Theoretische Biophysik, Humboldt-Universität zu Berlin, Invalidenstrasse 42, D-10115 Berlin, Germany.
Bioinformatics. 2010 Feb 1;26(3):421-2. doi: 10.1093/bioinformatics/btp642. Epub 2009 Nov 17.
Systems Biology Markup Language (SBML) is the leading exchange format for mathematical models in Systems Biology. Semantic annotations link model elements with external knowledge via unique database identifiers and ontology terms, enabling software to check and process models by their biochemical meaning. Such information is essential for model merging, one of the key steps towards the construction of large kinetic models. SemanticSBML is a tool that helps users to check and edit MIRIAM annotations and SBO terms in SBML models. Using a large collection of biochemical names and database identifiers, it supports modellers in finding the right annotations and in merging existing models. Initially, an element matching is derived from the MIRIAM annotations and conflicting element attributes are categorized and highlighted. Conflicts can then be resolved automatically or manually, allowing the user to control the merging process in detail.
SemanticSBML comes as a free software written in Python and released under the GPL 3. A Debian package, a source package for other Linux distributions, a Windows installer and an online version of semanticSBML with limited functionality are available at http://www.semanticsbml.org. A preinstalled version can be found on the Linux live DVD SB.OS, available at http://www.sbos.eu.
Supplementary data are available at Bioinformatics online.
系统生物学标记语言（SBML）是系统生物学中数学模型的主要交换格式。语义注释通过唯一的数据库标识符和本体论术语将模型元素与外部知识联系起来，使软件能够根据其生化意义检查和处理模型。此类信息对于模型合并至关重要，模型合并是构建大型动力学模型的关键步骤之一。SemanticSBML 是一种帮助用户检查和编辑 SBML 模型中 MIRIAM 注释和 SBO 术语的工具。它使用大量生化名称和数据库标识符，支持建模人员找到正确的注释并合并现有模型。最初，从 MIRIAM 注释中推导出元素匹配，然后对冲突的元素属性进行分类和突出显示。然后可以自动或手动解决冲突，使用户可以详细控制合并过程。
SemanticSBML 是用 Python 编写的免费软件，根据 GPL 3 发布。可在 http://www.semanticsbml.org 获得 Debian 软件包、适用于其他 Linux 发行版的源代码包、Windows 安装程序和具有有限功能的在线 SemanticSBML 版本。SB.OS 上的 Linux 实时 DVD 提供了预安装版本，可在 http://www.sbos.eu 上找到。
补充数据可在生物信息学在线获得。
