Literature DB >> 12519944

The European Bioinformatics Institute's data resources.

Catherine Brooksbank1, 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.   

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.

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Year:  2003        PMID: 12519944      PMCID: PMC165513          DOI: 10.1093/nar/gkg066

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN: 0305-1048            Impact factor:   16.971


  33 in total

1.  AutoDep: a web-based system for deposition and validation of macromolecular structural -information.

Authors:  D Lin; N O Manning; J Jiang; E E Abola; D Stampf; J Prilusky; J L Sussman
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2000-07

2.  Minimum information about a microarray experiment (MIAME)-toward standards for microarray data.

Authors:  A Brazma; P Hingamp; J Quackenbush; G Sherlock; P Spellman; C Stoeckert; J Aach; W Ansorge; C A Ball; H C Causton; T Gaasterland; P Glenisson; F C Holstege; I F Kim; V Markowitz; J C Matese; H Parkinson; A Robinson; U Sarkans; S Schulze-Kremer; J Stewart; R Taylor; J Vilo; M Vingron
Journal:  Nat Genet       Date:  2001-12       Impact factor: 38.330

3.  The PROSITE database, its status in 2002.

Authors:  Laurent Falquet; Marco Pagni; Philipp Bucher; Nicolas Hulo; Christian J A Sigrist; Kay Hofmann; Amos Bairoch
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

4.  GenBank.

Authors:  Dennis A Benson; Ilene Karsch-Mizrachi; David J Lipman; James Ostell; Barbara A Rapp; David L Wheeler
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

5.  Creating the gene ontology resource: design and implementation.

Authors: 
Journal:  Genome Res       Date:  2001-08       Impact factor: 9.043

6.  The EBI SRS server-new features.

Authors:  Evgeny M Zdobnov; Rodrigo Lopez; Rolf Apweiler; Thure Etzold
Journal:  Bioinformatics       Date:  2002-08       Impact factor: 6.937

7.  Local alignment statistics.

Authors:  S F Altschul; W Gish
Journal:  Methods Enzymol       Date:  1996       Impact factor: 1.600

8.  Improved tools for biological sequence comparison.

Authors:  W R Pearson; D J Lipman
Journal:  Proc Natl Acad Sci U S A       Date:  1988-04       Impact factor: 11.205

9.  The Gene Ontology Annotation (GOA) Project--Application of GO in SWISS-PROT, TrEMBL and InterPro.

Authors:  Evelyn Camon; Daniel Barrell; Catherine Brooksbank; Michele Magrane; Rolf Apweiler
Journal:  Comp Funct Genomics       Date:  2003

10.  Design and implementation of microarray gene expression markup language (MAGE-ML).

Authors:  Paul T Spellman; Michael Miller; Jason Stewart; Charles Troup; Ugis Sarkans; Steve Chervitz; Derek Bernhart; Gavin Sherlock; Catherine Ball; Marc Lepage; Marcin Swiatek; W L Marks; Jason Goncalves; Scott Markel; Daniel Iordan; Mohammadreza Shojatalab; Angel Pizarro; Joe White; Robert Hubley; Eric Deutsch; Martin Senger; Bruce J Aronow; Alan Robinson; Doug Bassett; Christian J Stoeckert; Alvis Brazma
Journal:  Genome Biol       Date:  2002-08-23       Impact factor: 13.583

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  17 in total

1.  The EMBL Nucleotide Sequence Database.

Authors:  Tamara Kulikova; Philippe Aldebert; Nicola Althorpe; Wendy Baker; Kirsty Bates; Paul Browne; Alexandra van den Broek; Guy Cochrane; Karyn Duggan; Ruth Eberhardt; Nadeem Faruque; Maria Garcia-Pastor; Nicola Harte; Carola Kanz; Rasko Leinonen; Quan Lin; Vincent Lombard; Rodrigo Lopez; Renato Mancuso; Michelle McHale; Francesco Nardone; Ville Silventoinen; Peter Stoehr; Guenter Stoesser; Mary Ann Tuli; Katerina Tzouvara; Robert Vaughan; Dan Wu; Weimin Zhu; Rolf Apweiler
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

2.  Comparative analysis of MTF-1 binding sites between human and mouse.

Authors:  Minghui Wang; Fan Yang; Xiangzhe Zhang; Hongbo Zhao; Qishan Wang; Yuchun Pan
Journal:  Mamm Genome       Date:  2010-04-11       Impact factor: 2.957

Review 3.  Bioinformatics and molecular modeling in glycobiology.

Authors:  Martin Frank; Siegfried Schloissnig
Journal:  Cell Mol Life Sci       Date:  2010-04-04       Impact factor: 9.261

4.  WU-Blast2 server at the European Bioinformatics Institute.

Authors:  Rodrigo Lopez; Ville Silventoinen; Stephen Robinson; Asif Kibria; Warren Gish
Journal:  Nucleic Acids Res       Date:  2003-07-01       Impact factor: 16.971

5.  The expression of glyceraldehyde-3-phosphate dehydrogenase associated cell cycle (GACC) genes correlates with cancer stage and poor survival in patients with solid tumors.

Authors:  Dunrui Wang; Daniel R Moothart; Douglas R Lowy; Xiaolan Qian
Journal:  PLoS One       Date:  2013-04-19       Impact factor: 3.240

6.  GeneKeyDB: a lightweight, gene-centric, relational database to support data mining environments.

Authors:  S A Kirov; X Peng; E Baker; D Schmoyer; B Zhang; J Snoddy
Journal:  BMC Bioinformatics       Date:  2005-03-24       Impact factor: 3.169

7.  EMBL Nucleotide Sequence Database: developments in 2005.

Authors:  Guy Cochrane; Philippe Aldebert; Nicola Althorpe; Mikael Andersson; Wendy Baker; Alastair Baldwin; Kirsty Bates; Sumit Bhattacharyya; Paul Browne; Alexandra van den Broek; Matias Castro; Karyn Duggan; Ruth Eberhardt; Nadeem Faruque; John Gamble; Carola Kanz; Tamara Kulikova; Charles Lee; Rasko Leinonen; Quan Lin; Vincent Lombard; Rodrigo Lopez; Michelle McHale; Hamish McWilliam; Gaurab Mukherjee; Francesco Nardone; Maria Pilar Garcia Pastor; Siamak Sobhany; Peter Stoehr; Katerina Tzouvara; Robert Vaughan; Dan Wu; Weimin Zhu; Rolf Apweiler
Journal:  Nucleic Acids Res       Date:  2006-01-01       Impact factor: 16.971

8.  An automatic method for assessing structural importance of amino acid positions.

Authors:  Michael I Sadowski; David T Jones
Journal:  BMC Struct Biol       Date:  2009-03-04

9.  GEM System: automatic prototyping of cell-wide metabolic pathway models from genomes.

Authors:  Kazuharu Arakawa; Yohei Yamada; Kosaku Shinoda; Yoichi Nakayama; Masaru Tomita
Journal:  BMC Bioinformatics       Date:  2006-03-23       Impact factor: 3.169

10.  A nonsense mutation in COQ9 causes autosomal-recessive neonatal-onset primary coenzyme Q10 deficiency: a potentially treatable form of mitochondrial disease.

Authors:  Andrew J Duncan; Maria Bitner-Glindzicz; Brigitte Meunier; Harry Costello; Iain P Hargreaves; Luis C López; Michio Hirano; Catarina M Quinzii; Michael I Sadowski; John Hardy; Andrew Singleton; Peter T Clayton; Shamima Rahman
Journal:  Am J Hum Genet       Date:  2009-04-16       Impact factor: 11.025

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