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:
- 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.
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.
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.
In this demo we have indexed 5 different genomic datasets. Data has been organised in 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 Studies GRCh38
1000g - 1000 Genomes phase 3
|WGS Multi sample||2,504||82,587,763|
uk10k - UK10K
Family Studies GRCh37
|corpasome - Corpas Family||WES Family Multi sample||4|
platinum - Illumina Platinum
|GWS Family Multi sample||17|
Cancer Studies GRCh37
rams_cml - RAMS_CML
Chronic Myeloid Leukemia - Russian Academy of Medical Sciences
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.
We loaded the 1000 Genomes pedigree file, you can find a copy at http://resources.opencb.org/opencb/opencga/templates/demo/20130606_g1k.ped
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.
We simulated two different disorders and few phenotypes for the different members of the family. To be documented soon.
To be documented soon.
To be documented soon.
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