Using process diagrams for the graphical representation of biological networks
Using process diagrams for the graphical representation of biological networks
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DOI：
10.1038/nbt1111
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发表时间：
2005-08-01
影响因子：
46.9
通讯作者：
Oda, K
中科院分区：
文献类型：
--
作者：
Kitano, H;Funahashi, A;Oda, K
随着人们对理解生物网络（例如蛋白质-蛋白质相互作用网络和基因调控网络）的兴趣日益浓厚，以人类和机器可读形式表示和通信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，如系统生物学标记语言 (SBML) (http://www.sbml.org) 所示，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形表示，并提出了一组增强所表示信息的正式性和丰富性的符号。流程图是完全基于状态转换的图，可以以简单的方式转换为机器可读的形式，例如 SBML。它由图解网络编辑软件CellDesigner（http://www.celldesigner.org/）支持，并已用于表示各种规模的各种网络（从只有几个组件到数百个组件）。
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).