Related Experiment Video
Updated: May 17, 2026

A Web Tool for Generating High Quality Machine-readable Biological Pathways
Published on: February 8, 2017
Computational reconstruction of metabolic networks from KEGG
1Laboratory of Molecular Immunology, Institute of Basic Medical Sciences, Beijing, People's Republic of China. zhoutingting@bmi.ac.cn
Abstract:
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.
Related Concept Videos
Protein Networks
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Protein Networks
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Metabolism of Chemolithotrophs
Overview of Protein Metabolism
Amino acids play various roles in the body once they are absorbed into cells. They are restructured...
Overview of Metabolism
Plant Metabolism
Sunlight, the primary source of energy in plants, is first absorbed by the chlorophyll pigments present in their leaves. Plants then use this energy to carry out photosynthesis, where water is oxidized into oxygen and carbon dioxide...

