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UniProt: the Universal Protein knowledgebase.

Rolf Apweiler1, Amos Bairoch, Cathy H Wu

  • 1The EMBL Outstation--European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. apweiler@ebi.ac.uk

Nucleic Acids Research
|December 19, 2003
PubMed
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The Universal Protein Knowledgebase (UniProt) unites Swiss-Prot, TrEMBL, and PIR databases to offer a comprehensive, annotated protein sequence resource. This initiative provides enhanced data access and encourages community data submission for protein research.

Area of Science:

  • Bioinformatics
  • Proteomics
  • Molecular Biology

Background:

  • Protein sequence and functional information was previously fragmented across multiple databases.
  • A unified, authoritative resource was needed to streamline access for the scientific community.

Purpose of the Study:

  • To establish the Universal Protein Knowledgebase (UniProt) by integrating Swiss-Prot, TrEMBL, and PIR.
  • To create a comprehensive, classified, and accurately annotated protein sequence knowledgebase.
  • To provide robust query interfaces and extensive cross-references for protein data.

Main Methods:

  • Unification of existing protein database activities (Swiss-Prot, TrEMBL, PIR).
  • Establishment of a central database with manually curated (Swiss-Prot) and automatically classified/annotated (TrEMBL) sections.

Related Experiment Videos

  • Development of supplementary databases: UniProt Non-Redundant Reference (UniRef) for efficient searching and UniProt Archive (UniParc) for comprehensive daily updates.

    • Main Results:

    • The formation of the Universal Protein Knowledgebase (UniProt) consortium.
    • A unified resource offering both manually curated and automatically annotated protein entries.
    • Availability of specialized databases (UniRef, UniParc) for diverse search needs.
    • Online accessibility and downloadable data formats for broad user access.

    Conclusions:

    • UniProt provides a centralized, authoritative, and richly annotated resource for protein sequences and functions.
    • The consortium enhances data accessibility and usability for the global scientific community.
    • Community data submission is encouraged to further enrich the UniProt knowledgebase.