SBGNViz: A tool for visualization and complexity management of SBGN process description maps

Mecit Sari, Istemi Bahceci, Ugur Dogrusoz, Selcuk Onur Sumer, Bülent Arman Aksoy, Özgün Babur, Emek Demir

Research output: Contribution to journalArticle

13 Scopus citations

Abstract

Background Information about cellular processes and pathways is becoming increasingly available in detailed, computable standard formats such as BioPAX and SBGN. Effective visualization of this information is a key recurring requirement for biological data analysis, especially for -omic data. Biological data analysis is rapidly migrating to web based platforms; thus there is a substantial need for sophisticated web based pathway viewers that support these platforms and other use cases. Results Towards this goal, we developed a web based viewer named SBGNViz for process description maps in SBGN (SBGN-PD). SBGNViz can visualize both BioPAX and SBGN formats. Unique features of SBGNViz include the ability to nest nodes to arbitrary depths to represent molecular complexes and cellular locations, automatic pathway layout, editing and highlighting facilities to enable focus on sub-maps, and the ability to inspect pathway members for detailed information from EntrezGene. SBGNViz can be used within a web browser without any installation and can be readily embedded into web pages. SBGNViz has two editions built with ActionScript and JavaScript. The JavaScript edition, which also works on touch enabled devices, introduces novel methods for managing and reducing complexity of large SBGN-PD maps for more effective analysis. Conclusion SBGNViz fills an important gap by making the large and fast-growing corpus of rich pathway information accessible to web based platforms. SBGNViz can be used in a variety of contexts and in multiple scenarios ranging from visualization of the results of a single study in a web page to building data analysis platforms.

Original languageEnglish (US)
Article numbere0128985
JournalPloS one
Volume10
Issue number6
DOIs
StatePublished - Jun 1 2015

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)
  • General

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    Sari, M., Bahceci, I., Dogrusoz, U., Sumer, S. O., Aksoy, B. A., Babur, Ö., & Demir, E. (2015). SBGNViz: A tool for visualization and complexity management of SBGN process description maps. PloS one, 10(6), [e0128985]. https://doi.org/10.1371/journal.pone.0128985