The Universal Protein Resource (UniProt) in 2010.

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Authors: UniProt Consortium
Year: 2010
Journal: Nucleic acids research
PMID: 19843607
DOI: 10.1093/nar/gkp846
PMCID: PMC2808944

#	Section	Preview
20	PROGRESS REPORT — UniProtKB annotation — Integration with other databases	Integration between the three types of sequence-related databases (nucleic acid sequences, protein…
21	PROGRESS REPORT — Controlled vocabularies	Controlled vocabularies (CVs) (http://www.uniprot.org/docs/#vocabulary) are used to describe various…
22	PROGRESS REPORT — Controlled vocabularies — Plastid annotation controlled vocabulary	In the OG (OrGanelle) line (Encoded on subsection of the ‘Names and origin’ section,…
23	PROGRESS REPORT — Controlled vocabularies — Structuring of the metabolic pathway topic using UniPathway	The metabolism of living organisms can be understood as a network of biochemical reactions,…
24	PROGRESS REPORT — Controlled vocabularies — Structuring of the metabolic pathway topic using UniPathway	We have followed this classical approach in the UniPathway project (a collaborative project with the…
25	PROGRESS REPORT — Controlled vocabularies — Structuring of the metabolic pathway topic using UniPathway	The role of a protein in metabolism is described in the 'Pathway' subsection of the 'General…
26	PROGRESS REPORT — Controlled vocabularies — Structuring of the metabolic pathway topic using UniPathway	Examples:
27	PROGRESS REPORT — Controlled vocabularies — Structuring of the metabolic pathway topic using UniPathway	P49367: S. cerevisiae homoacotinase (EC 4.2.1.36) catalyzes the second step of the sub-pathway…
28	PROGRESS REPORT — Controlled vocabularies — Structuring of the metabolic pathway topic using UniPathway	CC -!- PATHWAY: Amino-acid biosynthesis; L-lysine biosynthesis via AAA
29	PROGRESS REPORT — Controlled vocabularies — Structuring of the metabolic pathway topic using UniPathway	CCpathway; L-alpha-aminoadipate from 2-oxoglutarate: step 2/4.
30	PROGRESS REPORT — Controlled vocabularies — Structuring of the metabolic pathway topic using UniPathway	Q980X0: S. solfataricus acetylglutamate/acetylaminoadipate kinase (EC 2.7.2.8 & EC 2.7.2.-)…
31	PROGRESS REPORT — Controlled vocabularies — Structuring of the metabolic pathway topic using UniPathway	CC -!- PATHWAY: Amino-acid biosynthesis; L-arginine biosynthesis; N(2)-
32	PROGRESS REPORT — Controlled vocabularies — Structuring of the metabolic pathway topic using UniPathway	CC acetyl-L-ornithine from L-glutamate: step 2/4.
33	PROGRESS REPORT — Controlled vocabularies — Structuring of the metabolic pathway topic using UniPathway	CC -!- PATHWAY: Amino-acid biosynthesis; L-lysine biosynthesis via AAA
34	PROGRESS REPORT — Controlled vocabularies — Structuring of the metabolic pathway topic using UniPathway	CC pathway; L-lysine from L-alpha-aminoadipate (Thermus route): step
35	PROGRESS REPORT — Controlled vocabularies — Structuring of the metabolic pathway topic using UniPathway	CC 2/5.
36	PROGRESS REPORT — Controlled vocabularies — Structuring of the metabolic pathway topic using UniPathway	The UniProt web site supplies direct links to UniPathway…
37	PROGRESS REPORT — Controlled vocabularies — Structuring of the metabolic pathway topic using UniPathway	UniProtKB/Swiss-Prot release 57.6 contains more than 105 000 distinct proteins (∼155 000 PATHWAY…
38	PROGRESS REPORT — Controlled vocabularies — Enzyme nomenclature in UniProt	EC numbers are used to describe enzyme reactions and are based on the recommendations of the…
39	PROGRESS REPORT — Controlled vocabularies — Enzyme nomenclature in UniProt	Examples:

Citation	PMID	DOI	Status
Cochrane, G et al., Nucleic Acids Res., 2009, Petabyte-scale innovations at the European Nucleotide Archive	18978013	10.1093/nar/gkn765	Cited
Fleischmann, W et al., Bioinformatics, 1999, A novel method for automatic functional annotation of proteins	10222410	10.1093/bioinformatics/15.3.228	Cited
Flicek, P et al., Nucleic Acids Res., 2008, Ensembl 2008	18000006	10.1093/nar/gkm988	Cited
Gattiker, A et al., Comput. Biol. Chem., 2003, Automated annotation of microbial proteomes in SWISS-PROT	12798039	10.1016/s1476-9271(02)00094-4	Cited
Gaudet, P et al., Database, 2009, Collaborative annotation of genes and proteins between UniProtKB/Swiss-Prot and dictyBase	20157489	10.1093/database/bap016	Cited
Hong, EL et al., Nucleic Acids Res., 2008, The Ontology annotations at SGD: new data sources and annotation methods	17982175	10.1093/nar/gkm909	Cited
Jain, E et al., BMC Bioinformatics, 2009, Infrastructure for the life sciences: design and implementation of the UniProt website	19426475	10.1186/1471-2105-10-136	Cited
Jensen, LJ et al., Nucleic Acids Res., 2009, STRING 8 – a global view on proteins and their functional interactions in 630 organisms	18940858	10.1093/nar/gkn760	Cited
Kanehisa, M et al., Nucleic Acids Res., 2008, KEGG for linking genomes to life and the environment	18077471	10.1093/nar/gkm882	Cited
Leinonen, R et al., Bioinformatics, 2009, UniProt archive	15044231	10.1093/bioinformatics/bth191	Cited
Natale, DA et al., Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. Bioinformatics Volume, 2004, Large-scale, classification-driven, rule-based functional annotation of proteins	—	—	—
Patient, S et al., Bioinformatics, 2008, UniProtJAPI: a remote API for accessing UniProt data	18390879	10.1093/bioinformatics/btn122	Cited
Pruitt, KD et al., Genome Res., 2009, The consensus coding sequence (CCDS) project: identifying a common protein-coding gene set for the human and mouse genomes	19498102	10.1101/gr.080531.108	Cited
Suzek, BE et al., Bioinformatics, 2007, UniRef: comprehensive and non-redundant UniProt reference clusters	17379688	10.1093/bioinformatics/btm098	Cited
Swarbreck, D et al., Nucleic Acids Res., 2008, The Arabidopsis Information Resource (TAIR): gene structure and function annotation	17986450	10.1093/nar/gkm965	Cited
Wieser, D et al., Bioinformatics, 2004, Filtering erroneous protein annotation	15262818	10.1093/bioinformatics/bth938	Cited
Wood, V et al., Nature, 2002, The genome sequence of Schizosaccharomyces pombe	11859360	10.1038/nature724	Cited
Wu, CH et al., Nucleic Acids Res., 2004, PIRSF: family classification system at the Protein Information Resource	14681371	10.1093/nar/gkh097	Cited

The Universal Protein Resource (UniProt) in 2010.

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