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graph2tab, a library to convert experimental workflow graphs into tabular formats

Motivations: Spreadsheet-like tabular formats are ever more popular in the biomedical field as a mean for experimental reporting. The problem of converting the graph of an experimental workflow into a table-based representation occurs in many such formats and is not easy to solve. Results: We descri...

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Detalles Bibliográficos
Autores principales: Brandizi, Marco, Kurbatova, Natalja, Sarkans, Ugis, Rocca-Serra, Philippe
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3371871/
https://www.ncbi.nlm.nih.gov/pubmed/22556367
http://dx.doi.org/10.1093/bioinformatics/bts258
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author Brandizi, Marco
Kurbatova, Natalja
Sarkans, Ugis
Rocca-Serra, Philippe
author_facet Brandizi, Marco
Kurbatova, Natalja
Sarkans, Ugis
Rocca-Serra, Philippe
author_sort Brandizi, Marco
collection PubMed
description Motivations: Spreadsheet-like tabular formats are ever more popular in the biomedical field as a mean for experimental reporting. The problem of converting the graph of an experimental workflow into a table-based representation occurs in many such formats and is not easy to solve. Results: We describe graph2tab, a library that implements methods to realise such a conversion in a size-optimised way. Our solution is generic and can be adapted to specific cases of data exporters or data converters that need to be implemented. Availability and Implementation: The library source code and documentation are available at http://github.com/ISA-tools/graph2tab. Contact: brandizi@ebi.ac.uk. Supplementary Information: A supplementary document describes the theoretical and technical details about the library implementation.
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spelling pubmed-33718712012-06-11 graph2tab, a library to convert experimental workflow graphs into tabular formats Brandizi, Marco Kurbatova, Natalja Sarkans, Ugis Rocca-Serra, Philippe Bioinformatics Applications Note Motivations: Spreadsheet-like tabular formats are ever more popular in the biomedical field as a mean for experimental reporting. The problem of converting the graph of an experimental workflow into a table-based representation occurs in many such formats and is not easy to solve. Results: We describe graph2tab, a library that implements methods to realise such a conversion in a size-optimised way. Our solution is generic and can be adapted to specific cases of data exporters or data converters that need to be implemented. Availability and Implementation: The library source code and documentation are available at http://github.com/ISA-tools/graph2tab. Contact: brandizi@ebi.ac.uk. Supplementary Information: A supplementary document describes the theoretical and technical details about the library implementation. Oxford University Press 2012-06-15 2012-05-03 /pmc/articles/PMC3371871/ /pubmed/22556367 http://dx.doi.org/10.1093/bioinformatics/bts258 Text en © The Author(s) 2012. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/3.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Applications Note
Brandizi, Marco
Kurbatova, Natalja
Sarkans, Ugis
Rocca-Serra, Philippe
graph2tab, a library to convert experimental workflow graphs into tabular formats
title graph2tab, a library to convert experimental workflow graphs into tabular formats
title_full graph2tab, a library to convert experimental workflow graphs into tabular formats
title_fullStr graph2tab, a library to convert experimental workflow graphs into tabular formats
title_full_unstemmed graph2tab, a library to convert experimental workflow graphs into tabular formats
title_short graph2tab, a library to convert experimental workflow graphs into tabular formats
title_sort graph2tab, a library to convert experimental workflow graphs into tabular formats
topic Applications Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3371871/
https://www.ncbi.nlm.nih.gov/pubmed/22556367
http://dx.doi.org/10.1093/bioinformatics/bts258
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