Reactome diagram viewer: data structures and strategies to boost performance

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. Supplementary information Supplementary data are available at Bioinformatics online.

[1]  Inna Kuperstein,et al.  NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps , 2013, BMC Systems Biology.

[2]  Charles W. Krueger,et al.  Software reuse , 1992, CSUR.

[3]  Peter D'Eustachio,et al.  Reactome knowledgebase of human biological pathways and processes. , 2011, Methods in molecular biology.

[4]  Pankaj K. Agarwal,et al.  Geometric Range Searching and Its Relatives , 2007 .

[5]  Lincoln Stein,et al.  Reactome knowledgebase of human biological pathways and processes , 2008, Nucleic Acids Res..

[6]  Susumu Goto,et al.  Data, information, knowledge and principle: back to metabolism in KEGG , 2013, Nucleic Acids Res..

[7]  Clemente Izurieta,et al.  Comparison of JSON and XML Data Interchange Formats: A Case Study , 2009, CAINE.

[8]  Donald E. Knuth,et al.  The Art of Computer Programming, Vol. 3: Sorting and Searching , 1974 .

[9]  Guanhua Wang.  Improving Data Transmission in Web Applications via the Translation between XML and JSON , 2011, 2011 Third International Conference on Communications and Mobile Computing.

[10]  Peter J. Denning,et al.  The locality principle , 2005, CACM.

[11]  Yan Chen,et al.  Comparison between JSON and XML in Applications Based on AJAX , 2012, 2012 International Conference on Computer Science and Service System.

[12]  Piotr Gawron,et al.  MINERVA—a platform for visualization and curation of molecular interaction networks , 2016, npj Systems Biology and Applications.

[13]  Henning Hermjakob,et al.  The Reactome pathway knowledgebase , 2013, Nucleic Acids Res..

[14]  Ryan Miller,et al.  WikiPathways: capturing the full diversity of pathway knowledge , 2015, Nucleic Acids Res..

[15]  Sarala M. Wimalaratne,et al.  The Systems Biology Graphical Notation , 2009, Nature Biotechnology.

[16]  Jon Louis Bentley,et al.  Quad trees a data structure for retrieval on composite keys , 1974, Acta Informatica.

[17]  Peter J. Denning,et al.  The working set model for program behavior , 1968, CACM.

[18]  Virpi Roto,et al.  User Experience Evaluation Methods in Academic and Industrial Contexts , 2009 .

[19]  Christina Freytag,et al.  Designing And Engineering Time The Psychology Of Time Perception In Software , 2016 .

[20]  Lincoln Stein,et al.  Reactome pathway analysis: a high-performance in-memory approach , 2017, BMC Bioinformatics.

[21]  Gary D. Bader,et al.  Pathway Commons, a web resource for biological pathway data , 2010, Nucleic Acids Res..