OpenCGA uses a two-level structure to organise datasets, these are Projects and Studies and are used to organise HGVA data and metadata:
- Projects is the top-level and can contain one or more studies. Projects are specific for one species and assembly, all studies in a project are stored and indexed together in the same database and, therefore, they share the variant annotation.
- Study, in turn, represents a particular dataset which can contain samples metadata and cohorts, and obviously all the genomic variants. For example, the 1000 Genomes Project is defined as a study in OpenCGA and belongs to Reference GRCh37 project. You can also define cohorts in the studies, they are just a set of samples defined within a study. For example, populations and super-populations within The 1000 Genomes Project are defined as cohorts, so EUR, AMR or GBR are examples of cohorts.
You can get more information about data organisation at OpenCGA Catalog Data Management. Projects and Studies have a unique alias to ease their usage from the command-line and REST API, you can find more information about how to query data programmatically at RESTful Web Services and Clients. Please, see next section the full list and organisation of the currently available Projects and Studies (datasets) in HVGVA.
In this sections you can find all datasets loaded in HGVA and how they are organised in Projects and Studies (see previous section).
Project name (alias)
|HGVA Version (date)|
|Name||Alias||v1 (Dec. 2016)||v2 (Jan. 2018)|
|1000 Genomes Project GRCh37||1kG_phase3||Phase 3 2016-05||Phase 3 2016-05|
|Exome Sequencing Project (ESP6500)||ESP6500||2016-05||2016-05|
|Exome Aggregation Consortium (ExAC)||EXAC||0.3.1 2016-05||0.3.1 2016-05|
|Genome of the Netherlands (GoNL)||GONL||Release 5 2016-05||Release 5 2016-05|
|Genome Aggregation Database (gnomAD Exomes)||GNOMAD_EXOMES||-|
|Genome Aggregation Database (gnomAD Genomes)||GNOMAD_GENOMES||-|
|Spanish Medical Genome Project (MGP)||MGP||2016-12||2016-12|
|1000 Genomes Project GRCh38||1kG_phase3||Phase 3 2016-10||Phase 3 2016-10|
|UK10K Project (*)||UK10K||-|
|Genome Aggregation Database (gnomAD Exomes) (*)||GNOMAD_EXOMES||-|
|Genome Aggregation Database (gnomAD Genomes) (*)||GNOMAD_GENOMES||-|
|QIMR Berghofer Melanoma||QIMR_Berghofer_Melanoma||2016-12||2016-12|
|Chronic Myeloid Leukemia - Russian Academy of Medical Sciences||RAMS_CML||2016-12||2016-12|
(*) Liftover carried out by Genomics England (GEL)
Variant annotation was carried out by the CellBase project. Please, check CellBase documentation for details on additional data sources: Data sources and species