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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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Display SCVs for VCI interpretations submitted to ClinVar #63

Open wrightmw opened 3 years ago

wrightmw commented 3 years ago

Add a new "Submission Accession" column at the end of the "All interpretations for this variant in the Variant Curation Interface (VCI)" table.

This should display the SCVs for the current interpretation displayed in ClinVar for this variant by each affiliation. These SCVs should be a hyperlink back to the SCV within ClinVar.

The likely source of the information to populate this column would be the data stream from Monster.

Streaming and Consuming ClinVar weekly changes The B/G dev team will provide a stream which will contain the weekly additions, updates and deletions from ClinVar. From that stream the VCI team should be able to build a consumer service that looks for SCVs by clinvar submitter id (a field you may need to capture as well for each affiliation). When an SCV for a given affiliation is found, then they SHOULD be linkable at the interpretation level using the UUID for the interpretation (not the snapshot currently - we should discuss this). There will be some rules and logic to help deal with alternative matching scenarios in the event that UUIDs do not work out (i.e. historical or changes to general vs snapshot UUIDs over time). With a successful match any of the data from ClinVar will be available to update the associated persistent store in VCI for the interp snapshot.

Considerations for Fields to capture... I would label the column ClinVar Submission vs Submission Accession. I would also consider capturing the date it was submitted to ClinVar and possibly the date it was released (or created/published) in ClinVar.

Considerations for tracking/structuring stored SCV id and version in VCI db.... You may want to consider whether you should keep the SCV version element separate from the SCV id or simply keep it together as an SCV accession as most people think of it. It is likely that you will want to track the "approved" snapshots association to a specific SCV version. And it is good to bear in mind that it is possible but not likely that the SCV# can change for the same approved interpretation between approved versions. (NOTE: this is rare, but when a submitter submits to clinvar they can delete and or replace existing SCVs previously submitted. And then re-submit thus creating a new SCV id).

  1. The submitter IDs are being collated in column G of the affiliations google sheet. These need to be added to the individual affiliation files in our database.
  2. The ClinVar submission format generated by users in the VCI needs to be updated to include these submitter IDs (see #2206)
  3. Add SCV to ClinVar entries for each affiliation on Basic Info Tab, mapped via the stored Submitter IDs (updates via streaming service)

Replaced https://github.com/ClinGen/clincoded/issues/2183

wrightmw commented 3 years ago

From https://github.com/ClinGen/clincoded/issues/2222

Create new "ClinVar Submitter ID" field in the affiliation files. Here is a list of the IDs to be added:

Screen Shot 2020-07-10 at 08 07 20

These submitter IDs need to be added to affiliations files in the interfaces so they are available for programmatic use, such as bringing in the correct SCVs (#2183) and for ClinVar submission (#2206).