Nature Biotechnology
23, 961 - 966 (2005)
Published online: 4 August 2005; | doi:10.1038/nbt1111
Using process diagrams for the graphical representation of biological networksHiroaki Kitano1, 2, 3, 4, Akira Funahashi1, 3, 4, Yukiko Matsuoka1, 3
& Kanae Oda1, 41
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 should be addressed to Hiroaki Kitano kitano@symbio.jst.go.jp 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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