SBtab: a flexible table format for data exchange in systems biology.
SBtab: a flexible table format for data exchange in systems biology.
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DOI：
10.1093/bioinformatics/btw179
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发表时间：
2016-08-15
期刊：
影响因子：
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通讯作者：
Liebermeister W
中科院分区：
文献类型：
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作者：
Lubitz T;Hahn J;Bergmann FT;Noor E;Klipp E;Liebermeister W
SBtab是一种基于表格的系统生物学数据格式，旨在支持自动化数据集成和模型构建。它使用电子表格的结构，并定义了表结构、受控词汇表和语义注释的约定。该格式带有用于实验数据和符合SBML的模型结构的预定义表格类型，并且可以轻松地进行自定义以覆盖新类型的数据。可用性和实现：SBtab文档可以使用任何文本编辑器或电子表格工具创建和编辑。网站www.sbtab.net提供语法验证和转换为SBML和HTML的在线工具，以及在MS Excel、MATLAB和R中使用SBtab的软件。独立的Python代码包含文件解析，验证，转换为SBML和HTML的功能以及SQLite数据库的接口，可集成到系统生物学工作流程中。SBtab的详细说明，包括表格类型和可用工具的示例和说明，可在www.sbtab.net上找到。联系人：wolfram. gmail.com
Summary: SBtab is a table-based data format for Systems Biology, designed to support automated data integration and model building. It uses the structure of spreadsheets and defines conventions for table structure, controlled vocabularies and semantic annotations. The format comes with predefined table types for experimental data and SBML-compliant model structures and can easily be customized to cover new types of data. Availability and Implementation: SBtab documents can be created and edited with any text editor or spreadsheet tool. The website www.sbtab.net provides online tools for syntax validation and conversion to SBML and HTML, as well as software for using SBtab in MS Excel, MATLAB and R. The stand-alone Python code contains functions for file parsing, validation, conversion to SBML and HTML and an interface to SQLite databases, to be integrated into Systems Biology workflows. A detailed specification of SBtab, including examples and descriptions of table types and available tools, can be found at www.sbtab.net. Contact: wolfram.liebermeister@gmail.com