korikuzma
commented
2 weeks ago This will be worked on in the afternoon.
Open larrybabb opened 2 months ago
korikuzma
commented
2 weeks ago This will be worked on in the afternoon.
Submitter Name
Larry Babb
Submitter Affiliation
Broad Institute
Project Details
ClinGen and the MetaKB dev teams are working together to develop a open-source clinvar submission service that will be based on GKS standardized submissions for germline, oncogenicity and somatic clinical impact statements. This work is in the very early stage but of interest to these two teams and likely many others in the community.
The project repo can be found here. I would like to assemble some interested parties to isolate an end-to-end example using the latest GKS VA profiles relevant to ClinVar. The clinvar-gks project from ClinGen has been working towards providing a downloadable representation of all SCVs in a ClinVar release in the same GA4GH GKS format that would be used as input to this tool.
The aim would be to select one type of statement and rough out a prototype of an end-to-end submission to clinvar with the components described by the main design diagram. We have a test api from ncbi to work with and should be able to identify the key elements to make this tool useful to the open-source community and get it on the fast track to adoption.
Required Skills
python coding knowledge of VA profile schemas starting with Variant... found here