Perspective abstract

Nature Biotechnology 23, 961 - 966 (2005)
Published online: 4 August 2005 | doi:10.1038/nbt1111

Using process diagrams for the graphical representation of biological networks

Hiroaki Kitano1,2,3,4, Akira Funahashi1,3,4, Yukiko Matsuoka1,3 & Kanae Oda1,4

With the increased interest in understanding biological networks, such as protein-protein interaction networks and gene regulatory networks, methods for representing and communicating such networks in both human- and machine-readable form have become increasingly important. Although there has been significant progress in machine-readable representation of networks, as exemplified by the Systems Biology Mark-up Language (SBML) ( issues in human-readable representation have been largely ignored. This article discusses human-readable diagrammatic representations and proposes a set of notations that enhances the formality and richness of the information represented. The process diagram is a fully state transition–based diagram that can be translated into machine-readable forms such as SBML in a straightforward way. It is supported by CellDesigner, a diagrammatic network editing software (, and has been used to represent a variety of networks of various sizes (from only a few components to several hundred components).

  1. The Systems Biology Institute, Suite 6A, M31 6-31-15 Jingumae, Shibuya, Tokyo, 150-0001 Japan.
  2. Sony Computer Science Laboratories, Inc., 3-14-13 Higashi-gotanda, Shinagwa, Tokyo, 141-0022 Japan.
  3. ERATO-SORST Kitano Symbiotic Systems Project, Japan Science and Technology Agency, Suite 6A, M31 6-31-15 Jingumae, Shibuya, Tokyo, 150-0001 Japan.
  4. Department of Fundamental Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku, Yokohama 223-8522 Japan.

Correspondence to: Hiroaki Kitano1,2,3,4 e-mail:


These links to content published by NPG are automatically generated.


A comprehensive modular map of molecular interactions in RB/E2F pathway

Molecular Systems Biology Review (04 Mar 2008)


Circuit diagrams for biological networks

Molecular Systems Biology News and Views (17 Jan 2006)

Escalating model sizes and complexities call for standardized forms of representation

Molecular Systems Biology News and Views (25 May 2005)