Reactome – A Knowledgebase of Biological Pathways

  • Esther Schmidt
  • Ewan Birney
  • David Croft
  • Bernard de Bono
  • Peter D’Eustachio
  • Marc Gillespie
  • Gopal Gopinath
  • Bijay Jassal
  • Suzanna Lewis
  • Lisa Matthews
  • Lincoln Stein
  • Imre Vastrik
  • Guanming Wu
Conference paper

DOI: 10.1007/11915034_95

Part of the Lecture Notes in Computer Science book series (LNCS, volume 4277)
Cite this paper as:
Schmidt E. et al. (2006) Reactome – A Knowledgebase of Biological Pathways. In: Meersman R., Tari Z., Herrero P. (eds) On the Move to Meaningful Internet Systems 2006: OTM 2006 Workshops. OTM 2006. Lecture Notes in Computer Science, vol 4277. Springer, Berlin, Heidelberg

Abstract

Reactome (www.reactome.org) is a curated database describing very diverse biological processes in a computationally accessible format. The data is provided by experts in the field and subject to a peer review process. The core unit of the Reactome data model is the reaction. The entities participating in reactions form a network of biological interactions. Reactions are grouped into pathways. Reactome data are cross-referenced to a wide selection of publically available databases (such as UniProt, Ensembl, GO, PubMed), facilitating overall integration of biological data. In addition to the manually curated, mainly human reactions, electronically inferred reactions to a wide range of other species, are presented on the website. All Reactome reactions are displayed as arrows on a Reactionmap. The Skypainter tool allows visualisation of user-supplied data by colouring the Reactionmap. Reactome data are freely available and can be downloaded in a number of formats.

Keywords

knowledgebase pathways biological processes 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Esther Schmidt
    • 1
  • Ewan Birney
    • 1
  • David Croft
    • 1
  • Bernard de Bono
    • 1
  • Peter D’Eustachio
    • 2
  • Marc Gillespie
    • 2
  • Gopal Gopinath
    • 2
  • Bijay Jassal
    • 1
  • Suzanna Lewis
    • 3
  • Lisa Matthews
    • 2
  • Lincoln Stein
    • 2
  • Imre Vastrik
    • 1
  • Guanming Wu
    • 2
  1. 1.European Bioinformatics Institute, (EMBL-EBI)Hinxton, CambridgeshireUK
  2. 2.Cold Spring Harbor LaboratoryCold Spring HarborNew YorkUSA
  3. 3.Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyUSA

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