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phenopolis / phenopolis_genomics_browser

Python API and React frontend for the Phenopolis Genomics Browser
https://dev-live.phenopolis.org
MIT License
31 stars 2 forks source link

add endpoint for candidate variants and pubmed #15

Open pontikos opened 4 years ago

pontikos commented 4 years ago

Allow users to specify candidate variants and link to pubmed publications of the case.

priesgo commented 4 years ago

Can we think of this as a classification endpoint?

Users will provide an ACMG classification ie: pathogenic, likely pathogenic, benign, etc. and optionally a publication to support it (and I would say also a free text field to let them explain why the classification). Also, it may be useful to support multiple classifications for the same variant, maybe limit that to one per user (at least let's assume that for a given user only the latest is the valid one even if we keep the history in the database). This would allow us to have identify conflicting classifications, classifications with a high consensus, etc.

pontikos commented 4 years ago

Yes having user-specific entries or at least logging the user who made the change is (see auditing issue https://github.com/phenopolis/phenopolis_api/issues/21 ) is really important and a great idea :) Can we create a separate issue for this?

For however, I think, let's just keep this simple and maybe just extend the "edit individual" endpoint to allow for more fields (i.e candidate variant and pubmed_id) to be specified ?

You will need to add more columns to the individual table or create a new table to store this. I let you decide what you think is best.

You could also do this one https://github.com/phenopolis/phenopolis_api/issues/17 at the same time and add field to store links to other related individuals?

When that is done we can @YuanTian1991 to extend the frontend.