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EBISPOT / goci

GWAS Catalog Ontology and Curation Infrastructure
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Publication of studies with errors should be blocked in curation interface #145

Open ljwh2 opened 4 years ago

ljwh2 commented 4 years ago

Recently we had some examples where studies were published with no reported trait or discovery sample information (mentioned here: [https://github.com/EBISPOT/goci/issues/144]). Publication of studies with these major errors should be prohibited in the curation interface, in the same way as publishing with no EFO trait is prohibited.

The full list of errors which should block publication (for the ones in italics the functionality already exists): No EFO trait No genotyping technology No Reported trait No text in Discovery sample information No structured ancestry

The expected behaviour is:

  1. Curator sets status to "publish study" (either in "Curator information" tab or from Curation homepage)
  2. Curator is presented with error message: "Study: Smith J, pubmed = 12345678 requires review before publication because" followed by "no reported trait assigned" "no Discovery sample information entered" "no structured ancestry assigned" This error message lists all errors blocking publication.

See attached screenshot for current error message, generated by attempting to publish a study with no data. Screenshot 2020-08-03 at 17.23.35.png

ljwh2 commented 4 years ago

Note, curators think this feature used to exist for reported trait

ljwh2 commented 4 years ago

There is one additional place where the status can be set to published, which is the publication view:

https://www.ebi.ac.uk/gwas/curation/publication/32693751

Attempting to publishing from here does not currently generate any error messages (including EFO and genotyping technology shown in screenshot above). This status change should generate the same error messages as described above.

JalMacArthur commented 4 years ago

Discussed on 19th Aug - decided this needs further investigation to determine what QC of data is required and at what points. Taking into account submitted and curated data. Suggest meeting and discussion between Laura, Jackie, Tudor, Yomi.