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. 2005 Jan 1;33(Database issue):D428-32.
doi: 10.1093/nar/gki072.

Reactome: a knowledgebase of biological pathways

G Joshi-Tope  1 , M Gillespie, I Vastrik, P D'Eustachio, E Schmidt, B de Bono, B Jassal, G R Gopinath, G R Wu, L Matthews, S Lewis, E Birney, L Stein
Affiliations

Reactome: a knowledgebase of biological pathways

G Joshi-Tope et al. Nucleic Acids Res. .

Abstract

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.

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Figures

Figure 1
Figure 1
The Reaction map shows the reactions annotated in Reactome. The reaction clusters of top-level processes are shown.
Figure 2
Figure 2
Screenshots of an example Advanced Search query are shown. The database was queried to find all reactions in H.sapiens that have ATP as input, ADP as output.
Figure 3
Figure 3
The OMIM Morbid Map of the Human Genome lists all genes whose mutant forms are causally associated with human disease. Each Reactome event in which, one or more such gene products are involved as input, catalyst or regulator is shown in red. Some examples of diseases that map to Reactome reactions are shown.
See this image and copyright information in PMC

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