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Nucleic Acids Research 2005 33(Database Issue):D154-D159; doi:10.1093/nar/gki070
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Nucleic Acids Research, 2005, Vol. 33, Database issue D154-D159
© 2005, the authors
Nucleic Acids Research, Vol. 33, Database issue © Oxford University Press 2005; all rights reserved

The Universal Protein Resource (UniProt)

Amos Bairoch, Rolf Apweiler1,*, Cathy H. Wu2, Winona C. Barker3, Brigitte Boeckmann, Serenella Ferro, Elisabeth Gasteiger, Hongzhan Huang2, Rodrigo Lopez1, Michele Magrane1, Maria J. Martin1, Darren A. Natale2, Claire O'Donovan1, Nicole Redaschi and Lai-Su L. Yeh3

Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 rue Michel Servet, 1211 Geneva 4, Switzerland, 1 The EMBL Outstation—The European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, 2 Department of Biochemistry and Molecular Biology and 3 National Biomedical Research Foundation, Georgetown University Medical Center, 3900 Reservoir Road, NW, Box 571414, WA 20057-1414, USA

* To whom correspondence should be addressed: Tel: +44 0 1223 494435; Fax: +44 0 1223 494468; Email: apweiler{at}ebi.ac.uk

Received September 14, 2004; Revised and Accepted October 5, 2004

The Universal Protein Resource (UniProt) provides the scientific community with a single, centralized, authoritative resource for protein sequences and functional information. Formed by uniting the Swiss-Prot, TrEMBL and PIR protein database activities, the UniProt consortium produces three layers of protein sequence databases: the UniProt Archive (UniParc), the UniProt Knowledgebase (UniProt) and the UniProt Reference (UniRef) databases. The UniProt Knowledgebase is a comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase with extensive cross-references. This centrepiece consists of two sections: UniProt/Swiss-Prot, with fully, manually curated entries; and UniProt/TrEMBL, enriched with automated classification and annotation. During 2004, tens of thousands of Knowledgebase records got manually annotated or updated; we introduced a new comment line topic: TOXIC DOSE to store information on the acute toxicity of a toxin; the UniProt keyword list got augmented by additional keywords; we improved the documentation of the keywords and are continuously overhauling and standardizing the annotation of post-translational modifications. Furthermore, we introduced a new documentation file of the strains and their synonyms. Many new database cross-references were introduced and we started to make use of Digital Object Identifiers. We also achieved in collaboration with the Macromolecular Structure Database group at EBI an improved integration with structural databases by residue level mapping of sequences from the Protein Data Bank entries onto corresponding UniProt entries. For convenient sequence searches we provide the UniRef non-redundant sequence databases. The comprehensive UniParc database stores the complete body of publicly available protein sequence data. The UniProt databases can be accessed online (http://www.uniprot.org) or downloaded in several formats (ftp://ftp.uniprot.org/pub). New releases are published every two weeks.

The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use permissions, please contact journals.permissions{at}oupjournals.org.


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Bioinformatics, February 1, 2007; 23(3): 267 - 271.
[Abstract] [Full Text] [PDF]

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J. S. Kaminker, Y. Zhang, A. Waugh, P. M. Haverty, B. Peters, D. Sebisanovic, J. Stinson, W. F. Forrest, J. F. Bazan, S. Seshagiri, et al.
Distinguishing Cancer-Associated Missense Mutations from Common Polymorphisms
Cancer Res., January 15, 2007; 67(2): 465 - 473.
[Abstract] [Full Text] [PDF]

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 Nucleic Acids ResHome page
D. S. Wishart, D. Tzur, C. Knox, R. Eisner, A. C. Guo, N. Young, D. Cheng, K. Jewell, D. Arndt, S. Sawhney, et al.
HMDB: the Human Metabolome Database
Nucleic Acids Res., January 12, 2007; 35(suppl_1): D521 - D526.
[Abstract] [Full Text] [PDF]

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A. Andreeva, A. Prlic, T. J. P. Hubbard, and A. G. Murzin
SISYPHUS--structural alignments for proteins with non-trivial relationships
Nucleic Acids Res., January 12, 2007; 35(suppl_1): D253 - D259.
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G. L. Holliday, D. E. Almonacid, G. J. Bartlett, N. M. O'Boyle, J. W. Torrance, P. Murray-Rust, J. B. O. Mitchell, and J. M. Thornton
MACiE (Mechanism, Annotation and Classification in Enzymes): novel tools for searching catalytic mechanisms
Nucleic Acids Res., January 12, 2007; 35(suppl_1): D515 - D520.
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K. L. Childs, J. P. Hamilton, W. Zhu, E. Ly, F. Cheung, H. Wu, P. D. Rabinowicz, C. D. Town, C. R. Buell, and A. P. Chan
The TIGR Plant Transcript Assemblies database
Nucleic Acids Res., January 12, 2007; 35(suppl_1): D846 - D851.
[Abstract] [Full Text] [PDF]

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M. M. Gromiha, Y. Yabuki, S. Kundu, S. Suharnan, and M. Suwa
TMBETA-GENOME: database for annotated {beta}-barrel membrane proteins in genomic sequences
Nucleic Acids Res., January 12, 2007; 35(suppl_1): D314 - D316.
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 Nucleic Acids ResHome page
N. D'Agostino, M. Aversano, L. Frusciante, and M. L. Chiusano
TomatEST database: in silico exploitation of EST data to explore expression patterns in tomato species
Nucleic Acids Res., January 12, 2007; 35(suppl_1): D901 - D905.
[Abstract] [Full Text] [PDF]

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G. Lopez, A. Valencia, and M. Tress
FireDB--a database of functionally important residues from proteins of known structure
Nucleic Acids Res., January 12, 2007; 35(suppl_1): D219 - D223.
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L. H. Greene, T. E. Lewis, S. Addou, A. Cuff, T. Dallman, M. Dibley, O. Redfern, F. Pearl, R. Nambudiry, A. Reid, et al.
The CATH domain structure database: new protocols and classification levels give a more comprehensive resource for exploring evolution
Nucleic Acids Res., January 12, 2007; 35(suppl_1): D291 - D297.
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 Nucleic Acids ResHome page
M. L. Riley, T. Schmidt, I. I. Artamonova, C. Wagner, A. Volz, K. Heumann, H.-W. Mewes, and D. Frishman
PEDANT genome database: 10 years online
Nucleic Acids Res., January 12, 2007; 35(suppl_1): D354 - D357.
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 Mol Biol EvolHome page
H. Kidron, S. Repo, M. S. Johnson, and T. A. Salminen
Functional Classification of Amino Acid Decarboxylases from the Alanine Racemase Structural Family by Phylogenetic Studies
Mol. Biol. Evol., January 1, 2007; 24(1): 79 - 89.
[Abstract] [Full Text] [PDF]


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