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

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 ta...

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Autores principales: Lubitz, Timo, Hahn, Jens, Bergmann, Frank T., Noor, Elad, Klipp, Edda, Liebermeister, Wolfram
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4978929/
https://www.ncbi.nlm.nih.gov/pubmed/27153616
http://dx.doi.org/10.1093/bioinformatics/btw179
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author Lubitz, Timo
Hahn, Jens
Bergmann, Frank T.
Noor, Elad
Klipp, Edda
Liebermeister, Wolfram
author_facet Lubitz, Timo
Hahn, Jens
Bergmann, Frank T.
Noor, Elad
Klipp, Edda
Liebermeister, Wolfram
author_sort Lubitz, Timo
collection PubMed
description 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
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spelling pubmed-49789292016-08-11 SBtab: a flexible table format for data exchange in systems biology Lubitz, Timo Hahn, Jens Bergmann, Frank T. Noor, Elad Klipp, Edda Liebermeister, Wolfram Bioinformatics Applications Notes 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 Oxford University Press 2016-08-15 2016-04-08 /pmc/articles/PMC4978929/ /pubmed/27153616 http://dx.doi.org/10.1093/bioinformatics/btw179 Text en © The Author 2016. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Applications Notes
Lubitz, Timo
Hahn, Jens
Bergmann, Frank T.
Noor, Elad
Klipp, Edda
Liebermeister, Wolfram
SBtab: a flexible table format for data exchange in systems biology
title SBtab: a flexible table format for data exchange in systems biology
title_full SBtab: a flexible table format for data exchange in systems biology
title_fullStr SBtab: a flexible table format for data exchange in systems biology
title_full_unstemmed SBtab: a flexible table format for data exchange in systems biology
title_short SBtab: a flexible table format for data exchange in systems biology
title_sort sbtab: a flexible table format for data exchange in systems biology
topic Applications Notes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4978929/
https://www.ncbi.nlm.nih.gov/pubmed/27153616
http://dx.doi.org/10.1093/bioinformatics/btw179
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