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 different ways to query and operate OpenCGA using the REST web service 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.
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 facilitate the testing and development for all users. We have indexed and annotated 5 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 or somatic calls.
We have created a read-only user called demouser with password demouser. This user is not the owner of the data but has been given VIEW access to all data in all studies, this is a very common configuration in OpenCGA installations where the owner of the data grant access to other users.
Indexed 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 is organised in 3 projects and 5 studies.
Project Name
Study ID and Name
VCF File Type
Samples
Variants
Population Studies GRCh38
1000g - 1000 Genomes Project Phase 3
Name
Multi sample
2,504
uk10k
UK10K Project
Aggregated
10,000
46,624,127
Family Studies GRCh37
platinum
Platinum
Family Multi sample
3
8,456,984
corpasome - Corpas Family
Family Multi sample
4
300,711
GRCh38 Somatic
rams_cml
Chronic Myeloid Leukemia - Russian Academy of Medical Sciences
