title: SBGNViz: A Tool for Visualization and Complexity Management of SBGN Process Description Maps.
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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Computer Engineering Dept, Bilkent University, Ankara, Turkey.
authors.forename: Mecit
authors.initials: M
authors.lastname: Sari
authors.affiliation: Computer Engineering Dept, Bilkent University, Ankara, Turkey.
authors.forename: Istemi
authors.initials: I
authors.lastname: Bahceci
authors.affiliation: Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY, USA; Computer Engineering Dept, Bilkent University, Ankara, Turkey.
authors.forename: Ugur
authors.initials: U
authors.lastname: Dogrusoz
authors.affiliation: Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY, USA.
authors.forename: Selcuk Onur
authors.initials: SO
authors.lastname: Sumer
authors.affiliation: Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY, USA; Tri-Institutional Training Program in Computational Biology and Medicine, New York, NY, USA.
authors.forename: Bülent Arman
authors.initials: BA
authors.lastname: Aksoy
authors.affiliation: Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY, USA.
authors.forename: Özgün
authors.initials: Ö
authors.lastname: Babur
authors.affiliation: Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY, USA.
authors.forename: Emek
authors.initials: E
authors.lastname: Demir
mesh_terms: D022126:Access to Information; D003196:Computer Graphics; D020407:Internet; D015398:Signal Transduction / Q000502:physiology*; D012984:Software; D013223:Statistics as Topic / Q000379:methods*; D049490:Systems Biology / Q000379:methods; D013672:Technology / Q000379:methods*; D064878:Web Browser