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Update clingen label #7926

Merged
merged 6 commits into from
Jul 10, 2024
Merged

Update clingen label #7926

merged 6 commits into from
Jul 10, 2024

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twhetzel
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@twhetzel twhetzel commented Jul 5, 2024

closes #7924

In cases where the clingen preferred term did not already exist as a synonym in Mondo, I added a new exact synonym. All synonyms in the gSheet should be tagged with CLINGEN_LABEL and an xref for the Clingen group listed in the gSheet. See email "Mondo-ClinGen interaction" for link to this gSheet.

@twhetzel twhetzel requested a review from sabrinatoro as a code owner July 5, 2024 22:27
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twhetzel commented Jul 7, 2024

UPDATE: I talked with Sabrina and she explained the information in OMIM and why it is modeled with these terms in Mondo (summary: the OMIM entry page also has an Included entry). So the resolution is to not add the requested exact synonym to MONDO:0014805 and notify ClinGen about this.


@sabrinatoro @nicolevasilevsky the QC is failing on ../sparql/qc/general/qc-duplicate-exact-synonym-no-abbrev.sparql due to these Mondo terms (MONDO:0014805 and MONDO:0958071) both now having the same value for an exact synonym based on the request in the gSheet related to this ticket/PR to use USP7-related neurodevelopmental disorder as the clingen preferred term for MONDO:0014805.

Both Orphanet and Mondo have these terms:

  • 'Hao-Fountain syndrome' MONDO:0014805 (Orphanet Classification level: Disorder)
    • 'Hao-Fountain syndrome due to 16p13.2 microdeletion' MONDO:0100528 (Orphanet Classification level: Subtype of disorder)
    • 'Hao-Fountain syndrome due to USP7 mutation' MONDO:0958071 (Orphanet Classification level: Subtype of disorder)

However, they all point to the same OMIM term: https://omim.org/entry/616863. OMIM describes HAO-FOUNTAIN SYNDROME as having evidence that Hao-Fountain syndrome (HAFOUS) is caused by heterozygous mutation in the USP7 gene (602519) on chromosome 16p13.2 and that some patients with a similar phenotype have larger heterozygous deletions of chromosome 16p13.2, including the USP7 gene and additional neighboring genes.

Should these three terms in Mondo be merged (MONDO:0014805, MONDO:0100528 and MONDO:0958071) or should only MONDO:0958071 contain the clingen label syonym type or another solution?

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@twhetzel I have 2 very minor comments. I am approving this PR so it can be merged as soon as these minor comments are addressed.

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@twhetzel twhetzel assigned sabrinatoro and unassigned twhetzel Jul 9, 2024
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Everything looks good. Thank you!

@sabrinatoro sabrinatoro merged commit afe53b0 into master Jul 10, 2024
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@sabrinatoro sabrinatoro deleted the issue-7924 branch July 10, 2024 05:38
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Add CLINGEN_LABEL to synonyms
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