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Bioinformatics. 2018 Apr 1;34(7):1208-1214. doi: 10.1093/bioinformatics/btx752.

Reactome diagram viewer: data structures and strategies to boost performance.

Author information

1
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK.
2
Open Targets, Wellcome Genome Campus, Hinxton CB10 1SD, UK.
3
Fundación Investigación INCLIVA, Universitat de València, Valencia, Spain.
4
Instituto de Medicina Genomica, Valencia, Spain.
5
NIH BD2K Center of Excellence and Department of Physiology, Medicine and Bioinformatics, University of California, Los Angeles, CA 90095, USA.
6
Ontario Institute for Cancer Research, Toronto ON M5G 0A3, Canada.
7
Department of Molecular Genetics, University of Toronto, Toronto ON M5G 0A3, Canada.
8
NYU Langone Medical Center, New York NY 10016, USA.
9
State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, National Center for Protein Sciences, Beijing 102206, China.

Abstract

Motivation:

Reactome is a free, open-source, open-data, curated and peer-reviewed knowledgebase of biomolecular pathways. For web-based pathway visualization, Reactome uses a custom pathway diagram viewer that has been evolved over the past years. Here, we present comprehensive enhancements in usability and performance based on extensive usability testing sessions and technology developments, aiming to optimize the viewer towards the needs of the community.

Results:

The pathway diagram viewer version 3 achieves consistently better performance, loading and rendering of 97% of the diagrams in Reactome in less than 1 s. Combining the multi-layer html5 canvas strategy with a space partitioning data structure minimizes CPU workload, enabling the introduction of new features that further enhance user experience. Through the use of highly optimized data structures and algorithms, Reactome has boosted the performance and usability of the new pathway diagram viewer, providing a robust, scalable and easy-to-integrate solution to pathway visualization. As graph-based visualization of complex data is a frequent challenge in bioinformatics, many of the individual strategies presented here are applicable to a wide range of web-based bioinformatics resources.

Availability and implementation:

Reactome is available online at: https://reactome.org. The diagram viewer is part of the Reactome pathway browser (https://reactome.org/PathwayBrowser/) and also available as a stand-alone widget at: https://reactome.org/dev/diagram/. The source code is freely available at: https://github.com/reactome-pwp/diagram.

Contact:

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

Supplementary information:

Supplementary data are available at Bioinformatics online.

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