European Bioinformatics Institute
|Key people||Janet Thornton
|Parent organization||European Molecular Biology Laboratory|
The European Bioinformatics Institute (EBI) is a centre for research and services in bioinformatics, and is part of European Molecular Biology Laboratory (EMBL).
EMBL-EBI is listed in the Registry of Research Data Repositories re3data.org.
About the EMBL-EBI
The roots of the EMBL-EBI lie in the EMBL Nucleotide Sequence Data Library (now known as EMBL-Bank), which was established in 1980 at the EMBL laboratories in Heidelberg, Germany and was the world's first nucleotide sequence database. The original goal was to establish a central computer database of DNA sequences, to supplement sequences submitted to journals. What began as a modest task of abstracting information from literature soon became a major database activity with direct electronic submissions of data and the need for highly skilled informatics staff. The task grew in scale with the start of the genome projects, and grew in visibility as the data became relevant to research in the commercial sector. It soon became apparent that the EMBL Nucleotide Sequence Data Library needed better financial security to ensure its long-term viability and to cope with the sheer scale of the task.
There was also a need for research and development to provide services, to collaborate with global partners to support the project, and to provide assistance to industry. To this end, in 1992, the EMBL Council voted to establish the European Bioinformatics Institute and to locate it at the Wellcome Trust Genome Campus in the United Kingdom where it would be in close proximity to the major sequencing efforts at the Wellcome Trust Sanger Institute. From 1992 through to 1995, a gradual transition of the activities in Heidelberg took place, until in September 1995 the EMBL-EBI occupied its current location on the Wellcome Trust Genome Campus.
When the EMBL-EBI moved to Hinxton it hosted two databases, one for nucleotide sequences (the EMBL Data Library, now known as EMBL-Bank) and one for protein sequences (Swiss-Prot–TrEMBL, now known as UniProt). Since then, the EMBL-EBI has diversified to provide data resources in all the major molecular domains and expanded to include a broad research base. It provides user support and offers advanced training in bioinformatics.
As part of EMBL, the largest part of EMBL-EBI's funding comes from the governments of EMBL's 20 member states. Other major funders include the European Commission, Wellcome Trust, US National Institutes of Health, UK Research Councils, EMBL-EBI's industry partners and the UK Department of Trade and Industry. In addition, the Wellcome Trust provides the facilities for the EMBL-EBI on its Genome Campus at Hinxton, and the UK Research Councils have provided funds for EMBL-EBI's facilities in Hinxton.Coordinates:
Resources at the EMBL-EBI
The EMBL-EBI hosts a number of publicly open, free to use life science resources, including biomedical databases, analysis tools and bio-ontologies. These include:
- ArrayExpress - archive of gene expression experiments
- BioModels Database - a database of computational models relevant to the life sciences
- Chemical Entities of Biological Interest (ChEBI) - database and ontology of molecular entities
- European Nucleotide Archive (ENA) - resource of nucleotide sequencing information
- Ensembl project - genome databases for vertebrates and other eukaryotic species (joint with Wellcome Trust Sanger Institute)
- Europe PubMed Central - database offering free access to collection of biomedical research literature
- Experimental Factor Ontology (EFO) - ontology of experimental variables for biomedical data
- Expression Atlas - database of summary information on which genes are expressed under which conditions
- Gene ontology - ontology of gene functions and processes
- Protein Data Bank in Europe - European resource for the collection, organisation and dissemination of data on biological macromolecular structures
- Proteomics Identifications Database (PRIDE) - repository of mass spectrometry (MS) based proteomics
- UniProt - database of protein sequence and functional information (joint with Swiss Institute of Bioinformatics and Protein Information Resource)
Notes and references
- http://www.ebi.ac.uk/about/background Background
- "EBI Entry in re3data.org". www.re3data.org. Retrieved 28 August 2014.
- Attwood T.K., Gisel A., Eriksson N-E. and Bongcam-Rudloff E. (2011). "Concepts, Historical Milestones and the Central Place of Bioinformatics in Modern Biology: A European Perspective". Bioinformatics - Trends and Methodologies. InTech. Retrieved 8 Jan 2012.
- Stoesser, G.; Sterk, P.; Tuli, M.; Stoehr, P.; Cameron, G. (1997). "The EMBL Nucleotide Sequence Database". Nucleic Acids Research 25 (1): 7–14. doi:10.1093/nar/25.1.7. PMC 146376. PMID 9016493.
- Kneale, G.; Kennard, O. (1984). "The EMBL nucleotide sequence data library". Biochemical Society transactions 12 (6): 1011–1014. PMID 6530028.
- Wright, V. A.; Vaughan, B. W.; Laurent, T.; Lopez, R.; Brooksbank, C.; Schneider, M. V. (2010). "Bioinformatics training: Selecting an appropriate learning content management system--an example from the European Bioinformatics Institute". Briefings in Bioinformatics 11 (6): 552–562. doi:10.1093/bib/bbq023. PMID 20601435.
- National Center for Biotechnology Information
- Gene ontology
- Proteomics Identifications Database (PRIDE)