- The European Bioinformatics Institute in 2016: Data growth and integration. [PMID: 26673705]
Charles E Cook, Mary Todd Bergman, Robert D Finn, Guy Cochrane, Ewan Birney, Rolf Apweiler
Nucleic acids research 2016:44(D1)
2 Citations (Google Scholar as of 2016-04-07)
Abstract: New technologies are revolutionising biological research and its applications by making it easier and cheaper to generate ever-greater volumes and types of data. In response, the services and infrastructure of the European Bioinformatics Institute (EMBL-EBI, www.ebi.ac.uk) are continually expanding: total disk capacity increases significantly every year to keep pace with demand (75 petabytes as of December 2015), and interoperability between resources remains a strategic priority. Since 2014 we have launched two new resources: the European Variation Archive for genetic variation data and EMPIAR for two-dimensional electron microscopy data, as well as a Resource Description Framework platform. We also launched the Embassy Cloud service, which allows users to run large analyses in a virtual environment next to EMBL-EBI's vast public data resources. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.
- The European Bioinformatics Institute's data resources 2014. [PMID: 24271396]
Catherine Brooksbank, Mary Todd Bergman, Rolf Apweiler, Ewan Birney, Janet Thornton
Nucleic acids research 2014:42(Database issue)
24 Citations (Google Scholar as of 2016-01-18)
Abstract: Molecular Biology has been at the heart of the 'big data' revolution from its very beginning, and the need for access to biological data is a common thread running from the 1965 publication of Dayhoff's 'Atlas of Protein Sequence and Structure' through the Human Genome Project in the late 1990s and early 2000s to today's population-scale sequencing initiatives. The European Bioinformatics Institute (EMBL-EBI; http://www.ebi.ac.uk) is one of three organizations worldwide that provides free access to comprehensive, integrated molecular data sets. Here, we summarize the principles underpinning the development of these public resources and provide an overview of EMBL-EBI's database collection to complement the reviews of individual databases provided elsewhere in this issue.
- The European Bioinformatics Institute's data resources. [PMID: 19934258]
Catherine Brooksbank, Graham Cameron, Janet Thornton
Nucleic acids research 2010:38(Database issue)
38 Citations (Google Scholar as of 2016-06-09)
Abstract: The wide uptake of next-generation sequencing and other ultra-high throughput technologies by life scientists with a diverse range of interests, spanning fundamental biological research, medicine, agriculture and environmental science, has led to unprecedented growth in the amount of data generated. It has also put the need for unrestricted access to biological data at the centre of biology. The European Bioinformatics Institute (EMBL-EBI) is unique in Europe and is one of only two organisations worldwide providing access to a comprehensive, integrated set of these collections. Here, we describe how the EMBL-EBI's biomolecular databases are evolving to cope with increasing levels of submission, a growing and diversifying user base, and the demand for new types of data. All of the resources described here can be accessed from the EMBL-EBI website: http://www.ebi.ac.uk.
- The European Bioinformatics Institute's data resources: towards systems biology. [PMID: 15608238]
Catherine Brooksbank, Graham Cameron, Janet Thornton
Nucleic acids research 2005:33(Database issue)
120 Citations (Google Scholar as of 2016-06-09)
Abstract: Genomic and post-genomic biological research has provided fine-grain insights into the molecular processes of life, but also threatens to drown biomedical researchers in data. Moreover, as new high-throughput technologies are developed, the types of data that are gathered en masse are diversifying. The need to collect, store and curate all this information in ways that allow its efficient retrieval and exploitation is greater than ever. The European Bioinformatics Institute's (EBI's) databases and tools have evolved to meet the changing needs of molecular biologists: since we last wrote about our services in the 2003 issue of Nucleic Acids Research, we have launched new databases covering protein-protein interactions (IntAct), pathways (Reactome) and small molecules (ChEBI). Our existing core databases have continued to evolve to meet the changing needs of biomedical researchers, and we have developed new data-access tools that help biologists to move intuitively through the different data types, thereby helping them to put the parts together to understand biology at the systems level. The EBI's data resources are all available on our website at http://www.ebi.ac.uk.
- The European Bioinformatics Institute's data resources. [PMID: 12519944]
Catherine Brooksbank, Evelyn Camon, Midori A Harris, Michele Magrane, Maria Jesus Martin, Nicola Mulder, Claire O'Donovan, Helen Parkinson, Mary Ann Tuli, Rolf Apweiler, Ewan Birney, Alvis Brazma, Kim Henrick, Rodrigo Lopez, Guenter Stoesser, Peter Stoehr, Graham Cameron
Nucleic acids research 2003:31(1)
61 Citations (Google Scholar as of 2016-06-09)
Abstract: As the amount of biological data grows, so does the need for biologists to store and access this information in central repositories in a free and unambiguous manner. The European Bioinformatics Institute (EBI) hosts six core databases, which store information on DNA sequences (EMBL-Bank), protein sequences (SWISS-PROT and TrEMBL), protein structure (MSD), whole genomes (Ensembl) and gene expression (ArrayExpress). But just as a cell would be useless if it couldn't transcribe DNA or translate RNA, our resources would be compromised if each existed in isolation. We have therefore developed a range of tools that not only facilitate the deposition and retrieval of biological information, but also allow users to carry out searches that reflect the interconnectedness of biological information. The EBI's databases and tools are all available on our website at www.ebi.ac.uk.
- The EMBL Nucleotide Sequence Database. [PMID: 11752244]
Guenter Stoesser, Wendy Baker, Alexandra van den Broek, Evelyn Camon, Maria Garcia-Pastor, Carola Kanz, Tamara Kulikova, Rasko Leinonen, Quan Lin, Vincent Lombard, Rodrigo Lopez, Nicole Redaschi, Peter Stoehr, Mary Ann Tuli, Katerina Tzouvara, Robert Vaughan
Nucleic acids research 2002:30(1)
170 Citations (Google Scholar as of 2016-06-09)
Abstract: The EMBL Nucleotide Sequence Database (aka EMBL-Bank; http://www.ebi.ac.uk/embl/) incorporates, organises and distributes nucleotide sequences from all available public sources. EMBL-Bank is located and maintained at the European Bioinformatics Institute (EBI) near Cambridge, UK. In an international collaboration with DDBJ (Japan) and GenBank (USA), data are exchanged amongst the collaborating databases on a daily basis. Major contributors to the EMBL database are individual scientists and genome project groups. Webin is the preferred web-based submission system for individual submitters, whilst automatic procedures allow incorporation of sequence data from large-scale genome sequencing centres and from the European Patent Office (EPO). Database releases are produced quarterly. Network services allow free access to the most up-to-date data collection via FTP, email and World Wide Web interfaces. EBI's Sequence Retrieval System (SRS), a network browser for databanks in molecular biology, integrates and links the main nucleotide and protein databases plus many other specialized databases. For sequence similarity searching, a variety of tools (e.g. Blitz, Fasta, BLAST) are available which allow external users to compare their own sequences against the latest data in the EMBL Nucleotide Sequence Database and SWISS-PROT. All resources can be accessed via the EBI home page at http://www.ebi.ac.uk.
- The European Bioinformatics Institute (EBI) databases. [PMID: 8594602]
P Rodriguez-Tomé, P J Stoehr, G N Cameron, T P Flores
Nucleic acids research 1996:24(1)
95 Citations (Google Scholar as of 2016-06-09)
Abstract: The European Bioinformatics Institute (EBI) maintains and distributes the EMBL Nucleotide Sequence database, Europe's primary nucleotide sequence data resource. The EBI also maintains and distributes the SWISS-PROT Protein Sequence database, in collaboration with Amos Bairoch of the University of Geneva. Over fifty additional specialist molecular biology databases, as well as software and documentation of interest to molecular biologists are available. The EBI network services include database searching and sequence similarity searching facilities.
- The European Bioinformatics Institute (EBI) databases. [PMID: 7937043]
D B Emmert, P J Stoehr, G Stoesser, G N Cameron
Nucleic acids research 1994:22(17)
100 Citations (Google Scholar as of 2016-06-09)
Abstract: This paper describes the databases and services of the European Bioinformatics Institute (EBI). In collaboration with DDBJ and GenBank/NCBI, the EBI maintains and distributes the EMBL Nucleotide Sequence Database, Europe's primary nucleotide sequence data resource. The EBI also maintains and distributes the SWISS-PROT Protein Sequence Database, in collaboration with Amos Bairoch of the University of Geneva. Over thirty additional specialist molecular biology databases, as well as software and documentation of interest to molecular biologists, are also available. The EBI network services include database searching, entry retrieval, and sequence similarity searching facilities.