title: From metabolic reactions to networks and pathways.
abstract: Enzymatic reactions form a hypergraph structure and their translation into a graph structure accompanies an information loss. This chapter introduces well-known topological transformations from metabolic reactions to a graph, and discusses their advantages and disadvantages. Also discussed is the legitimacy of defining cofactors or currency metabolites, and suitable application area of each representation.
authors.affiliation: Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha, Kashiwa, Japan. arita@k.u-tokyo.ac.jp
authors.forename: Masanori
authors.initials: M
authors.lastname: Arita
mesh_terms: D004798:Enzymes / Q000378:metabolism*; D055641:Mathematical Concepts; D053858:Metabolic Networks and Pathways / Q000502:physiology*; D055432:Metabolomics / Q000379:methods*; D008954:Models, Biological; D049490:Systems Biology / Q000379:methods*
chemical_list: D004798:Enzymes