Using process diagrams for the graphical representation of biological networks

Hiroaki Kitano, Akira Funahashi, Yukiko Matsuoka, Kanae Oda

Research output: Contribution to journalArticle

302 Citations (Scopus)

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).

Original languageEnglish
Pages (from-to)961-966
Number of pages6
JournalNature Biotechnology
Volume23
Issue number8
DOIs
Publication statusPublished - 2005 Aug
Externally publishedYes

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Systems Biology
Proteins
Language
Protein Interaction Maps
Genes
Gene Regulatory Networks
Software

ASJC Scopus subject areas

  • Microbiology

Cite this

Using process diagrams for the graphical representation of biological networks. / Kitano, Hiroaki; Funahashi, Akira; Matsuoka, Yukiko; Oda, Kanae.

In: Nature Biotechnology, Vol. 23, No. 8, 08.2005, p. 961-966.

Research output: Contribution to journalArticle

Kitano, Hiroaki ; Funahashi, Akira ; Matsuoka, Yukiko ; Oda, Kanae. / Using process diagrams for the graphical representation of biological networks. In: Nature Biotechnology. 2005 ; Vol. 23, No. 8. pp. 961-966.
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