The European Bioinformatics Institute in 2017: data coordination and integration

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.

Biotechnology, Big Data and Artificial Intelligence

“…Empirical data suggests that nucleotide and proteomics data generation is growing at an exponential rate. Researchers at the European Bioinformatics Institute (EMBL‐EBI) have monitored the growth of the different types of data stored in their servers and concluded that it is doubling roughly every year (see Figure ). This exponential growth raises significant challenges to the organizations that have the mission of storing and organizing such data but provides a bounty for biotechnology researchers who have the ability to explore and exploit the ever‐increasing information stored in servers, worldwide.…”

“…Growth of data stored by EMBL‐EBI, for different types of data. Reprinted from Cook et al, with permission.…”

Structural biology data archiving – where we are and what lies ahead

“…The main archives for cellular structural biology are EMDB (tomograms) and Electron Microscopy Public Image Archive (EMPIAR) [9] (raw data related to EMDB entries, as well as 3D reconstructions from other bioimaging techniques that are not supported by EMDB, such as 3D-SEM and SXT). EMBL-EBI [10] is directly involved in the running and operation of all these archives, with the exception of BMRB and SASBDB (with whom we collaborate). URLs for the websites of the archives mentioned here and in the following section can be found in Table 1.…”

Biomedical Image Processing with Containers and Deep Learning: An Automated Analysis Pipeline

“…Archiving and indexing large datasets is a nontrivial, but a possible task, as demonstrated by the plethora of database repositories currently in use for biology research, electron microscopy, microarray analysis, radiology, or multidiscipline research …”