EBISPOT / goci

GWAS Catalog Ontology and Curation Infrastructure
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Full submission GCSTs list needs to be accessible from the depocuration app. #801

Open earlEBI opened 2 years ago

earlEBI commented 2 years ago

As a curator, when assigning traits (incl. reported traits, EFOs and background EFOs) in the depocuration app, I need to be able to access the full list of GCSTs and study tags for the submission from within the depocuration app, without having to open a different app (e.g. deposition). For studies that were added in the original submission template via the deposition app, the GCST and study tag must always remain the same as in that original template. If an edit has already been made in depo-curation (including assigning traits to the original studies; or creating and assigning traits to new studies) then this full list of GCSTs and study tags should include those changes.

It is important that the list of GCSTs matches the original submission for any studies that are in the original submission, so that if a study tag has been inadvertently edited, the upload will fail due to a mismatch and draw attention to the problem. However, trait annotations or additional studies that were added through previous edits in depo-curation should be preserved, so that they are not accidentally left out and wiped when the new template is uploaded.

One useful solution would be to provide a download button on the studies tab which acts in the same way as the download button on the samples tab, which provides a prefilled template with GCSTs and study tags already filled in, and the additional columns for reported trait, EFO, background EFO, which may be empty (if this is the first edit) or filled (if this is a subsequent edit).

Samples tab: Screenshot 2022-07-25 at 13.53.22.png

Samples download prefilled template: Screenshot 2022-07-25 at 13.53.54.png

Studies tab: Screenshot 2022-07-25 at 13.57.26.png

Suggested studies template to be prefilled with GCST and study tag only (if no edits have been made in depo-curation yet): Screenshot 2022-07-25 at 15.26.46.png

Suggested studies template to be prefilled with GCST, study tag and trait annotations (if edits have been made in depo-curation already): Screenshot 2022-07-25 at 15.24.51.png

ljwh2 commented 3 months ago

Note, the EFO Shortform is the most important field to display (separated by pipes if multiple)