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 facilitate the testing and development for all 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.
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.
Indexed Data
This demo consists of three projects and five studies. These represents different assemblies and 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:
Project ID and Name
Study ID - Name
VCF File Type
Samples
Variants
population
Population Studies GRCh38
1000g - 1000 Genomes phase 3
WGS Multi sample
2,504
82,587,763
uk10k - UK10K
WGS Aggregated
10,000
46,624,127
family
Family Studies GRCh37
corpasome - Corpas Family
WES Family Multi sample
4
300,711
platinum - Illumina Platinum
GWS Family Multi sample
17
12,263,246
cancer
Cancer Studies GRCh37
rams_cml - RAMS_CML
Chronic Myeloid Leukemia - Russian Academy of Medical Sciences