SBGN-ED – working with the Systems Biology Graphical Notation

Abstract

The Systems Biology Graphical Notation - SBGN [1] provides a standard for the visual representation of biochemical and cellular processes. SBGN aims to improve information exchange and to support the collaborative creation of large maps based on individual modules. The language contains three views of biological processes covering different levels of detail:(1) Process Description (PD): this sublanguage provides a detailed presentation of the temporal dependencies of biological interactions in a network;(2) Entity Relationship (ER): this sublanguage displays the relationships in which a given entity can participate in a network; and(3) Activity Flow (AF): this sublanguage shows the flow of information between biological entities in an abstract way.SBGN aims to support a more efficient and accurate communication of biological knowledge between different research communities. However, to increase its usage, tools for editing, validating, layouting and translating SBGN maps are desirable.We present novel developments in SBGN-ED [2], a tool which allows the creation of all three types of SBGN maps from scratch or the editing of existing maps, the validation of these maps for syntactical and semantical correctness, the translation of networks from databases such as KEGG into SBGN and the export of SBGN maps into several file and image formats. SBGN-ED is based on the Vanted system [3] for the integration, analysis and visualisation of experimental data within biological networks and functional hierarchies. We furthermore present some applications based on SBGN-ED such as RIMAS [4].SBGN-ED is freely available from http://www.sbgn-ed.org. The web site contains also tutorials and example files.[1] N. Le Novère et al. (2009) The systems biology graphical notation. Nature Biotechnology, 27: 735–741.[2] B.H. Junker, C. Klukas and F. Schreiber (2006) VANTED: a system for advanced data analysis and visualization in the context of biological networks. BMC Bioinformatics, 7: 109.1–109.13.[3] T. Czauderna, C. Klukas and F. Schreiber (2010) Editing, validating, and translating of SBGN maps. Bioinformatics, 26(18): 2340-2341.[3] A. Junker, A. Hartmann, F. Schreiber, H. Bäumlein (2010) An engineers view on regulation of seed development. Trends in Plant Science 15(6): 303-307.