Rebuilding KEGG Maps: Algorithms and Benefits

Static drawings of biological pathways are still an important research tool for biologists. Gerhard Michal created his seminal drawings of metabolic networks in the 1960s and thus defined canonical representations of some key pathways. The Kyoto Encyclopedia of Genes and Genomes (KEGG) provides the most popular static drawings of biological networks of different types, used in a huge number of publications. These drawings are so widely known that they are immediately recognizable to most biologists. This enables collaborative work and simplifies the communication of analysis results. Automatic layout of these pathway maps is complicated by the fact that the information available from KEGG does not contain the entire layout information of the reference maps. Here we present a fully automated algorithm for interactive KEGG layout construction. The algorithm conserves the original KEGG layout to the extent possible while improving readability by removing unnecessary elements (in organism-specific maps). Multiple pathway maps can be laid out simultaneously to facilitate the navigation of larger networks. The algorithm supports the hierarchical layout of sub networks and thus supports interactive exploration of large datasets.