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Open Access Highly Accessed Methodology article

Conversion of KEGG metabolic pathways to SBGN maps including automatic layout

Tobias Czauderna1*, Michael Wybrow2, Kim Marriott2 and Falk Schreiber123

Author Affiliations

1 Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany

2 Caulfield School of Information Technology, Monash University, Victoria 3145, Australia

3 Institute of Computer Science, Martin Luther University Halle‐Wittenberg, Halle (Saale), Germany

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BMC Bioinformatics 2013, 14:250  doi:10.1186/1471-2105-14-250

Published: 16 August 2013



Biologists make frequent use of databases containing large and complex biological networks. One popular database is the Kyoto Encyclopedia of Genes and Genomes (KEGG) which uses its own graphical representation and manual layout for pathways. While some general drawing conventions exist for biological networks, arbitrary graphical representations are very common. Recently, a new standard has been established for displaying biological processes, the Systems Biology Graphical Notation (SBGN), which aims to unify the look of such maps. Ideally, online repositories such as KEGG would automatically provide networks in a variety of notations including SBGN. Unfortunately, this is non‐trivial, since converting between notations may add, remove or otherwise alter map elements so that the existing layout cannot be simply reused.


Here we describe a methodology for automatic translation of KEGG metabolic pathways into the SBGN format. We infer important properties of the KEGG layout and treat these as layout constraints that are maintained during the conversion to SBGN maps.


This allows for the drawing and layout conventions of SBGN to be followed while creating maps that are still recognizably the original KEGG pathways. This article details the steps in this process and provides examples of the final result.