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The European Bioinformatics Institute in 2018: Tools, Infrastructure and Training Charles E Published online 16 November 2018 Nucleic Acids Research, 2019, Vol. 47, Database issue D15–D22 doi: 10.1093/nar/gky1124 The European Bioinformatics Institute in 2018: tools, infrastructure and training Charles E. Cook *, Rodrigo Lopez , Oana Stroe, Guy Cochrane , Cath Brooksbank , Ewan Birney and Rolf Apweiler European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK Received October 03, 2018; Revised October 19, 2018; Editorial Decision October 19, 2018; Accepted November 11, 2018 ABSTRACT resources (https://www.ebi.ac.uk/services/). These include archival resources storing primary data submitted by re- The European Bioinformatics Institute (https://www. searchers and knowledgebases that add value to archival ebi.ac.uk/) archives, curates and analyses life sci- resources through curation and analysis. All data resources ences data produced by researchers throughout the are available through web interfaces and most are also ac- world, and makes these data available for re-use cessible using application programming interfaces (APIs) globally (https://www.ebi.ac.uk/). Data volumes con- that provide users with high-throughput methods for data tinue to grow exponentially: total raw storage capac- access. Additionally, we provide in excess of 150 tools, also ity now exceeds 160 petabytes, and we manage these through web interfaces and APIs, that allow our users to increasing data flows while maintaining the quality analyse their own data and data downloaded from EMBL- of our services. This year we have improved the effi- EBI and other public repositories (1). We describe our tools ciency of our computational infrastructure and dou- infrastructure in greater detail below. A fundamental tenet of our mission is that all hosted bled the bandwidth of our connection to the world- data, tools and infrastructure are freely available worldwide, wide web. We report two new data resources, the and that data are represented in and shared in a variety of Single Cell Expression Atlas (https://www.ebi.ac.uk/ structured and standard formats for consumption by both gxa/sc/), which is a component of the Expression At- people and machines. EMBL-EBI’s data resources are part las; and the PDBe-Knowledgebase (https://www.ebi. of a worldwide infrastructure of life sciences data resources ac.uk/pdbe/pdbe-kb), which collates functional an- and many of our resources are run in collaboration with notations and predictions for structure data in the partners around the world, as we described last year (2). Protein Data Bank. Additionally, Europe PMC (http: Continued international collaboration is crucial to ensur- //europepmc.org/) has added preprint abstracts to ing that the life sciences data infrastructure provides open its search results, supplementing results from peer- access archiving and added-value to ever-growing volumes reviewed publications. EMBL-EBI maintains over 150 of data submitted to these resources by researchers around the globe. EMBL-EBI is a node in the ELIXIR infrastruc- analytical bioinformatics tools that complement our ture (https://www.elixir-europe.org/)(2) in Europe and is data resources. We make these tools available for actively engaged in efforts to increase the efficiency of the users through a web interface as well as program- global infrastructure for life sciences data resources (3). matically using application programming interfaces, We continuously review our data services through con- whilst ensuring the latest versions are available for sultation with our users and monitor new technologies and our users. Our training team, with support from all advances in research in order to ensure that these services of our staff, continued to provide on-site, off-site and provide those users with the resources they need to under- web-based training opportunities for thousands of take their work. In this update we summarize growth in our researchers worldwide this year. data resources, describe new data services that have been in- troduced this year and provide an overview of the extensive INTRODUCTION and broad collection of data analysis tools that complement our data resources. A primary mission of EMBL-EBI is to collect, organize, Our discovery tools and ontologies transcend scien- add value and make available biomolecular science data tific boundaries, bringing together biologists, clinicians, to the global life sciences community. To fulfil this mis- physicists, mathematicians and software engineers from sion, we support and provide to our users over 40 data *To whom correspondence should be addressed. Tel: +44 1223 494665; Email: [email protected] C The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. D16 Nucleic Acids Research, 2019, Vol. 47, Database issue academia, industry and healthcare. By connecting diverse single cell RNA-Seq studies. The Single Cell Atlas’ pipelines skills and expertise we are enabling the creative exploration annotate and re-analyse data from publicly available stud- of complex questions in biology today. ies, store them in standardized formats and allow search- ing and display of gene expression in individual cells from EMBL-EBI DATA RESOURCES IN 2018 different tissues or experimental conditions, such as dis- eases. The Single Cell Expression Atlas currently contains EMBL-EBI data resources cover the entire range of bio- data for nine species: Anopheles gambiae, Caenorhabditis logical sciences from raw DNA sequences to curated pro- elegans, Danio rerio, Drosophila melanogaster, Homo sapi- teins, chemicals, structures, systems, pathways, ontologies ens, Mus musculus, Plasmodium berghei, Rattus norvegi- and literature. These resources are shown graphically in Fig- cus and Schistosoma mansoni. Datasets from additional ure 1, with the complete list of services available online at species, as well as more functionality for their exploration https://www.ebi.ac.uk/services. Updates for 18 of these re- on the web, will be made available over new releases in sources also appear in this annual database issue of Nucleic due course. The resource will also host datasets from Acids Research. the Human Cell Atlas (https://www.humancellatlas.org/) as these become available (https://www.humancellatlas.org/ DATA GROWTH files/HCA WhitePaper 18Oct2017.pdf). Submissions to our data resources, fuelled by decreas- ing costs and new technologies, continue to increase Protein Data Bank in Europe––knowledge base exponentially (Figure 2). As always, data volumes are Protein Data Bank in Europe––Knowledge Base (PDBe- largest for nucleic acid sequences in the European Nu- KB; pdbe-kb.org) is a community-driven resource managed cleotide Archive (ENA, https://www.ebi.ac.uk/ena) and the bythePDBeteam(http://www.ebi.ac.uk/pdbe/), collating European Genome-phenome Archive (https://ega-archive. functional annotations and predictions to provide biologi- org/). We have during the past two years seen notable cal context for structure data in the PDB archive. PDBe-KB growth in submissions of mass spectrometry proteomics is a collaborative effort between PDBe and a diverse group data to the PRIDE database (https://www.ebi.ac.uk/pride/ of bioinformatics resources and research teams. PDBe-KB archive/), and as a category proteomics data has since 2016 consolidates into one resource the curated and enriched had the second largest storage footprint, after nucleotide se- data from a number of data projects, briefly described be- quences, among our data resources. low. Our total disk capacity, including all backups and space Structure Integration with Function, Taxonomy and Se- reserved for immediate future growth, grew from 120 quence (SIFTS, http://www.ebi.ac.uk/pdbe/docs/sifts/)pro- petabytes at the end of 2016 and will reach just over 160 vides residue-level mappings between UniProtKB (https: petabytes by the end of 2018 (Figure 3). //www.uniprot.org) and PDB entries, allowing for easy The two key components of EMBL-EBI’s provision of all transfer of value-added annotations between protein services, both data resources and tools, are interconnectiv- structures and sequences (6). In that vein, SIFTS pro- ity and interoperability. As we reported previously, our data vides cross-references to the IntEnz (https://www.ebi.ac.uk/ resources are internally linked through a dense network of intenz/), GO (http://geneontology.org), Pfam (7), InterPro cross references that allow them to share information on re- (8), SCOP (http://scop.mrc-lmb.cam.ac.uk/scop/), CATH lated data or biological entities (4). Our unified search en- (http://www.cathdb.info), PubMed (https://www.ncbi.nlm. gine indexes connections between data resources and pro- nih.gov/pubmed/), Ensembl (9) and Homologene (https: vides navigable links between them (5). We continue to ex- //www.ncbi.nlm.nih.gov/homologene) resources. The infor- pand this search engine, which has now been integrated into mation is updated and released every week at the same over 20 of our data resources, improving the user experience time as the release of new PDB entries and is widely by allowing users to locate, view and download most infor- used by resources such as RCSB PDB (https://www.rcsb. mation and data related
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