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Published 20 hours ago • verified publisher icon EBISPOT

Delete BoW/submission and change GCST

Open eks-ebi opened this issue 1 month ago • 19 comments

Background:

The author made a previous submission (body of work GCP000131, 1 study: GCST90013791). The submission was deleted from the deposition database, however the metadata and sumstats from the original submission still exist in the search UI: https://www.ebi.ac.uk/gwas/studies/GCST90013791. There was also some confusion when the original submission was deleted, which means that there is another study (GCST90017149) in Mongo that is no longer needed

I have now created a new sumstats+metadata submission: https://www.ebi.ac.uk/gwas/depo-curation/submissions/6792317da2be5f000111fd92 Thisis linked to the PMID (39749473), contains all the submitted data (sumstats and metadata) and has been fully curated. It is ready for import, but first we need to remove all traces of the old submission, and change the GCST in the new submission to match the original one (GCST90013791)

I need developer help with the following tasks:

  • [x] Make sure we have deleted everything linked to the original body of work (GCP000131) and the existing study (GCST90013791) - I think it is already deleted from deposition db, but it would be worth double checking. I think the existing data for this GCST also needs to be removed from Oracle so it does not appear in the search UI, downloads etc.
  • [x] Delete GCST90017149 from deposition db (this is not needed, and does not need to be replaced by anything)
  • [x] Change the GCST for the new submission (6792317da2be5f000111fd92) from GCST90502918 > GCST90013791 to match what the author has cited in their paper
  • [x] Once the GCST is updated, I will import the new submission and publish to Catalog
  • [x] Make sure the old summary statistics have been removed from the FTP: http://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/GCST90013001-GCST90014000/GCST90013791/
  • [x] Make sure the summary statistics from the new submission have been copied to the correct GCST folder in the FTP: http://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/GCST90013001-GCST90014000/GCST90013791/

eks-ebi avatar Jan 24 '25 15:01 eks-ebi