Chapter

On the Move to Meaningful Internet Systems 2006: OTM 2006 Workshops

Volume 4277 of the series Lecture Notes in Computer Science pp 710-719

Reactome – A Knowledgebase of Biological Pathways

  • Esther SchmidtAffiliated withEuropean Bioinformatics Institute, (EMBL-EBI)
  • , Ewan BirneyAffiliated withEuropean Bioinformatics Institute, (EMBL-EBI)
  • , David CroftAffiliated withEuropean Bioinformatics Institute, (EMBL-EBI)
  • , Bernard de BonoAffiliated withEuropean Bioinformatics Institute, (EMBL-EBI)
  • , Peter D’EustachioAffiliated withCold Spring Harbor Laboratory, Cold Spring Harbor
  • , Marc GillespieAffiliated withCold Spring Harbor Laboratory, Cold Spring Harbor
  • , Gopal GopinathAffiliated withCold Spring Harbor Laboratory, Cold Spring Harbor
  • , Bijay JassalAffiliated withEuropean Bioinformatics Institute, (EMBL-EBI)
  • , Suzanna LewisAffiliated withDepartment of Molecular and Cell Biology, University of California, Berkeley
    • , Lisa MatthewsAffiliated withCold Spring Harbor Laboratory, Cold Spring Harbor
    • , Lincoln SteinAffiliated withCold Spring Harbor Laboratory, Cold Spring Harbor
    • , Imre VastrikAffiliated withEuropean Bioinformatics Institute, (EMBL-EBI)
    • , Guanming WuAffiliated withCold Spring Harbor Laboratory, Cold Spring Harbor

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