Annotate lineages with names (eg: Delta) - Githubissues

TRON-Bioinformatics / covigator

CoVigator - Monitoring SARS-CoV-2 mutations

MIT License

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Annotate lineages with names (eg: Delta) #61

Closed priesgo closed 1 year ago

priesgo commented 1 year ago

I initially thought of having a new lineages table in the database, where the PK is the Pangolin lineage identifier (ie: B.1.1.7) and additionally we have metadata about like WHO designation (ie: Delta), flag of VOC, parent lineage, etc.

This is a good resource to fetch such data: https://github.com/cov-lineages/constellations There may be others.

Subtasks:

[ ] Define data model for the lineage table
[ ] Research the best resource to fetch such information
[ ] Integrate this data in the CoVigator package (via git submodule if possible)
[ ] Load data in DB at DB startup

priesgo commented 1 year ago

Add maybe a radio button into the lineages tab to switch to WHO names (eg: alpha, delta) instead of pangolin ids