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

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dc.citation.issueNumber6en_US
dc.citation.volumeNumber10en_US
dc.contributor.authorSari, M.en_US
dc.contributor.authorBahceci I.en_US
dc.contributor.authorDogrusoz, U.en_US
dc.contributor.authorSumer, S.O.en_US
dc.contributor.authorAksoy, B.A.en_US
dc.contributor.authorBabur O.en_US
dc.contributor.authorDemir, E.en_US
dc.date.accessioned2016-02-08T09:51:11Z
dc.date.available2016-02-08T09:51:11Z
dc.date.issued2015en_US
dc.departmentDepartment of Computer Engineeringen_US
dc.description.abstractBackground 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. © 2015 Sari et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.en_US
dc.description.provenanceMade available in DSpace on 2016-02-08T09:51:11Z (GMT). No. of bitstreams: 1 bilkent-research-paper.pdf: 70227 bytes, checksum: 26e812c6f5156f83f0e77b261a471b5a (MD5) Previous issue date: 2015en
dc.identifier.doi10.1371/journal.pone.0128985en_US
dc.identifier.issn19326203
dc.identifier.urihttp://hdl.handle.net/11693/21791
dc.language.isoEnglishen_US
dc.publisherPublic Library of Scienceen_US
dc.relation.isversionofhttp://dx.doi.org/10.1371/journal.pone.0128985en_US
dc.source.titlePLoS ONEen_US
dc.subjectalgorithmen_US
dc.subjectArticleen_US
dc.subjectautomationen_US
dc.subjectcomputer programen_US
dc.subjectgene mappingen_US
dc.subjectsearch engineen_US
dc.titleSBGNViz: A tool for visualization and complexity management of SBGN process description mapsen_US
dc.typeArticleen_US

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