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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...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2012
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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. |
format | Online Article Text |
id | pubmed-3371871 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
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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