There are three main ways to access OpenCGA data:

RESTful Web Services

OpenCGA implements a comprehensive and well-designed REST web service API, this consists of more than 200 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 through the REST web services API:

• REST Client Libs: four different client libraries have been 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 make easy facilitate the testing and development for all bioinformaticians and developers.

Data

This demo consists of three users. We have loaded and indexed 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 exomes and genomes; or cancer 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. As in most OpenCGA installations where normal users are not the owners of the data, demouser has been given VIEW access to all demo user data, this is a very common configuration in 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.

Genomic Data

In this demo we have indexed 5 different genomic datasets. Data has been organised in 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 

data is organised in 3 projects and 5 studies. You can find some useful information in this table:

Credentials

OpenCGA host URL is available at

Clinical Data

In order to make this demo more useful to users we have loaded or simulated some clinical data, this allows to exploit OpenCGA analysis such as GWAS or clinical interpretation. You can find clinical data for each study in the following sections.

1000g

We loaded the 1000 Genomes pedigree file, you can find a copy at http://

resources.

We have created a read-only user called demouser with password demouser.

opencb.org/opencb/opencga/templates/demo/20130606_g1k.ped 

uk10k

There is no possible clinical data in this study. This is a WGS aggregated dataset so no samples or genotypes were present in the dataset and, therefore, no Individuals or Samples have been created.  

corpasome

We simulated two different disorders and few phenotypes for the different members of the family. To be documented soon.

platinum

To be documented soon.

rams_cml

To be documented soon.