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EBISPOT / xgwas-curator-tasks

An internal repo for GWAS curators to track issues
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Study with no beta direction #9

Closed ljwh2 closed 10 months ago

ljwh2 commented 1 year ago

https://www.ebi.ac.uk/gwas/studies/GCST000069 has no beta unit or direction.

earlEBI commented 11 months ago

@ljwh2 I've added 'increase' in this case but I think there might be more cases like this still in the Catalog, because the unit is % variance, see table: https://www.nature.com/articles/ng2108/tables/1 and curation notes: http://ves-ebi-e4.ebi.ac.uk:8080/gwas/curation/studies/64/notes '% variance' was put into the 'OR/beta description' field which isn't shown in the UI but is put into the associations download 95% CI (TEXT)' field:

assocs in UI.png

assocs download.png The following are other GCSTs which I think are affected in the same way: GCST000565 GCST000473 GCST000069 GCST000519 GCST000556

I don't know if this is just specific to associations with '% variance' as unit... or if it's wrong to change to 'increase' but we have to put a direction these days to pass validation.

earlEBI commented 11 months ago

All those studies above are from <=2010. Here's an example of a study curated in 2017 with % variance increase: https://www.ebi.ac.uk/gwas/studies/GCST004921 Two studies from 2009 were re-curated in 2017 and there are curation notes mentioning that % variance had to be moved to beta unit the same as I have done: http://ves-ebi-e4.ebi.ac.uk:8080/gwas/curation/studies/5245/notes

earlEBI commented 11 months ago

GCST000069: also had to add CoR in order to republish. Done.

ljwh2 commented 11 months ago

@eks-ebi to create new ticket for wider problem, check if these GCSTs are included

eks-ebi commented 10 months ago

closing this ticket as referenced in new broader ticket