Reactome: a database of reactions, pathways and biological processes

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.

DOI: 10.1093/nar/gkq1018

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@inproceedings{Croft2011ReactomeAD, title={Reactome: a database of reactions, pathways and biological processes}, author={David Croft and Gavin O'Kelly and Guanming Wu and Robin Haw and Marc E Gillespie and Lisa Matthews and Michael Caudy and Phani Garapati and Gopal Gopinath and Bijay Jassal and Steven Jupe and Irina Kalatskaya and Shahana Mahajan and Bruce May and Nelson Ndegwa and Esther Schmidt and Veronica Shamovsky and Christina K. Yung and Ewan Birney and Henning Hermjakob and Peter D'Eustachio and Lincoln Stein}, booktitle={Nucleic Acids Research}, year={2011} }