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 metadata, cohorts, 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, see below the full list of currently available datasets (studies) in HGVA and how they are organized in different projects.
Studies
Project name (alias)
Studies
Version/Date
HGVA v1 (Dec. 2016)
HGVA v2 (Jul. 2017)
Reference GRCh37 (reference_grch37)
1000 genomes project GRCh37
Phase 3 2016-05
To be decided
Exome Sequencing Project
2016-05
To be decided
Exome Aggregation Consortium
0.3.1 2016-05
To be decided
Genome of the Netherlands
Release 5 2016-05
To be decided
UK10K project
2016-05
To be decided
Spanish Medical Genome Project
2016-12
To be decided
Reference GRCh38
(reference_grch38)
1000 genomes project GRCh38
Phase 3 2016-10
To be decided
Cancer GRCh37
(cancer_grch37)
QIMR Berghofer Melanoma
2016-12
To be decided
Chronic Myeloid Leukemia - Russian Academy of Medical Sciences
2016-12
To be decided
Variant annotation was carried out by the CellBase project. Please, check CellBase documentation for details on additional data sources: Data sources and species