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- Title
Using process diagrams for the graphical representation of biological networks.
- Authors
Kitano, Hiroaki; Funahashi, Akira; Matsuoka, Yukiko; Oda, Kanae
- 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).
- Subjects
MOLECULAR association; PROTEIN-protein interactions; LIFE sciences; COMPUTER software; GRAPHIC methods; CHARTS, diagrams, etc.
- Publication
Nature Biotechnology, 2005, Vol 23, Issue 8, p961
- ISSN
1087-0156
- Publication type
Article
- DOI
10.1038/nbt1111