title: CySBGN: a Cytoscape plug-in to integrate SBGN maps.
abstract: BACKGROUND
  A standard graphical notation is essential to facilitate exchange of network representations of biological processes. Towards this end, the Systems Biology Graphical Notation (SBGN) has been proposed, and it is already supported by a number of tools. However, support for SBGN in Cytoscape, one of the most widely used platforms in biology to visualise and analyse networks, is limited, and in particular it is not possible to import SBGN diagrams.
  
  
  RESULTS
  We have developed CySBGN, a Cytoscape plug-in that extends the use of Cytoscape visualisation and analysis features to SBGN maps. CySBGN adds support for Cytoscape users to visualize any of the three complementary SBGN languages: Process Description, Entity Relationship, and Activity Flow. The interoperability with other tools (CySBML plug-in and Systems Biology Format Converter) was also established allowing an automated generation of SBGN diagrams based on previously imported SBML models. The plug-in was tested using a suite of 53 different test cases that covers almost all possible entities, shapes, and connections. A rendering comparison with other tools that support SBGN was performed. To illustrate the interoperability with other Cytoscape functionalities, we present two analysis examples, shortest path calculation, and motif identification in a metabolic network.
  
  
  CONCLUSIONS
  CySBGN imports, modifies and analyzes SBGN diagrams in Cytoscape, and thus allows the application of the large palette of tools and plug-ins in this platform to networks and pathways in SBGN format.
authors: EMBL - European Bioinformatics Institute, Cambridge, UK.
authors: Emanuel
authors: E
authors: Gonçalves
authors: Martijn
authors: M
authors: van Iersel
authors: Julio
authors: J
authors: Saez-Rodriguez
mesh_terms: D003196:Computer Graphics; D053858:Metabolic Networks and Pathways; D010944:Plants / Q000378:metabolism; D012984:Software; D049490:Systems Biology; D018511:Systems Integration