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There are three main

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 data in OpenCGA. You can get more info at RESTful Web Services.

We have implemented three ways to access OpenCGA data :

  • RESTful Web Services and Clients
  • Command Line Interface (CLI)
    • Web data mining and visualisation

    through the REST web services:

    • REST Client Libs: four different client libraries have been developed: Java, Python, R and Javascript. This allows a easy integration in any bioinformatic pipeline.
    • Command Line: users and administrators can use opencga.sh command line to query and operate OpenCGA. 
    • 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 the testing and development for all bioinformaticians and developers.

    Data

    This demo consists of three projects and five studies. These represents different assembly and type of data such as multi sample VCF, aggregated VCF or family genome or exome. The data 


    ProjectStudy ID and NameSamplesVCF FilesVCF File TypeVariants
    Population Studies GRCh38

    1000g - 1000 Genomes Project Phase 3

    Name

    		2,50424Multi sample

    uk10k

    UK10K Project

    		10,0001Agregated46,624,127
    Family Studies GRCh37platinum - Platinum

    NA12877, NA12877 and NA12877 samples from platinum genomes

    		33Multi sample

    8,456,984

    corpasome - Corpas Family

    This study simulates two disorders and some phenotypes in the Corpas family for training purposes

    		44Multi sample

    300,711

    GRCh38 Somatic

    rams_cml

    Chronic Myeloid Leukemia - Russian Academy of Medical Sciences

    		1111Somatic121,384


    Credentials

    OpenCGA host URL is available at

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

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

    You can check Swagger at: http://bioinfo.hpc.cam.ac.uk/opencga-prod/webservices/


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