Spotlight: Reactome

This week, we’re pleased to profile the Reactome database in our weekly Spotlight series. Thanks to Robin Haw and Peter D’Eustachio from Reactome for taking the time to talk with us, and for registering the Reactome BioGPS plugin.

In one tweet or less, introduce us to your website.
Reactome is a free, open source, expert-authored, peer-reviewed and highly reliable knowledgebase of pathways and reactions in human biology.

Why is your database unique and special?
The Reactome data model generalizes the concept of a biochemical reaction to encompass any transformation of an input set of physical entities into an output set, and thus allows us to capture processes ranging from signaling, the regulation of cell cycle progression, transcriptional regulation, DNA repair, influenza and HIV replication in infected host cells and blood coagulation to classical intermediary metabolism in a single internally consistent, computationally navigable format. In addition to manually curated human pathways, Reactome provides orthology-based computational predictions of pathways for 22 model organisms. Additional curated pathway web resources that use the Reactome data model have been created by collaborating groups for the plant Arabidopsis, fruit fly and chicken. All of Reactome’s content and software infrastructure are publicly available under open source terms.

Why did you create your website?
The rationale behind Reactome is to convey the rich information in the visual representations of biological pathways familiar from textbooks and articles in a computationally accessible, detailed, and freely accessible format.

Who is your target audience?
The website’s textbook-like format allows biologists, clinicians, scientists, teachers and students the opportunity to browse and search Reactome. For chemo- and bioinformaticians we provide our interaction, reaction and pathway data in formats that include downloadable flat, MySQL, BioPAX, SBML and PSI-MITAB files and also provide access through our Web Services APIs.

What’s your greatest success story so far?
We are particularly proud of constructing the most nearly comprehensive pathway annotation of the network of reactions and processes triggered by EGF (Epidermal Growth Factor) signaling (Bauer-Mehren et al. 2009).

What improvements are coming in the future?
Curators are updating old pathways and curating new ones that focus on stem cell biology, epigenetic regulation, developmental processes and human disease. A redesign of our website together with the development of new and improved pathway analysis and visualization tools is currently underway. We are particularly excited about the upcoming release of a SBGN-based Entity Level-Viewer to display pathway diagrams and support interrogation of user-generated expression data. Reactome will continue to support Cytoscape, SBML and BioPAX development groups. We are eager for contributions from the community and would welcome inquiries from researchers interested in contributing information on pathways in their area of expertise. Please contact helpreactomeorg  (helpreactomeorg)  .

Who is the team behind your website?
Reactome is a collaboration amongst groups at the Ontario Institute for Cancer Research, New York University Medical Center, Cold Spring Harbor Laboratory, and The European Bioinformatics Institute. The team, led by Lincoln Stein, Ewan Birney, Peter D’Eustachio and Henning Hermjakob, includes curators and developers Michael Caudy, David Croft, Phani Garapati, Marc Gillespie, Robin Haw, Bijay Jassal, Steve Jupe, Alexander Kanapin, Lisa Matthews, Bruce May, Gavin O’Kelly, Esther Schmidt and Guanming Wu. The development of Reactome is supported by grant P41 HG003751 from the National Human Genome Research Institute at the US National Institutes of Health and grant LSHG-CT-2003-518254 from The European Union (6th Framework Programme).

If you have a chance to check out the site, the Reactome developer team is soliciting feedback via a user survey. Thanks to the Robin, Peter and the Reactome team for registering their site as a BioGPS plugin, and for participating in our Spotlight series.