The Universal Protein Resource (UniProt) in 2010.

💬 Chat with this paper

paper Cited Public

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

#	Section	Preview
0	INTRODUCTION	UniProt strives to provide a centralized repository of protein sequences with comprehensive coverage…
1	THE UNIPROT DATABASES — The UniProt Knowledgebase (UniProtKB)	UniProtKB consists of two sections, UniProtKB/Swiss-Prot and UniProtKB/TrEMBL. The former contains…
2	THE UNIPROT DATABASES — The UniProt Knowledgebase (UniProtKB)	in Spearmint (2) or manually curated rules (UniRule) (3–6) based on protein families.…
3	THE UNIPROT DATABASES — The UniProt Reference Clusters (UniRef)	UniRef provides clustered sets of all sequences from UniProtKB (including splice forms as separate…
4	THE UNIPROT DATABASES — The UniProt Reference Clusters (UniRef)	sequence and name; the number of members and the lowest common taxonomy node are also included.…
5	THE UNIPROT DATABASES — UniProt Archive (UniParc)	UniParc is the main sequence storehouse and is a comprehensive repository that reflects the history…
6	THE UNIPROT DATABASES — The UniProt Metagenomic and Environmental Sequences database (UniMES)	The UniProt Knowledgebase contains entries with a known taxonomic source. However, the expanding…
7	MANUAL ANNOTATION IN UNIPROTKB	UniProtKB/Swiss-Prot contains manually annotated records with information extracted from literature…
8	MANUAL ANNOTATION IN UNIPROTKB	The annotation activities of the UniProtKB/Swiss-Prot can be divided into two parts.
9	MANUAL ANNOTATION IN UNIPROTKB — Model organism-oriented annotation	UniProtKB/Swiss-Prot provides annotated entries for many species, but concentrates on the annotation…
10	MANUAL ANNOTATION IN UNIPROTKB — Transversal annotation	Transversal annotation focuses on issues common to all organisms, such as post-translational…
11	MANUAL ANNOTATION IN UNIPROTKB — Transversal annotation	For more information on UniProt’s annotation programs, please see…
12	PROGRESS REPORT — UniProtKB annotation — Revisiting the human proteome	Following the publication in UniProt release 14.1 of the first draft of the complete human proteome,…
13	PROGRESS REPORT — UniProtKB annotation — Revisiting the human proteome	As part of the review process, we are using information extraction tools such as the STRING database…
14	PROGRESS REPORT — UniProtKB annotation — Revisiting the human proteome	a collaborative effort to identify a core set of consistently annotated and high quality human and…
15	PROGRESS REPORT — UniProtKB annotation — Complete Schizosaccharomyces pombe proteome in UniProtKB/Swiss-Prot	The annotation effort towards proteins from model organisms recently led to the integration into…
16	PROGRESS REPORT — UniProtKB annotation — Complete Schizosaccharomyces pombe proteome in UniProtKB/Swiss-Prot	The availability of the complete set of both S. cerevisiae and S. pombe proteins and the…
17	PROGRESS REPORT — UniProtKB annotation — Viral protein annotation program (VPAP)	Started in 2004, the viral protein annotation program seeks to provide a detailed review on viral…
18	PROGRESS REPORT — UniProtKB annotation — Viral protein annotation program (VPAP)	UniProtKB/Swiss-Prot release 57.6 contains 14 233 annotated viral entries. Viral entries are created…
19	PROGRESS REPORT — UniProtKB annotation — Dictyostelium annotation program	UniProt and dictyBase, the model organism database (MOD) for Dictyostelium discoideum, have…

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.

In this knowledge base