Update on Activities at the Universal Protein Resource (UniProt) in 2013

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2012 Nov 20

PMID 23161681

Citations 423

Affiliations

Soon will be listed here.

Abstract

The mission of the Universal Protein Resource (UniProt) (http://www.uniprot.org) is to support biological research by providing a freely accessible, stable, comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase. It integrates, interprets and standardizes data from numerous resources to achieve the most comprehensive catalogue of protein sequences and functional annotation. UniProt comprises four major components, each optimized for different uses, the UniProt Archive, the UniProt Knowledgebase, the UniProt Reference Clusters and the UniProt Metagenomic and Environmental Sequence Database. UniProt is produced by the UniProt Consortium, which consists of groups from the European Bioinformatics Institute (EBI), the SIB Swiss Institute of Bioinformatics (SIB) and the Protein Information Resource (PIR). UniProt is updated and distributed every 4 weeks and can be accessed online for searches or downloads.

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References

Kasprzyk A . BioMart: driving a paradigm change in biological data management. Database (Oxford). 2011; 2011:bar049. PMC: 3215098. DOI: 10.1093/database/bar049. View

Suzek B, Huang H, McGarvey P, Mazumder R, Wu C . UniRef: comprehensive and non-redundant UniProt reference clusters. Bioinformatics. 2007; 23(10):1282-8. DOI: 10.1093/bioinformatics/btm098. View

Leinonen R, Diez F, Binns D, Fleischmann W, Lopez R, Apweiler R . UniProt archive. Bioinformatics. 2004; 20(17):3236-7. DOI: 10.1093/bioinformatics/bth191. View

Kersey P, Staines D, Lawson D, Kulesha E, Derwent P, Humphrey J . Ensembl Genomes: an integrative resource for genome-scale data from non-vertebrate species. Nucleic Acids Res. 2011; 40(Database issue):D91-7. PMC: 3245118. DOI: 10.1093/nar/gkr895. View

Lima T, Auchincloss A, Coudert E, Keller G, Michoud K, Rivoire C . HAMAP: a database of completely sequenced microbial proteome sets and manually curated microbial protein families in UniProtKB/Swiss-Prot. Nucleic Acids Res. 2008; 37(Database issue):D471-8. PMC: 2686602. DOI: 10.1093/nar/gkn661. View

Jain E, Bairoch A, Duvaud S, Phan I, Redaschi N, Suzek B . Infrastructure for the life sciences: design and implementation of the UniProt website. BMC Bioinformatics. 2009; 10:136. PMC: 2686714. DOI: 10.1186/1471-2105-10-136. View

Patient S, Wieser D, Kleen M, Kretschmann E, Martin M, Apweiler R . UniProtJAPI: a remote API for accessing UniProt data. Bioinformatics. 2008; 24(10):1321-2. DOI: 10.1093/bioinformatics/btn122. View

Kretschmann E, Fleischmann W, Apweiler R . Automatic rule generation for protein annotation with the C4.5 data mining algorithm applied on SWISS-PROT. Bioinformatics. 2001; 17(10):920-6. DOI: 10.1093/bioinformatics/17.10.920. View

Flicek P, Amode M, Barrell D, Beal K, Brent S, Carvalho-Silva D . Ensembl 2012. Nucleic Acids Res. 2011; 40(Database issue):D84-90. PMC: 3245178. DOI: 10.1093/nar/gkr991. View

10.

Vizcaino J, Cote R, Reisinger F, Foster J, Mueller M, Rameseder J . A guide to the Proteomics Identifications Database proteomics data repository. Proteomics. 2009; 9(18):4276-83. PMC: 2970915. DOI: 10.1002/pmic.200900402. View

11.

Vasudevan S, Vinayaka C, Natale D, Huang H, Kahsay R, Wu C . Structure-guided rule-based annotation of protein functional sites in UniProt knowledgebase. Methods Mol Biol. 2010; 694:91-105. DOI: 10.1007/978-1-60761-977-2_7. View

12.

Chen C, Natale D, Finn R, Huang H, Zhang J, Wu C . Representative proteomes: a stable, scalable and unbiased proteome set for sequence analysis and functional annotation. PLoS One. 2011; 6(4):e18910. PMC: 3083393. DOI: 10.1371/journal.pone.0018910. View

13.

Pruitt K, Tatusova T, Brown G, Maglott D . NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy. Nucleic Acids Res. 2011; 40(Database issue):D130-5. PMC: 3245008. DOI: 10.1093/nar/gkr1079. View

14.

Morgat A, Coissac E, Coudert E, Axelsen K, Keller G, Bairoch A . UniPathway: a resource for the exploration and annotation of metabolic pathways. Nucleic Acids Res. 2011; 40(Database issue):D761-9. PMC: 3245108. DOI: 10.1093/nar/gkr1023. View

15.

Klimke W, ODonovan C, White O, Brister J, Clark K, Fedorov B . Solving the Problem: Genome Annotation Standards before the Data Deluge. Stand Genomic Sci. 2011; 5(1):168-93. PMC: 3236044. DOI: 10.4056/sigs.2084864. View

16.

. Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res. 2011; 40(Database issue):D71-5. PMC: 3245120. DOI: 10.1093/nar/gkr981. View

17.

Fleischmann W, Moller S, Gateau A, Apweiler R . A novel method for automatic functional annotation of proteins. Bioinformatics. 1999; 15(3):228-33. DOI: 10.1093/bioinformatics/15.3.228. View

18.

Hunter S, Jones P, Mitchell A, Apweiler R, Attwood T, Bateman A . InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res. 2011; 40(Database issue):D306-12. PMC: 3245097. DOI: 10.1093/nar/gkr948. View

19.

Karsch-Mizrachi I, Nakamura Y, Cochrane G . The International Nucleotide Sequence Database Collaboration. Nucleic Acids Res. 2011; 40(Database issue):D33-7. PMC: 3244996. DOI: 10.1093/nar/gkr1006. View