Reactome: a database of reactions, pathways and biological processes

David Croft(European Bioinformatics Institute), Gavin O’Kelly(European Bioinformatics Institute), Guanming Wu(Ontario Institute for Cancer Research), Robin Haw(Ontario Institute for Cancer Research), Marc Gillespie(St. John's University), Lisa Matthews(New York University), Michael Caudy(Ontario Institute for Cancer Research), Phani Garapati(European Bioinformatics Institute), Gopal Gopinath(Center for Food Safety and Applied Nutrition), Bijay Jassal(European Bioinformatics Institute), S Jupe(European Bioinformatics Institute), Irina Kalatskaya(Ontario Institute for Cancer Research), Sandeep Mahajan(City University of New York), Bruce May(Ontario Institute for Cancer Research), Nelson Ndegwa(European Bioinformatics Institute), Esther Schmidt(European Bioinformatics Institute), Veronica Shamovsky(New York University), Christina K. Yung(Ontario Institute for Cancer Research), Ewan Birney(European Bioinformatics Institute), Henning Hermjakob(European Bioinformatics Institute), Peter D’Eustachio(New York University), Lincoln Stein(Ontario Institute for Cancer Research)
Nucleic Acids Research
November 9, 2010
10.1093/nar/gkq1018
Cited by 1,789Open Access
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Abstract

Reactome (http://www.reactome.org) is a collaboration among groups at the Ontario Institute for Cancer Research, Cold Spring Harbor Laboratory, New York University School of Medicine and The European Bioinformatics Institute, to develop an open source curated bioinformatics database of human pathways and reactions. Recently, we developed a new web site with improved tools for pathway browsing and data analysis. The Pathway Browser is an Systems Biology Graphical Notation (SBGN)-based visualization system that supports zooming, scrolling and event highlighting. It exploits PSIQUIC web services to overlay our curated pathways with molecular interaction data from the Reactome Functional Interaction Network and external interaction databases such as IntAct, BioGRID, ChEMBL, iRefIndex, MINT and STRING. Our Pathway and Expression Analysis tools enable ID mapping, pathway assignment and overrepresentation analysis of user-supplied data sets. To support pathway annotation and analysis in other species, we continue to make orthology-based inferences of pathways in non-human species, applying Ensembl Compara to identify orthologs of curated human proteins in each of 20 other species. The resulting inferred pathway sets can be browsed and analyzed with our Species Comparison tool. Collaborations are also underway to create manually curated data sets on the Reactome framework for chicken, Drosophila and rice.

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