Genomics HTTP Server

[skeenan]

Background

The GA4GH has defined an API in the schemas which provides interfaces to the common genomic data types. The data types are meant to be accessed over an HTTP API, and Ensembl, EBI, and UCSC all have implementations of these schemas.

It is possible to take advantage of the good work done to define these interfaces to create your own genomics API. This gives you the most flexibility for connecting to databases and designing data ingestion methods. The GA4GH constrains the types of queries to those that could be implemented easily. With your server you can add extensions that provide the features to suit individual use case.

Designing and implementing your own genomics API has never been so easy and fun!

Major tasks

• Implement a genomics protocol (Reads, Variants, RNA...) based on the GA4GH schemas.
• Select a database or data representation method.
• Write controller functions that perform queries against your database.
• Ingest or generate simulated data that your API will present.
• Implement an extension or query not represented in the GA4GH schemas.

  Ideal candidates

We provide the boilerplate in your language of choice that will allow you to quickly move into writing functional code. Basic knowledge of HTTP server and client concepts is required. Some experience with databases will be helpful, as will experience with genomics data types.

[marcdubybroad]

Is there a way to participate remotely via Slack? I am not attending ASHG this year. My experience is 10 years Java with Spring, MySQL, 1 year developing REST services for the Broad's AMP t2d portal.

[magaliruffier]

I'd be interested to attend

[kozbo]

@magaliruffier Great!

[david4096]

http://1kgenomes.ga4gh.org/swagger