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 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
Project
Study ID and Name
Samples
VCF Files
VCF File Type
Variants
Population Studies GRCh38
1000g - 1000 Genomes Project Phase 3
Name
2,504
24
Multi sample
uk10k
UK10K Project
10,000
1
Agregated
46,624,127
Family Studies GRCh37
platinum - Platinum
NA12877, NA12877 and NA12877 samples from platinum genomes
3
3
Multi sample
8,456,984
corpasome - Corpas Family
This study simulates two disorders and some phenotypes in the Corpas family for training purposes
4
4
Multi sample
300,711
GRCh38 Somatic
rams_cml
Chronic Myeloid Leukemia - Russian Academy of Medical Sciences
