Computational reconstruction of metabolic networks from KEGG.

Reconstruction of metabolic networks from metabolites, enzymes, and reactions is the foundation of the network-based study on metabolism. In this chapter, we describe a practical method for reconstructing metabolic networks from KEGG. This method makes use of organism-specific pathway data in the KEGG/PATHWAY database to reconstruct metabolic networks on pathway level, and the pathway hierarchy data in the KEGG/ORTHOLOGY database to guide the network reconstruction on higher levels. By calling upon the KEGG Web services, this method ensures the data used in the reconstruction are correct and up-to-date. The incorporation of a local relational database allows caching of pathway data improves performance and speeds up network reconstruction. Some applications of reconstructed networks on network alignment and network topology analysis are exampled and notes are stated in the end.