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Reactome


NAR Molecular Biology Database Collection entry number 612
Croft D, Mundo AF, Haw R, Milacic M, Weiser J, Wu G, Caudy M, Garapati P, Gillespie M, Kamdar MR, Jassal B, Jupe S, Matthews L, May B, Palatnik S, Rothfels K, Shamovsky V, Song H, Williams M, Birney E, Hermjakob H, Stein L, D'Eustachio P.
European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada, College of Pharmacy and Health Sciences, St. John's University, Queens, NY 11439, USA, NYU School of Medicine, New York, NY 10016, USA, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA and Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A1, Canada.

Database Description

Reactome is a curated database of biological processes in humans. It covers biological pathways ranging from the basic processes of metabolism to high-level processes such as hormonal signalling. While Reactome is targeted at human pathways, it also includes many individual biochemical reactions from non-human systems such as rat, mouse, fugu fish and zebra fish. This makes the database relevant to the large number of researchers who work on model organisms. All the information in Reactome is backed up by its provenance: either a literature citation or an electronic inference based on sequence similarity. Our ontology ensures that the various events are linked in an appropriate spatial and temporal context.

The basic information in Reactome is provided by bench biologists who are experts in that domain of biology. The information is then managed and edited by the Reactome staff at CSHL and the EBI, and entered into a relational database. They are then reviewed by other biological researchers for consistency and accuracy. Following peer-review, the information is published to the web.

Reactome supersedes an earlier project called The Genome Knowledgebase and incorporates all the information previously available in its predecessor. Reactome sports a radically redesigned user interface in which the entire set of human pathways known to the database are represented as a series of constellations in a "starry sky." The starry sky can be used to navigate through the universe of human reactions and is invaluable to visualize connections between pathways, some of which will be surprising to biologists who are not familiar with pathways outside their domain of research.

References

Joshi-Tope G., Vastrik I., Gopinathrao G., Matthews L., Schmidt E., Gillespie M., D'Eustachio P., Jassal B., Lewis S., Wu G., Birney E., and Stein L. 2003. The Genome Knowledgebase: A Resource for Biologists and Bioinformaticists. Cold Spring Harbor Symposia on Quantitative Biology. Volume LXVIII. 2003 Cold Spring Harbor laboratory Press 0-87969-709-1/04.

Subcategory: Metabolic pathways

Go to the abstract in the NAR 2014 Database Issue.
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