Using process diagrams for the graphical representation of biological networks View Full Text


Ontology type: schema:ScholarlyArticle     


Article Info

DATE

2005-08

AUTHORS

Hiroaki Kitano, Akira Funahashi, Yukiko Matsuoka, Kanae Oda

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). More... »

PAGES

961-966

Identifiers

URI

http://scigraph.springernature.com/pub.10.1038/nbt1111

DOI

http://dx.doi.org/10.1038/nbt1111

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1036467908

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/16082367


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