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) (http://www.sbml.org) 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 (http://www.celldesigner.org/), and has been used to represent a variety of networks of various sizes (from only a few components to several hundred components).

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  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: kitano@symbio.jst.go.jp



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