RESTful Web Services

OpenCGA implements a comprehensive and well-designed REST web service API, this consists of more than 200 endpoints that allow to query and fully operate all web services to allow querying and operating data in OpenCGA. You can get more info at RESTful Web Services page.

We have implemented three different ways to query and operate OpenCGA using through the REST web service services API:

• REST Client Libs: four different client libraries have been developed: Java, Python, R and Javascript. This allows a easy integration in any bioinformatic pipeline.implemented to ease the use of REST web services, This allows bioinformaticians to easily integrate OpenCGA in any pipeline. The four libraries are equally functional and fully maintained, these are Java, Python (available at PyPI), R and JavaScript
• Command Line: users and administrators can use opencga.sh command line to query and operate OpenCGA. 
• IVA Web Application: an interactive web application called IVA has been developed to query and visualisation OpenCGA data.

OpenCGA Demo

We have deployed a public demo installation to facilitate the testing and development for all users. We have loaded and indexed and annotated 5 five different datasets organised in 3 projects and 5 studies, these cover the most typical data use cases today such as multi-sample VCF, family data exomes and genomes; or somatic callscancer somatic data. All documentation examples and tutorials use this demo installation.

Connecting to demo installation

OpenCGA demo REST URL is available at:

http://bioinfo.hpc.cam.ac.uk/opencga-prod/ 

you can check REST API and documentation at http://bioinfo.hpc.cam.ac.uk/opencga-prod/webservices/.

We have created a read-only user called demouser with password demouser. This user is As in most OpenCGA installations where normal users are not the owner owners of the data but , demouser has been given VIEW access to all demo user data in all studies, this is a very common configuration in OpenCGA installations OpenCGA  where the owner of the data grant access to other users. In this demo installation the owner of the data is demo user, while demouser user is the public  user created to query data.

Indexed Data

This demo consists of three projects and five studies. These represents different assembly assemblies and type of data types such as multi sample VCF, aggregated VCF or family genome or exome. The data is organised in 3 projects and 5 studies. You can find some useful information in this table:

Example