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Nucleic Acids Res. 2016 Jan 4;44(D1):D481-7. doi: 10.1093/nar/gkv1351. Epub 2015 Dec 9.

The Reactome pathway Knowledgebase.

Author information

  • 1European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
  • 2Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada College of Pharmacy and Health Sciences, St John's University, Queens, NY 11439, USA.
  • 3Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada.
  • 4NYU School of Medicine, New York, NY 10016, USA.
  • 5Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A1, Canada Lincoln.Stein@oicr.on.ca.
  • 6European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK National Center for Protein Sciences, Beijing, China hhe@ebi.ac.uk.
  • 7NYU School of Medicine, New York, NY 10016, USA deustp01@med.nyu.edu.

Abstract

The Reactome Knowledgebase (www.reactome.org) provides molecular details of signal transduction, transport, DNA replication, metabolism and other cellular processes as an ordered network of molecular transformations-an extended version of a classic metabolic map, in a single consistent data model. Reactome functions both as an archive of biological processes and as a tool for discovering unexpected functional relationships in data such as gene expression pattern surveys or somatic mutation catalogues from tumour cells. Over the last two years we redeveloped major components of the Reactome web interface to improve usability, responsiveness and data visualization. A new pathway diagram viewer provides a faster, clearer interface and smooth zooming from the entire reaction network to the details of individual reactions. Tool performance for analysis of user datasets has been substantially improved, now generating detailed results for genome-wide expression datasets within seconds. The analysis module can now be accessed through a RESTFul interface, facilitating its inclusion in third party applications. A new overview module allows the visualization of analysis results on a genome-wide Reactome pathway hierarchy using a single screen page. The search interface now provides auto-completion as well as a faceted search to narrow result lists efficiently.

PMID:
26656494
PMCID:
PMC4702931
DOI:
10.1093/nar/gkv1351
[PubMed - indexed for MEDLINE]
Free PMC Article
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