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. 2018 Jan 4;46(D1):D21-D29.
doi: 10.1093/nar/gkx1154.

The European Bioinformatics Institute in 2017: data coordination and integration

Charles E Cook  1 , Mary T Bergman  1 , Guy Cochrane  1 , Rolf Apweiler  1 , Ewan Birney  1
Affiliations

The European Bioinformatics Institute in 2017: data coordination and integration

Charles E Cook et al. Nucleic Acids Res. .

Abstract

The European Bioinformatics Institute (EMBL-EBI) supports life-science research throughout the world by providing open data, open-source software and analytical tools, and technical infrastructure (https://www.ebi.ac.uk). We accommodate an increasingly diverse range of data types and integrate them, so that biologists in all disciplines can explore life in ever-increasing detail. We maintain over 40 data resources, many of which are run collaboratively with partners in 16 countries (https://www.ebi.ac.uk/services). Submissions continue to increase exponentially: our data storage has doubled in less than two years to 120 petabytes. Recent advances in cellular imaging and single-cell sequencing techniques are generating a vast amount of high-dimensional data, bringing to light new cell types and new perspectives on anatomy. Accordingly, one of our main focus areas is integrating high-quality information from bioimaging, biobanking and other types of molecular data. This is reflected in our deep involvement in Open Targets, stewarding of plant phenotyping standards (MIAPPE) and partnership in the Human Cell Atlas data coordination platform, as well as the 2017 launch of the Omics Discovery Index. This update gives a birds-eye view of EMBL-EBI's approach to data integration and service development as genomics begins to enter the clinic.

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Figures

Figure 1.
Figure 1.
Selection of core data resources at EMBL-EBI. Updates in this issue: BioModels (15), EBI Metagenomics (39), ENA (6), Ensembl (7), Ensembl Genomes (8), Europe PMC (9), Expression Atlas (21), Mechanism and Catalytic Site Atlas (M-CSA) (45), MEROPS (46), Protein Data Bank in Europe (PDBe) (12), Reactome (47), Rfam (48) and WormBase (49). For a complete lists of EMBL-EBI resources see https://www.ebi.ac.uk/services.
Figure 2.
Figure 2.
Major database collaborations. Many EMBL-EBI data resources are collaborations with other organizations around the world. These collaborations allow us to share the effort of collecting and serving data to our users and to provide collectively more and better analytical tools. This map visually demonstrates the shared global network that supports open data for the biological sciences.
Figure 3.
Figure 3.
(A) Data accumulation at EMBL-EBI by data type: nucleotide sequence, mass spectrometry and microarray; (B) Data accumulation by archive: Proteomics identifications (PRIDE) (13), EGA (5), ArrayExpress (AE) (2), European Nucleotide Archive (ENA) (6) and Metabolights (16). The Y-axis for both charts is logarithmic, so growth in all data types is exponential. In all data resources shown here, growth rates are predicted to continue increasing, with notable sustained exponential growth in PRIDE, the EGA and MetaboLights. All have doubling times of around 12 months.
See this image and copyright information in PMC

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