Reactome diagram viewer: data structures and strategies to boost performance

被引：128
作者：
Fabregat, Antonio [1 ,2 ]
Sidiropoulos, Konstantinos [1 ]
Viteri, Guilherme [1 ]
Marin-Garcia, Pablo [3 ,4 ]
Ping, Peipei [5 ,6 ]
Stein, Lincoln [7 ,8 ]
D'Eustachio, Peter [9 ]
Hermjakob, Henning [1 ,10 ]
机构：
[1] EBI, EMBL, Wellcome Genome Campus, Hinxton CB10 1SD, England
[2] Open Targets, Wellcome Genome Campus, Hinxton CB10 1SD, England
[3] Univ Valencia, Fdn Invest INCLIVA, Valencia, Spain
[4] Inst Med Genom, Valencia, Spain
[5] Univ Calif Los Angeles, NIH, Ctr Excellence BD2K, Los Angeles, CA 90095 USA
[6] Univ Calif Los Angeles, Dept Physiol Med & Bioinformat, Los Angeles, CA 90095 USA
[7] Ontario Inst Canc Res, Toronto, ON M5G 0A3, Canada
[8] Univ Toronto, Dept Mol Genet, Toronto, ON M5G 0A3, Canada
[9] NYU, Langone Med Ctr, 550 1St Ave, New York, NY 10016 USA
[10] Natl Ctr Prot Sci, Beijing Inst Radiat Med, Beijing Proteome Res Ctr, State Key Lab Prote, Beijing 102206, Peoples R China
来源：
BIOINFORMATICS | 2018年 / 34卷 / 07期
基金：
美国国家卫生研究院;
关键词：
D O I：
10.1093/bioinformatics/btx752
中图分类号：
Q5 [生物化学];
学科分类号：
071010 ; 081704 ;
摘要：
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.
引用
收藏
页码：1208 / 1214
页数：7
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