Beacon API

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Miro Cupak

Talk on Beacon API at the Global Alliance for Genomics and Health Plenary Meeting 2016, Vancouver, BC, Canada.

Software

Beacon API
Miro Cupak
Jordi Rambla
17/10/2016

Road to Beacon API
https://github.com/ga4gh/beacon-team

Before
Beacon 0.1 (2014)
● Really simple (2 records)
● true/false response.
https://github.com/ga4gh/beacon-team
Beacon 0.2 (2015)
● Complex (9 records)
● true/false/overlap/null response.
● Datasets.
● Simple data use conditions.
● Self description.
● Not well adopted.
● Not polished enough.
● Too vague.

Now
● Beacon 0.3 (2016).
● Simplified 0.2.
● Based on real needs.
https://github.com/ga4gh/beacon-team
● Improved support for datasets and cross-dataset queries.
● Modular and extensible.
● Data versioning.
● Various improvements to the data model.
● Tooling.
https://github.com/ga4gh/beacon-team/releases/tag/v0.3.0

Next
● Beacon 0.4 (in progress).
https://github.com/ga4gh/beacon-team
● Support for complex variants.
● Improved data use conditions.
● Documentation.
● Developer experience.
● Various minor improvements.

Case study
● EGA & ELIXIR Beacons
○ Docker backend & web
○ Tools
○ Apache 2.0 licence
● Links
○ ELIXIR API repository
○ ELIXIR web repo
○ EGA Beacon
https://github.com/ga4gh/beacon-team

Future
● Stabilize the API, indeed more: simplify and flexibilize
○ Always have the expected response when omitting parameters (optional for non-core)
● Planned
○ Beacon Network API
○ Triple-A access levels
● Need further discussion, because dependencies from other GA4GH groups or could
depart from “simplicity” principal
■ Quantitative Variants
■ GA4GH Objects inside Beacon response
■ Genotype + Phenotype queries ~ “Clinical” Beacons
● Parallel works on
○ Security, Privacy, ELSI...
https://github.com/ga4gh/beacon-team

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