Drilling into Experimental Data at the EMBL-EBI Archives

Earlier in this workshop we discussed the Ensembl Genome Browser. Much of the data that is shown in the browser is served from the submission based EMBL-EBI archival services. In this presentation I shall describe how one can go from the Ensembl Genome Browser into the archived experimental data focussing predominantly on genetic variation datasets at the European Variation Archive (EVA; www.ebi.ac.uk/eva) and the underlying genome sequence data at the European Nucleotide Archive (ENA; www.ebi.ac/uk/ena). Finally I shall show how all of the data at EMBL-EBI is cross-linked using BioSamples (www.ebi.ac.uk/biosamples) to ensure that users are able to find datasets of relevance regardless of entry point into the system.

The EVA archives Variant Call Format (VCF) files, which are the community standard for describing and sharing genetic variation data. Submitted VCF files are validated (https://github.com/EBIvariation/vcf-validator) and also associated with rich metadata to ensure that these datasets are of most benefit to downstream users. Data archived at the EVA are normalized and annotated using a variety of standardized methods, including Ensembl’s Variant Effect Predictor (http://www.ensembl.org/info/docs/tools/vep/index.html). I shall present the ways in which users can mine these data by using browsers on the EVA website to construct both study-centric and global queries, filtering on any combination of species, methodology, variant type, phenotype, consequence or allele frequency and how results from these queries can be downloaded in a variety of formats including VCF and CSV. Additionally, EVA provides a comprehensive REST web services API, to allow programmatic access, and hence the integration of these data with other resources, such as Ensembl, and this shall also be presented.

The ENA is one of the largest and most established archives at EMBL-EBI and accepts submission of experimental data directly from DNA sequencing machines, assembly data including alignments to multi-omics datasets that contain many data types. I shall present how one can browse from detailed variant data at EVA to the supporting alignment data at ENA to the underlying genomic sequence read data at ENA using BioSamples information. This therefore permits the user to complete the journey from genomic locus at the Ensembl Genome Browser through to the raw underlying information.