ClinGen / gene-and-variant-curation-tools

ClinGen's gene and variant curation interfaces (GCI & VCI). Developed by Stanford ClinGen team.
https://curation.clinicalgenome.org/
MIT License
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Flag any PMIDs in the GCI/VCI that are actually preprints #351

Open bmpbowen opened 11 months ago

bmpbowen commented 11 months ago

NLM is piloting the assignment of PMIDs for preprints in PubMed. As this was not an intended use of the current PMID features in the VCI and GCI, we need to:

1) Block any new preprint PMIDs from being added to the GCI and VCI 2) Retrospectively add a flag to the VCI and GCI for any PMIDs added in the past year that are actually preprints, and notify GCEPs if any preprint evidence used in curations has since been published as it may need to be re-curated

Note: Eventually, while we will support adding preprints to the VCI/GCI, we will do so via DOIs, not via PMIDs, because there is no guarantee that PMID support for preprints will extend past the NLM pilot phase.

bmpbowen commented 11 months ago

We also need to 1) quantify how many PMIDs added in the last year came from a preprint server using the PubMed title field. 2) Need to add a warning for users for every new attempt to add a PMID that is a preprint see mock-up here: https://docs.google.com/presentation/d/1qmfqNArfykpCYjwH7w9x0tgfU3XCqLKy/edit#slide=id.g2682b19f92a_0_0

wrightmw commented 1 month ago

The NLM pilot (https://www.ncbi.nlm.nih.gov/pmc/about/nihpreprints/) for preprints in PubMed seems likely to continue. The GCWG on Oct 9th decided to go ahead with allowing preprints via PMIDs to be added to the GCI.

  1. Remove block on adding preprint PMIDs
  2. Flag each preprint PMID with "Preprint"to make sure it is abundantly clear to users both within the GCI and downstream on the website, that this PMID is for a preprint
  3. Investigate how a preprint PMID could be replaced with the final published PMID
  4. Investigate how we could be notified of when the published PMID is available

Also: Retrospectively add a flag to the GCI for any PMIDs added in the past year that are actually preprints, and notify GCEPs if any preprint evidence used in curations has since been published as it may need to be re-curated

@courtneythaxton Does this adequately reflect the new scope of this?