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Nucleic Acids Research 2005 33(Database Issue):D428-D432; doi:10.1093/nar/gki072
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Nucleic Acids Research, 2005, Vol. 33, Database issue D428-D432
© 2005, the authors
Nucleic Acids Research, Vol. 33, Database issue © Oxford University Press 2005; all rights reserved

Reactome: a knowledgebase of biological pathways

G. Joshi-Tope1,*, M. Gillespie1,3, I. Vastrik2, P. D'Eustachio1,4, E. Schmidt2, B. de Bono2, B. Jassal2, G.R. Gopinath1, G.R. Wu1, L. Matthews1, S. Lewis5, E. Birney2 and L. Stein1

1 Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA, 2 European Bioinformatics Institute, Hinxton, Cambridge, UK, 3 St Johns University, NY, USA, 4 New York University School of Medicine, NY, USA and 5 University of California, Berkeley, CA, USA

* To whom correspondence should be addressed. Tel: +1 516 367 6904; Fax: +1 516 367 6851; Email: joshi{at}cshl.org

Received August 19, 2004; Revised and Accepted October 6, 2004

Reactome, located at http://www.reactome.org is a curated, peer-reviewed resource of human biological processes. Given the genetic makeup of an organism, the complete set of possible reactions constitutes its reactome. The basic unit of the Reactome database is a reaction; reactions are then grouped into causal chains to form pathways. The Reactome data model allows us to represent many diverse processes in the human system, including the pathways of intermediary metabolism, regulatory pathways, and signal transduction, and high-level processes, such as the cell cycle. Reactome provides a qualitative framework, on which quantitative data can be superimposed. Tools have been developed to facilitate custom data entry and annotation by expert biologists, and to allow visualization and exploration of the finished dataset as an interactive process map. Although our primary curational domain is pathways from Homo sapiens, we regularly create electronic projections of human pathways onto other organisms via putative orthologs, thus making Reactome relevant to model organism research communities. The database is publicly available under open source terms, which allows both its content and its software infrastructure to be freely used and redistributed.

The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use permissions, please contact journals.permissions{at}oupjournals.org.


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