Using process diagrams for the graphical representation of biological networks.

Nat Biotechnol

The Systems Biology Institute, Suite 6A, M31 6-31-15 Jingumae, Shibuya, Tokyo, 150-0001 Japan.

Published: August 2005

AI Article Synopsis

  • Increased interest in biological networks has led to the need for effective methods to represent these networks in human- and machine-readable formats.
  • Progress in machine-readable formats like SBML is noted, but human-readable representations have not received as much attention.
  • The article introduces diagrammatic notations, particularly the process diagram, which enhances information representation and can be easily translated into machine-readable forms, supported by tools like CellDesigner.

Article 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).

Download full-text PDF

Source
http://dx.doi.org/10.1038/nbt1111DOI Listing

Publication Analysis

Top Keywords

biological networks
8
networks
7
process diagrams
4
diagrams graphical
4
graphical representation
4
representation biological
4
networks increased
4
increased interest
4
interest understanding
4
understanding biological
4

Similar Publications

Want AI Summaries of new PubMed Abstracts delivered to your In-box?

Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!