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griffithlab / civic-meeting

Repo for advertising and organizing CIViC unconference/meeting activities
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ClinGen VCI <-> Evidence Registry <-> CIViC Integration (VHL collaboration) #38

Closed malachig closed 2 years ago

malachig commented 5 years ago

Some people from the Stanford VCI are coming and we would like to discuss technical details of how we could use the Evidence Registry (Baylor) to help VCI users leverage curation work previously done in CIViC to make final pathogenicity assertions in the VCI.

malachig commented 5 years ago

Discussed with Matt Wright and Jimmy Zhen. Evidence Registry has been renamed Linked Data Hub? The name change is to avoid confusion with the Evidence Repo (a different application that will be used to publish final assertions that have been published from the ClinGen VCI).

Linked Data Hub is where the Baylor group is store external data for the ClinGen VCI (or anyone else) to pull in via a public API. Also planning to link into population data, functional data, etc.

We need to ask Ronak Patel for access to the demo URL for this resource.

Matt and Jimmy informed me that they are waiting for the first version of this to be finalized before working on the integration piece with VCI. The FDA application has taken development precedence for now.

As a short term plan. We discussed the possibility of linking from within VCI to CIViC for those entries where possible (via ClinGen Allele Registry ID? Or chromosome location). Could CIViC create a URL that would actually be constructed with the CAID?

Medium term we discussed using the Linked Data Hub to associate specific pieces of evidence in CIViC with the appropriate section in ClinGen VCI based on the evidence codes.

Our options would be much more flexible if CIViC captured the evidence level evidence codes in a structured format instead of in the evidence statement.