Reactome enhanced pathway visualization.

Journal: Bioinformatics (Oxford, England)
PMID: 29077811

Abstract

MOTIVATION: Reactome is a free, open-source, open-data, curated and peer-reviewed knowledge base of biomolecular pathways. Pathways are arranged in a hierarchical structure that largely corresponds to the GO biological process hierarchy, allowing the user to navigate from high level concepts like immune system to detailed pathway diagrams showing biomolecular events like membrane transport or phosphorylation. Here, we present new developments in the Reactome visualization system that facilitate navigation through the pathway hierarchy and enable efficient reuse of Reactome visualizations for users' own research presentations and publications.

Authors

  • Konstantinos Sidiropoulos
    European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK.
  • Guilherme Viteri
    European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK.
  • Cristoffer Sevilla
    European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK.
  • Steve Jupe
    European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK.
  • Marissa Webber
    Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada.
  • Marija Orlic-Milacic
    Ontario Institute for Cancer Research, Toronto, ON, Canada.
  • Bijay Jassal
    Ontario Institute for Cancer Research, Toronto, ON, Canada.
  • Bruce May
    Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada.
  • Veronica Shamovsky
    Department of Biochemistry & Molecular Pharmacology, NYU School of Medicine, New York, New York, United States of America.
  • Corina Duenas
    European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK.
  • Karen Rothfels
    Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada.
  • Lisa Matthews
    Department of Biochemistry & Molecular Pharmacology, NYU. Langone Medical Center, New York, NY, United States.
  • Heeyeon Song
    Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada.
  • Lincoln Stein
    Informatics and Bio-computing, Ontario Institute for Cancer Research, Toronto, Ontario, Canada.
  • Robin Haw
    Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada.
  • Peter D'Eustachio
    Department of Biochemistry & Molecular Pharmacology, NYU. Langone Medical Center, New York, NY, United States.
  • Peipei Ping
    From the NIH BD2K Center of Excellence for Biomedical Computing at UCLA, Los Angeles, CA (P.P., K.W., A.B.); and NIH BD2K KnowEng Center of Excellence for Biomedical Computing at UIUC, Urbana, IL (J.H.). pping38@g.ucla.edu.
  • Henning Hermjakob
    European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
  • Antonio Fabregat
    European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK.

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