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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Criteria-evidence selection in variant curation #66

Open wrightmw opened 3 years ago

wrightmw commented 3 years ago

Replaces https://github.com/ClinGen/clincoded/issues/2032

Directly linking or specifying the evidence that is used for criteria evaluation.

We need this workflow to allow curators to specify if they used evidence from an external source, that is not available in the VCI. i.e. in preference users should indicate the evidence within the VCI.... if it includes evidence not available in the VCI, we should encourage them to add this evidence to the VCI so they can then indicate it... but if not we should provide them the option to describe the provenance of the data (preferably in a structured way)

Draft specifications are here, including notes notes from the VCI small proxy call on 7/20/20. https://docs.google.com/presentation/d/1z97px8hjI3BIsWd_g0BSNy_6Nrxf1UeIuT5WjDP7gdI/edit#slide=id.g8da1fb38ad_0_5

Summary of current discussion:

  1. Allow users to select all evidence displayed in the VCI
  2. Provide structured way for users to specify evidence not displayed in the VCI
  3. We plan to build this in a staged development process.
  4. We also plan to build towards a long-term goal of providing auto-generated text for criteria explanations.

Further notes:(from Xi):

  1. We appear to be exporting to the Erepo all evidence comments (all PMIDs) EXCEPT for the case segregation tab
  2. For the case segregation tab we are not exporting the comments for evidence at this time. This is intentional (we are running the non-published source pilot), but confusing to our users.
  3. In the long run we need to have a private option/process for notes for non-published evidence, but export desired comments to the eRepo for all tabs. See #2225

Note: this likely requires data modeling of the evidence as well as the case-segregation tab.