Krause Falko, Schulz Marvin, Swainston Neil, Liebermeister Wolfram
Max Planck Institute for Molecular Genetics, Dep. Computational Molecular Biology, Berlin, Germany.
Methods Enzymol. 2011;500:371-95. doi: 10.1016/B978-0-12-385118-5.00019-0.
Systems biology models can be reused within new simulation scenarios, as parts of more complex models or as sources of biochemical knowledge. Reusability does not come by itself but has to be ensured while creating a model. Most important, models should be designed to remain valid in different contexts-for example, for different experimental conditions-and be published in a standardized and well-documented form. Creating reusable models is worthwhile, but it requires some efforts when a model is developed, implemented, documented, and published. Minimum requirements for published systems biology models have been formulated by the MIRIAM initiative. Main criteria are completeness of information and documentation, availability of machine-readable models in standard formats, and semantic annotations connecting the model elements with entries in biological Web resources. In this chapter, we discuss the assumptions behind bottom-up modeling; present important standards like MIRIAM, the Systems Biology Markup Language (SBML), and the Systems Biology Graphical Notation (SBGN); and describe software tools and services for handling semantic annotations. Finally, we show how standards can facilitate the construction of large metabolic network models.
系统生物学模型可在新的模拟场景中重复使用，作为更复杂模型的组成部分或作为生化知识的来源。可重复使用性并非自然而然就能实现，而是在创建模型时必须加以确保。最重要的是，模型应设计为在不同背景下保持有效——例如，针对不同的实验条件——并以标准化且记录完善的形式发布。创建可重复使用的模型是值得的，但在开发、实施、记录和发布模型时需要付出一些努力。MIRIAM计划已经制定了已发布的系统生物学模型的最低要求。主要标准包括信息和文档的完整性、标准格式的机器可读模型的可用性，以及将模型元素与生物网络资源中的条目相连接的语义注释。在本章中，我们讨论自下而上建模背后的假设；介绍诸如MIRIAM、系统生物学标记语言（SBML）和系统生物学图形符号（SBGN）等重要标准；并描述用于处理语义注释的软件工具和服务。最后，我们展示标准如何促进大型代谢网络模型的构建。
