The Universal Protein Resource (UniProt)
Open accessAbstract
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.
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The creation of large databases such as GenBank and UniProt have led to gene and protein sequence data being deposited in a common format.
“The creation of large databases such as GenBank and UniProt have led to gene and protein sequence data being deposited in a common format.”
From Open Science 2.0: Towards a truly collaborative research ecosystem (2023) · cites this paper as [86]
This standardization fueled a revolution in bioinformatics, allowing large-scale analysis at the touch of a button.
“This standardization fueled a revolution in bioinformatics, allowing large-scale analysis at the touch of a button [84–87].”
From Open Science 2.0: Towards a truly collaborative research ecosystem (2023) · cites this paper as [86]
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- Authors
- Bairoch, A.
- Affiliations
- SIB Swiss Institute of Bioinformatics (CH)
- Corresponding author
- Bairoch, A.
- ORCID
- Bairoch, A.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2004-12-17
- Volume
- 33
- Issue
- Database issue
- Pages
- D154-D159
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC540024
- OpenAlex
- W2161062388
- Cited by
- 3,774
- References
- 29
- Citations by year
- 2026: 28 · 2025: 60 · 2024: 68 · 2023: 72 · 2022: 83 · 2021: 110 · 2020: 117 · 2019: 103 · 2018: 99 · 2017: 93 · 2016: 159 · 2015: 153 · 2014: 167 · 2013: 199 · 2012: 208
- FWCI
- 73.09
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- other-oa
- Locations
- Nucleic Acids Research (publishedVersion, other-oa)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Archive ouverte UNIGE (University of Geneva) (publishedVersion, other-oa)
- reroDoc Digital Library (submittedVersion)
- UCL Discovery (University College London) (submittedVersion)
- Archive ouverte UNIGE (University of Geneva) (submittedVersion, cc-by)
- Funders
- National Science Foundation (0205470, 0138188)
- Australian Government
- European Commission
- National Institutes of Health
- National Human Genome Research Institute (U01 HG02712-01, 1R01HGO2273-01, U01HG002712, R01HG002273)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Keywords
- UniProt, protein sequence databases, Swiss-Prot, TrEMBL, protein annotation, post-translational modification, protein toxicity, sequence-structure mapping, Protein Data Bank, digital object identifiers
- MeSH terms
- Amino Acid Sequence, Proteins, User-Computer Interface, Systems Integration, Databases, Protein
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