genomicVariations to return pathogenicity predictions

[dglemos]

Hello, This is more of a question. I need Beacon to return pathogenicity predictions such as CADD and EVE. The current schema does not specify any field for these types of predictions. Could we have a new section under VariantLevelData just for in silico predictions?

[mbaudis]

@dglemos I'm +1 for this; logical addition (although we at some point have to comb over the whole variant model anyway, especial regarding its integration w/ VRS 1.3++).

  VariantLevelData:
    type: object
    properties:
      clinicalInterpretations:
        type: array
        items:
          $ref: '#/definitions/PhenoClinicEffect'
      phenotypicEffects:
        type: array
        items:
          $ref: '#/definitions/PhenoClinicEffect'
      pathogenicityPredictions:
        type: array
        items:
          $ref: '#/definitions/PhenoClinicEffect'

... like that? And would the PhenoClinicEffect class be sufficient? Needs then also respective definitions/examples.

@costero-e Could you have a look into organizing this into the branch setup, e.g. which feature branch this should go to and set one up if needed? And feed back to @dglemos to give her a place to craft a PR against. We can edit.

[costero-e]

Yes @mbaudis , I will take a look at it tomorrow if the day gives me a chance as I have been very busy lately

[costero-e]

Alright, I have created a feature branch called genomicVariations and a subfeature branch called genomicVariations_add-pathogenicity-predictions. @dglemos you can modify this subfeature branch and PR to genomicVariations when you are ready

[dglemos]

@mbaudis @costero-e thank you for the response! I'm working on the PR, it may take a few weeks to be ready though. I'm also planning on adding other changes such as molecular interactions and a small update to the frequency schema.

[dglemos]

Hi @costero-e, I'm unable to push changes to the branch genomicVariations_add-pathogenicity-predictions. Can you please check the permissions?

[costero-e]

Hi @dglemos , I just sent you a collaboration request for you to be able to push into the branches. If you accept it you will be able to push now. Thank you.