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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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Ability to add tags sitewide #15

Open wrightmw opened 3 years ago

wrightmw commented 3 years ago

Tagging required in both GCI and VCI... parallel implementation.

Tag use cases:

  1. Alerts (e.g. new publication, new ClinVar entry, time for re-evaluation, etc) Auto-tags added by VCI
    • New ClinVar entry
      • Triggered by: new ClinVar entry for the variant that is a different (3-level: B/VUS/P) pathogenicity than the approved and submitted to ClinVar curation by the VCEP.
        • Re-evaluation:
      • Triggered by: 2 years from approval date for Likely Path/VUS interpretations. (Steven to check details)
  2. Bulk-tagging (e.g. VP added, ClinVar reports)
    • Added in bulk by system - triggered by curator action
    • Need two layers: 1: Action and 2: Additional info like ClinVar data, date submitted etc.
    • Need to be able to sort on both layers.
    • High priority but dependent on these features,
  3. Free text options (use case: workflow items)
    • ex: denote all variants that use data from a single paper, reviewed pending approval, awaiting patient data from lab.
    • Pre-populated set of options: Pilot Variant, Conflict Resolution, Re-curation, reasons for why variant was selected for curations.

See for scoping: https://broadinstitute.atlassian.net/browse/CSP-102 See for mockups: https://docs.google.com/presentation/d/1bhhzm8ZlkwNHGc2WI-UlcZC5m-TwDQMa5NSteG3sKwQ/edit#slide=id.g9ffe19a625_0_11

wrightmw commented 3 years ago

From https://github.com/ClinGen/clincoded/issues/2145 Approved VCEPs need to be able to mark an entry as "Under Review". This new status would be manually added by the curator, and should be able to be manually deleted...but otherwise by default it would be removed when a Publishing event occurs.

Note: making an interpretation status "Under Review" may need to trigger a status update message to the ERepo