Annotation and merging of SBML models with semanticSBML
Annotation and merging of SBML models with semanticSBML
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DOI：
10.1093/bioinformatics/btp642
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发表时间：
2010-02-01
期刊：
影响因子：
5.8
通讯作者：
Liebermeister, Wolfram
中科院分区：
文献类型：
--
作者：
Krause, Falko;Uhlendorf, Jannis;Liebermeister, Wolfram
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。语义注释通过惟一的数据库标识符和本体术语将模型元素与外部知识链接起来，使软件能够根据模型的生化含义检查和处理模型。这些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是一个帮助用户在SBML模型中检查和编辑MIRIAM注释和SBO术语的工具。使用大量生化名称和数据库标识符，它支持建模者找到正确的注释和合并现有模型。最初，从MIRIAM注释派生出元素匹配，对冲突的元素属性进行分类并突出显示。然后可以自动或手动解决冲突，允许用户详细控制合并过程。
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.