SBtab: a flexible table format for data exchange in systems biology

被引：23

作者：

Lubitz, Timo ^{[1
]}

Hahn, Jens ^{[1
]}

Bergmann, Frank T. ^{[2
]}

Noor, Elad ^{[3
]}

Klipp, Edda ^{[1
]}

Liebermeister, Wolfram ^{[4
]}

机构：

[1] Humboldt Univ, Inst Biol, Theoret Biophys, Berlin, Germany

[2] Heidelberg Univ, COS Bioquant, Heidelberg, Germany

[3] ETH, Inst Mol Syst Biol, Zurich, Switzerland

[4] Charite, Inst Biochem, Berlin, Germany

来源：

BIOINFORMATICS | 2016年 / 32卷 / 16期

关键词：

KINETIC-MODELS; MIRIAM;

D O I：

10.1093/bioinformatics/btw179

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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 pre-defined 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 websitewww.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

引用

页码：2559 / 2561

页数：3

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