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Data organisation
OpenCGA uses a hierarchical two-level structure to organize organise datasets. Briefly, Projects, Studies and Cohorts are these are Projects and Studies and are used to organize organise HGVA data and metadata:
- Projects can is the top-level and can contain one or more Studies. A project specifies a studies. Projects are specific for one species and assembly, all studies from the same 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 data set with/without dataset which can contain samples metadata, and cohorts, and obviously all the genomic variation datavariants. For example, The the 1000 Genomes Project is 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 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. Thus, so EUR, AMR or GBR are examples of cohorts.
Here you You can get more info information about data organisation at OpenCGA Catalog data modelsData Management. Projects and Studies have a unique alias to ease their usage. Please, see below the full list and organisation of the currently available datasets (loaded as studies) in HGVA and how they are organised in different projects Projects and Studies (datasets) in HVGVA.
Studies
Projects name (alias) | Studies | HGVA Version/Date | ||
|---|---|---|---|---|
| Name | Alias | v1 (Dec. 2016) | v2 (Jan. 2018) | |
| Reference GRCh37 (reference_grch37) | 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 | |
| UK10K Project | UK10k | 2016-05 | 2016-05 | |
| DiscovEHR | DISCOVEHR | - | ||
| Genome Aggregation Database (gnomAD Exomes) | GNOMAD_EXOMES | - | ||
| Genome Aggregation Database (gnomAD Genomes) | GNOMAD_GENOMES | - | ||
| Spanish Medical Genome Project (MGP) | MGP | 2016-12 | 2016-12 | |
Reference GRCh38 (reference_grch38) | 1000 Genomes Project GRCh38 | 1kG_phase3 | Phase 3 2016-10 | Phase 3 2016-10 |
| ESP6500 | ESP6500 | - | ||
| UK10K Project (*) | UK10K | - | ||
| DiscovEHR (*) | DISCOVEHR | - | ||
| Genome Aggregation Database (gnomAD Exomes) (*) | GNOMAD_EXOMES | - | ||
| Genome Aggregation Database (gnomAD Genomes) (*) | GNOMAD_GENOMES | - | ||
Cancer GRCh37 (cancer_grch37) | QIMR Berghofer Melanoma | QIMR_Berghofer_Melanoma | 2016-12 | 2016-12 |
| Chronic Myeloid Leukemia - Russian Academy of Medical Sciences | RAMS_CML | 2016-12 | 2016-12 | |
Platinum (platinum) | Illumina Platinum | illumina_platinum | 2015-08 | 2015-08 |
(*) A liftover carried aout 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
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