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SACGF / variantgrid

VariantGrid public repo
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Connect to external databases via API: Beacon, Match Maker Exchange, LOVD #40

Open davmlaw opened 6 years ago

davmlaw commented 6 years ago

A Beacon is a web service for genetic data sharing that can be queried for information about specific alleles.

https://docs.genomebeacons.org/

For v1 (not sure about current) the only downside is the endpoint is "/" ie the default for the domain! I'm sure we could make beacon.shariant.org or something and handle it.

MatchMaker exchange: https://www.matchmakerexchange.org/

LOVD - https://pypi.python.org/pypi/lovd/0.1.0

https://www.biogrid.org.au/

davmlaw commented 3 years ago

Thuong reports they get something useful around 20% of the time with MM - so might be worth making this easier / or automatic?

davmlaw commented 1 month ago

Looks pretty easy to do Beacon, but need to lodge our server somewhere can't access site, have raised an issue about it:

https://github.com/ga4gh-beacon/ga4gh-beacon.github.io/issues/1

Devs replied on there, and have provided a list of sites:

progenetix cancercelllines.org RefCNV

... and here is a list somebody at CRG started etc.:

https://docs.google.com/spreadsheets/d/1TetikAVPk_-UR6IShYCKA5PGJbR4Us_kCru3GCdnL6k/edit?gid=0#gid=0