title: Using process diagrams for the graphical representation of biological networks.
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).
authors.affiliation: The Systems Biology Institute, Suite 6A, M31 6-31-15 Jingumae, Shibuya, Tokyo, 150-0001 Japan. kitano@symbio.jst.go.jp
authors.forename: Hiroaki
authors.initials: H
authors.lastname: Kitano
authors.forename: Akira
authors.initials: A
authors.lastname: Funahashi
authors.forename: Yukiko
authors.initials: Y
authors.lastname: Matsuoka
authors.forename: Kanae
authors.initials: K
authors.lastname: Oda
mesh_terms: D000818:Animals; D003196:Computer Graphics; D003198:Computer Simulation; D005786:Gene Expression Regulation / Q000502:physiology*; D006801:Humans; D008954:Models, Biological; D015398:Signal Transduction / Q000502:physiology*; D049490:Systems Biology / Q000379:methods*; D014157:Transcription Factors / Q000378:metabolism*; D014584:User-Computer Interface
chemical_list: D014157:Transcription Factors