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Protein sequence databases have become a crucial resource for molecular biologists, both as repositories
for protein functional and structural data and as starting points for future experiments. The UniProt
consortium aims to support biological research by maintaining a high quality database that serves as a
stable, comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase,
with extensive cross-references and querying interfaces freely accessible to the scientific community.
The UniProt Consortium
The UniProt Consortium is comprised of the European Bioinformatics Institute
(EBI), the Swiss Institute
of Bioinformatics (SIB),
and the Protein Information Resource (PIR).
EBI, located at the Wellcome Trust
Genome Campus in Hinxton, UK, hosts a large resource of bioinformatics databases and services. SIB,
located in Geneva, Switzerland, maintains the ExPASy
(Expert Protein Analysis System) servers that are a central resource for
proteomics tools and databases. PIR, hosted by the National Biomedical Research Foundation
(NBRF) at the
Georgetown University Medical Center in
Washington, DC, USA, is heir to the oldest protein sequence database, Margaret Dayhoff's Atlas of
Protein Sequence and Structure. In 2002, EBI, SIB, and PIR joined forces as the UniProt Consortium.
The Roots of UniProt Databases
Each consortium member is heavily involved in protein database maintenance and annotation. Until
recently, EBI and SIB together produced Swiss-Prot
and TrEMBL, while PIR produced the
Protein Sequence Database (PIR-PSD).
These databases coexisted with differing protein sequence coverage and annotation priorities.
Swiss-Prot is recognized as the gold standard of protein annotation, with extensive cross-references,
literature citations, and computational analyses provided by expert curators. Recognizing that
sequence data were being generated at a pace exceeding Swiss-Prot's ability to keep up, TrEMBL
(Translated EMBL Nucleotide Sequence Data Library) was created to provide automated
annotations for those proteins not in Swiss-Prot. Meanwhile, PIR maintained the PIR-PSD and
related databases, including iProClass,
a database of protein sequences and curated families. The consortium members — all dedicated to the same goal
of providing expansive and meaningful protein annotation, and all with solid foundations stemming from decades
of activity — decided to pool their overlapping (and, importantly, their complementary) resources, efforts,
and expertise. The UniProt databases build upon these solid foundations.
Organization of UniProt Databases
The UniProt databases are:
The UniProt Archive (UniParc) provides a stable, comprehensive sequence collection without
redundant sequences by storing the complete body of publicly available protein sequence data.
The UniProt Knowledgebase (UniProtKB) is the central database of protein sequences with
accurate, consistent, and rich sequence and functional annotation.
The UniProt Reference Clusters (UniRef) databases provide non-redundant
reference clusters based on the UniProt knowledgebase (and
selected UniParc records)
in order to obtain complete coverage of sequence space at several
resolutions.
The UniProt Metagenomic and Environmental Sequences (UniMES) database is
a repository specifically developed for metagenomic and environmental data.
Funding for UniProt
UniProt is mainly supported by the National Institutes of Health (NIH)
grant 1 U01 HG02712-01.
Minor support for the EBI's involvement in UniProt comes from FELICS
(021902RII3) and from the NIH grant 1R01HGO2273-01.
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