Kitano Hiroaki, Funahashi Akira, Matsuoka Yukiko, Oda Kanae
The Systems Biology Institute, Suite 6A, M31 6-31-15 Jingumae, Shibuya, Tokyo, 150-0001 Japan.
Nat Biotechnol. 2005 Aug;23(8):961-6. doi: 10.1038/nbt1111.
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).
随着人们对理解生物网络（如蛋白质-蛋白质相互作用网络和基因调控网络）的兴趣日益浓厚，以人类可读和机器可读形式表示和交流此类网络的方法变得越来越重要。尽管在网络的机器可读表示方面取得了重大进展，例如以系统生物学标记语言（SBML）（http://www.sbml.org）为例，但人类可读表示方面的问题在很大程度上被忽视了。本文讨论了人类可读的图表表示法，并提出了一组能增强所表示信息的形式化和丰富性的符号。过程图是一种完全基于状态转换的图表，可以直接转换为诸如SBML等机器可读形式。它得到了图表网络编辑软件CellDesigner（http://www.celldesigner.org/）的支持，并已被用于表示各种规模的各种网络（从仅几个组件到几百个组件）。
