref: UMLS:C0080276 {source="MONDO:obsoleteEquivalent"}
property_value: exactMatch http://identifiers.org/snomedct/42030000
property_value: exactMatch http://linkedlifedata.com/resource/umls/id/C0080276
property_value: exactMatch http://purl.bioontology.org/ontology/ICD10CM/N00-N99
property_value: IAO:0000231 "out of scope" xsd:string {source="MONDO:excludeGroupingMorpho"}
property_value: IAO:0000233 https://github.com/monarch-initiative/mondo/issues/4113 xsd:anyURI
is_obsolete: true
consider: MONDO:0002118
consider: MONDO:0005039

Note that is_obsolete: true in this record, not sure if it's related to this issue.

@newgene newgene added the bug Something isn't working label Jun 28, 2023
@colleenXu
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@everaldorodrigo @newgene @andrewsu

This may be a good issue to review for addressing vs dropping

@newgene newgene assigned DylanWelzel and unassigned ericz1803 Feb 1, 2024
@newgene
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newgene commented Feb 1, 2024

assigned to @DylanWelzel since it's related to mydisease.info as well.

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