The Universal Protein Resource (UniProt): an expanding universe of protein information

By Cathy H. Wu, Rolf Apweiler, Amos Bairoch, D. Natale, W. C. Barker, Brigitte Boeckmann, Serenella Ferro, Elisabeth Gasteiger, Hongzhan Huang, Rodrigo Lopez and 6 more. Nucleic Acids Res., 2005

1,138 citations recorded by the source corpus.

The Universal Protein Resource (UniProt) provides a central resource on protein sequences and functional annotation with three database components, each addressing a key need in protein bioinformatics. The UniProt Knowledgebase (UniProtKB), comprising the manually annotated UniProtKB/Swiss-Prot section and the automatically annotated UniProtKB/TrEMBL section, is the preeminent storehouse of protein annotation. The extensive cross-references, functional and feature annotations and literature-based evidence attribution enable scientists to analyse proteins and query across databases. The UniProt Reference Clusters (UniRef) speed similarity searches via sequence space compression by merging sequences that are 100% (UniRef100), 90% (UniRef90) or 50% (UniRef50) identical. Finally, the UniProt Archive (UniParc) stores all publicly available protein sequences, containing the history of sequence data with links to the source databases. UniProt databases continue to grow in size and in availability of information. Recent and upcoming changes to database contents, formats, controlled vocabularies and services are described. New download availability includes all major releases of UniProtKB, sequence collections by taxonomic division and complete proteomes. A bibliography mapping service has been added, and an ID mapping service will be available soon. UniProt databases can be accessed online at or downloaded at .

Subfields: Molecular Biology, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/2a8972b2ba205088fb4de2dd1822306819591225

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Citations in the corpus

Lack of an HSP70 heat shock response in two Antarctic marine invertebrates (2008, methodology): “Consensus sequences were database searched using WU-blast2 (WU-blastx) (Altschul et al, 1997) against Uniprot (Boeckmann et al, 2003; Wu et al, 2006) to assign their HSP identity.”
DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis (2007, methodology): “The construction of the DAVID Knowledgebase consists of two major steps: 1) Improve cross-reference capability across redundant IDs, particularly for the IDs found in the NCBI and Uni- Prot systems [1, 2 ], with a novel algorithm”
The Edinburgh human metabolic network reconstruction and its functional analysis (2007, background): “A bow-tie connectivity structure is rediscovered from a functional rather than structural point of view, and the distribution of disease related metabolic reactions in the bow-tie structure was investigated.”
BisoGenet: a new tool for gene network building, visualization and analysis (2010, background): “Main protein information is provided by the major protein universal resource Uniprot[31].”
PredictSNP: Robust and Accurate Consensus Classifier for Prediction of Disease-Related Mutations (2014, background): “The final source was Humsavar [42], which is a distinct unit of UniProt containing 36,994 neutral and disease-related mutations found in Uni-protKB/SwissProt entries.”
Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data (2011, positive): “It extended the 3 ′ UTR in 2,918 transcripts (2,819 loci, median length, 20; average length, 248; Supplementary Fig.”
Automated Protein Structure Modeling with SWISS-MODEL Workspace and the Protein Model Portal (2012, background): “It is sufficient to provide the sequence or the UniProt accession code (80) of the protein of interest and select among a list of available tools:”
State of the nation in data integration for bioinformatics (2008, background): “For example, a Uniprot [6] entry refers to a class of proteins (via a representation of its primary structure), a class of variant proteins or some viral protein, whereas a KEGG [7] entry refers to a collection of proteins involved in some pathway.”
MitoCarta2.0: an updated inventory of mammalian mitochondrial proteins (2015, background): “Similarly, UniProt (27,28) includes over 1094 human genes linked to mitochondria (of which 76% are in MitoCarta2.”
Advancing translational research with the Semantic Web (2007, methodology): “Our approach was to collect gene and protein synonyms from a variety of public databases – Entrez Gene, UniProt, OMIM [77], and Enzyme [78].”
FlyMine: an integrated database for Drosophila and Anopheles genomics (2007, methodology): “Currently, we can load any data that conform to several different formats: GFF3 [30] for genome annotation and genomic features (for example, Dnase I footprints, microarray oligonucleotide and genome tiling amplimers), PSI-MI [31,32] for data describing protein interactions or complexes, MAGE [33,34”
The database of experimentally supported targets: a functional update of TarBase (2008, background): “The ‘Gene information’ category gathers mostly biological properties of the target gene like the protein type, Ensembl and SwissProt IDs and chromosome location, providing direct links to Ensembl, SwissProt and the UCSC browser respectively.”
PhosphoSitePlus, 2014: mutations, PTMs and recalibrations (2014, methodology): “We have always considered UniPROTKB SwissProt (9), followed by NCBI RefSeq NP (10), to be the most reliable protein sequence resource.”