The European Bioinformatics Institute in 2018: tools, infrastructure and training

Abstract

The European Bioinformatics Institute ( https://www.ebi.ac.uk/ ) archives, curates and analyses life sciences data produced by researchers throughout the world, and makes these data available for re-use globally ( https://www.ebi.ac.uk/ ). Data volumes continue to grow exponentially: total raw storage capacity now exceeds 160 petabytes, and we manage these increasing data flows while maintaining the quality of our services. This year we have improved the efficiency of our computational infrastructure and doubled the bandwidth of our connection to the worldwide web. We report two new data resources, the Single Cell Expression Atlas ( https://www.ebi.ac.uk/gxa/sc/ ), which is a component of the Expression Atlas; and the PDBe-Knowledgebase ( https://www.ebi.ac.uk/pdbe/pdbe-kb ), which collates functional annotations and predictions for structure data in the Protein Data Bank. Additionally, Europe PMC ( http://europepmc.org/ ) has added preprint abstracts to its search results, supplementing results from peer-reviewed publications. EMBL-EBI maintains over 150 analytical bioinformatics tools that complement our data resources. We make these tools available for users through a web interface as well as programmatically using application programming interfaces, whilst ensuring the latest versions are available for our users. Our training team, with support from all of our staff, continued to provide on-site, off-site and web-based training opportunities for thousands of researchers worldwide this year.

CD90/Thy-1, a Cancer-Associated Cell Surface Signaling Molecule

“…We recently demonstrated that CD90 expression is not only restricted to GBM stem-like cells but is also observed in more differentiated GBM cells (primary adherent lines) and in freshly dissociated GBM specimens (Avril et al, 2017a). Using the recent single-cell RNA sequencing datasets from stem-like and no-stem GBM cells and tumor migrating cells (Darmanis et al, 2017; Cook et al, 2018), we confirm herein that CD90 is expressed in tumor cells from the cancer site but also in migrating tumor cells, tumor-associated endothelial cells, and neighboring neuronal cells (Figure 2C). CD90 expression in kidney cancers is currently controversial.…”

Insect genomes: progress and challenges

“…Such databases have high maintenance costs and mainly play the role of data warehousing. This type of database is represented by the NCBI (Sayers et al ., ), the European Bioinformatics Institute (Cook et al ., ) and the Japanese Nucleic Acid Database (Kodama et al ., ), which are recognized as the three major gene databases. The second category reflects genome databases with particular focus on a group of species.…”

annonex2embl: automatic preparation of annotated DNA sequences for bulk submissions to ENA

“…Accordingly, a considerable fraction of submissions to public databases represents sequence data from large-scale investigations (Kans and Ouellette 2001;Gruenstaeudl and Hartmaring 2019). Data accumulation statistics for nucleotide sequences at ENA corroborate this trend Cook et al 2019). Most sequence databases have, consequently, adopted policies and methods to enable the submission of large-scale sequence datasets.…”