A graphical notation for biochemical networks

Abstract

A solid definition and comprehensive graphical representation of biological networks is essential for efficient and accurate dissemination of information on biological models. Several proposals have already been made toward this aim. The most well known representation of this kind is a molecular interaction map, or ‘Kohn Map’. However, although the molecular interaction map is a well-defined and compact notation, there are several drawbacks, such as difficulties in intuitive understanding of temporal changes of reactions and additional complexities arising from particular graphical representations. This article proposes several improvements to the molecular interaction map, as well as the use of the ‘process diagram’ to help understand temporal sequences of reactions.