4.7 Article

Reactome diagram viewer: data structures and strategies to boost performance

期刊

BIOINFORMATICS
卷 34, 期 7, 页码 1208-1214

出版社

OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btx752

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资金

  1. National Institutes of Health BD2K [U54 GM114833]
  2. National Human Genome Research Institute at the National Institutes of Health [U41 HG003751]
  3. European Bioinformatics Institute (EMBL-EBI)
  4. Open Targets (The target validation platform)
  5. Medicine by Design (University of Toronto)
  6. National Institutes of Health [U54 GM114833]
  7. NATIONAL HUMAN GENOME RESEARCH INSTITUTE [U41HG003751] Funding Source: NIH RePORTER
  8. NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES [U54GM114833] Funding Source: NIH RePORTER

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Motivation: Reactome is a free, open-source, open-data, curated and peer-reviewed knowledge-base 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.

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