Overview

The recently proposed Systems Biology Graphical Notation (SBGN, http://sbgn.org) is an emerging standard for graphical representations of biochemical and cellular processes studied in systems biology. This standardisation helps to communicate biological knowledge more efficient and accurate between different research communities in the life sciences. However, to support SBGN, tools for editing, validating and translating of SBGN maps are necessary.

We present SBGN-ED, a VANTED add-on which allows to create and edit all three types of SBGN maps, that is Process Description, Entity Relationship and Activity Flow, to validate these maps according to the SBGN specifications, to translate maps from the KEGG and MetaCrop pathway databases into SBGN, and to export SBGN maps into several file and image formats.

The VANTED system (Visualisation and Analysis of Networks containing Experimental Data) is an open source software that offers the possibility to load and edit graphs, which may represent biological pathways or functional hierarchies. It allows to integrate different *omics data into the functional context and provides a variety of functions for data mapping and processing, statistical analysis, and visualisation. With the VANTED Add-on interface it is easily possible to extend the functionality of the software.

News

24/10/2013 - SBGN-ED 1.5 released

16/08/2013 - SBGN-ED 1.4 released

07/08/2012 - SBGN-ED 1.3 released

16/05/2012 - SBGN-ED 1.2.1 released

21/02/2012 - SBGN-ED 1.2 released

02/11/2011 - SBGN-ED winner of the SBGN 2011 Competition - Best SBGN software support

06/10/2010 - SBGN-ED winner of the SBGN 2010 Competition - Best SBGN software support

How to cite SBGN-ED:

Czauderna, T., Klukas, C., Schreiber, F.: Editing, Validating, and Translating of SBGN Maps. Bioinformatics, 26(18):2340-2341, 2010.