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Data organisation

OpenCGA uses a hierarchical structure to organize datasets. Briefly, Projects, Studies and Cohorts are used to organize HGVA metadata:

  • Projects are entities which contain one or more Studies. 
  • Study, in turn, represents a particular data set with/without samples metadatacohorts, and obviously genomic variation data. For example, The 1000 Genomes Project is defined as a study in OpenCGA. Likewise, The Genome of the Netherlads or the Exome Aggregation Consortium are also two different studies, and so on.
  • Finally, a cohort is simply a set of samples defined within a study. For example, populations and super-populations within The 1000 Genomes Project are defined as cohorts. Thus, EUR, AMR or GBR are examples of cohorts.

Please, click on http://bioinfo.hpc.cam.ac.uk/hgva-1.0/... to get a full list of currently available datasets (studies) in HGVA and how they are organized in different projects.

Studies


Project


Studies

Version/Date
HGVA v1 (Dec. 2016)HGVA v2 (Jul. 2017)
Reference GRCh371000 genomes project GRCh37Phase 3 2016-05
1000 genomes project GRCh38Phase 3 2016-10
Exome Sequencing Project2016-05

Exome Aggregation Consortium0.3.1 2016-05

Genome of the NetherlandsRelease 5 2016-05

UK10K project2016-05

Spanish Medical Genome Project2016-12

QIMR Berghofer Melanoma2016-12

Chronic Myeloid Leukemia - Russian Academy of Medical Sciences2016-12

Variant annotation was carried out by the CellBase project. Please, check CellBase documentation for details on additional data sources: Data sources and species

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