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Nat Biotechnol. 2005 Aug;23(8):961-6.

Using process diagrams for the graphical representation of biological networks.

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1
The Systems Biology Institute, Suite 6A, M31 6-31-15 Jingumae, Shibuya, Tokyo, 150-0001 Japan. kitano@symbio.jst.go.jp

Abstract

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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PMID:
16082367
DOI:
10.1038/nbt1111
[Indexed for MEDLINE]

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