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Bioinformatics. 2017 Nov 1;33(21):3461-3467. doi: 10.1093/bioinformatics/btx441.

Reactome enhanced pathway visualization.

Author information

1
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK.
2
Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada.
3
NYU Langone Medical Center, New York, NY 10016, USA.
4
Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 0A3, Canada.
5
Department of Physiology, Medicine and Bioinformatics, NIH BD2K Center of Excellence, University of California, Los Angeles, CA 90095, USA.
6
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK.
7
State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, National Center for Protein Sciences - Beijing, Beijing 102206, China.
8
OpenTargets, Wellcome Genome Campus, Hinxton CB10 1SD, UK.

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.

Results:

For the higher levels of the hierarchy, Reactome now provides scalable, interactive textbook-style diagrams in SVG format, which are also freely downloadable and editable. Repeated diagram elements like 'mitochondrion' or 'receptor' are available as a library of graphic elements. Detailed lower-level diagrams are now downloadable in editable PPTX format as sets of interconnected objects.

Availability and implementation:

http://reactome.org.

Contact:

fabregat@ebi.ac.uk or hhe@ebi.ac.uk.

PMID:
29077811
PMCID:
PMC5860170
DOI:
10.1093/bioinformatics/btx441
[Indexed for MEDLINE]
Free PMC Article

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