EMBL-EBI Annual Scientific Report 2012

Paul FlicekDSc Washington University, 2004. HonoraryFaculty Member, Wellcome Trust Sanger Institutesince 2008.At EMBL-EBI since 2005. Team Leader since2007, Senior Scientist since 2011.European Nucleotide ArchiveThe ENA provides globally comprehensive primary datarepositories for nucleotide sequencing information. ENAcontent spans raw sequence reads, assembly and alignmentinformation and functional annotation of assembledsequences and genomes. ENA’s palette of services areprovided over the web and through a powerful programmaticinterface. ENA data and services form a core foundation uponwhich scientific understanding of biological systems has beenassembled. Our exploitation of these systems will continue todevelop. With ongoing focus on data presentation, integrationwithin ENA, integration with resources external to ENA, toolsprovision and services development, the team’s commitmentis to the utility of ENA content and achieving the broadestreach of sequencing applications.http://www.ebi.ac.uk/ena/EnsemblEnsembl produces and maintains both automatic andmanually curated annotation on selected eukaryoticgenomes. Automatic annotation is based on mRNA andprotein information. Ensembl provides valuable insights intovariation within and between species, and allows users tocompare whole genomes to identify conserved elements. It isintegrated with several other important molecular resources,for example UniProt, and can be accessed programmatically.Ensembl is developed as a joint project between EMBL-EBIand the Wellcome Trust Sanger Institute.http://www.ensembl.org/Ensembl GenomesThe falling costs of DNA sequencing have led to an explosionof reference genome sequences and genome-widemeasurements and interpretations. Ensembl Genomes(Kersey et al., 2012) provides portals for bacteria, protists,fungi, plants and invertebrate metazoa, offering access togenome-scale data through a set of programmatic andinteractive interfaces, exploiting developments originating inthe vertebrate-focused Ensembl project. Collectively, the twoprojects span the taxonomic space.EGAThe EGA contains exclusive data collected from individualswhose consent agreements authorise data release only forspecific research use or to bona fide researchers. Strictprotocols govern how information is managed, stored anddistributed by the EGA project. As an example, only membersof the EGA team are allowed to process data and only ina secure computing facility. Once processed, all data areencrypted for dissemination and the encryption keys aredelivered offline. An independent Ethics Committee auditsthe EGA protocols and infrastructure. The EGA help desk willanswer any requests at ega-helpdesk@ebi.ac.uk.http://www.ebi.ac.uk/ega/DGVaDGVa is a central archive that receives data from, anddistributes data to, a number of resources. The DGVaaccepts direct submissions from researchers and accessionnumbers for data objects included in these are given theprefix ‘e’. The DGVa also exchanges data on a regular basiswith dbVar (a peer archive hosted by NCBI in the USA). Dataobjects accessioned by dbVar have the prefix ‘n’. You canretrieve DGVa data from the data download page, searchthe DGVa using Biomart, and view the data in a genomiccontext using Ensembl. The DGVa also supplies data to DGV(Database of Genomic Variants, hosted by The Centre forApplied Genomics in Canada), where further curation andinterpretation is carried out.http://www.ebi.ac.uk/dgva/MetagenomicsOur Metagenomics service is an automated pipeline for theanalysis and archiving of metagenomic data, and providesinsights into the functional and metabolic potential of asample.http://www.ebi.ac.uk/metagenomics/http://www.ensemblgenomes.org/2012 EMBL-EBI Annual Scientific Report11