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EBISPOT / xgwas-curator-tasks

An internal repo for GWAS curators to track issues
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Incorrect EFOs in Catalog #30

Open ljwh2 opened 4 months ago

ljwh2 commented 4 months ago

4 staudies are annotated with HP_0000726, but this does not exist in EFO. they should be annotated with MONDO_0001627 which already exists in the Catalog.

The annotation needs correcting and the HP term should be deleted.

3 studies are annotated with an obsolete term for interleukin 12 beta 1 subunit: https://www.ebi.ac.uk/gwas/search?query=interleukin-12%20receptor%20subunit%20beta-1%20measurement

earlEBI commented 4 months ago

@ljwh2 It seems there are 9 studies from 6 publications annotated with the obsolete interleukin term, some of which were curated many years ago before the Depocuration App. Would it be more efficient for a developer to change the EFO for these? Or teach me how they would do it.

earlEBI commented 4 months ago

I've edited the 4 studies with the HP dementia term to the MONDO dementia term, but I'm unable to delete the HP term from depocuration as it says studies are still linked. I will try again after the next data release to see if it lets me then.

edit: was still not able to delete this term but remembered there are several terms which have been renamed with 'obsolete' in front of them to surmount this issue, so I have done the same for Dementia HP_0000726.