biojs-io-biom, a BioJS component for handling data in Biological Observation Matrix (BIOM) format

The Biological Observation Matrix (BIOM) format is widely used to store data from high-throughput studies. It aims at increasing interoperability of bioinformatic tools that process this data. However, due to multiple versions and implementation details, working with this format can be tricky. Curre...

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Detalles Bibliográficos
Autores principales: Ankenbrand, Markus J., Terhoeven, Niklas, Hohlfeld, Sonja, Förster, Frank, Keller, Alexander
Formato: Online Artículo Texto
Lenguaje:English
Publicado: F1000 Research Limited 2017
Materias:
Software Tool Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5224677/
https://www.ncbi.nlm.nih.gov/pubmed/28105307
http://dx.doi.org/10.12688/f1000research.9618.2
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author Ankenbrand, Markus J.
Terhoeven, Niklas
Hohlfeld, Sonja
Förster, Frank
Keller, Alexander
author_facet Ankenbrand, Markus J.
Terhoeven, Niklas
Hohlfeld, Sonja
Förster, Frank
Keller, Alexander
author_sort Ankenbrand, Markus J.
collection PubMed
description The Biological Observation Matrix (BIOM) format is widely used to store data from high-throughput studies. It aims at increasing interoperability of bioinformatic tools that process this data. However, due to multiple versions and implementation details, working with this format can be tricky. Currently, libraries in Python, R and Perl are available, whilst such for JavaScript are lacking. Here, we present a BioJS component for parsing BIOM data in all format versions. It supports import, modification, and export via a unified interface. This module aims to facilitate the development of web applications that use BIOM data. Finally, we demonstrate its usefulness by two applications that already use this component. Availability: https://github.com/molbiodiv/biojs-io-biom, https://dx.doi.org/10.5281/zenodo.218277
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spelling pubmed-52246772017-01-18 biojs-io-biom, a BioJS component for handling data in Biological Observation Matrix (BIOM) format Ankenbrand, Markus J. Terhoeven, Niklas Hohlfeld, Sonja Förster, Frank Keller, Alexander F1000Res Software Tool Article The Biological Observation Matrix (BIOM) format is widely used to store data from high-throughput studies. It aims at increasing interoperability of bioinformatic tools that process this data. However, due to multiple versions and implementation details, working with this format can be tricky. Currently, libraries in Python, R and Perl are available, whilst such for JavaScript are lacking. Here, we present a BioJS component for parsing BIOM data in all format versions. It supports import, modification, and export via a unified interface. This module aims to facilitate the development of web applications that use BIOM data. Finally, we demonstrate its usefulness by two applications that already use this component. Availability: https://github.com/molbiodiv/biojs-io-biom, https://dx.doi.org/10.5281/zenodo.218277 F1000 Research Limited 2017-01-09 /pmc/articles/PMC5224677/ /pubmed/28105307 http://dx.doi.org/10.12688/f1000research.9618.2 Text en Copyright: © 2017 Ankenbrand MJ et al. http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Software Tool Article
Ankenbrand, Markus J.
Terhoeven, Niklas
Hohlfeld, Sonja
Förster, Frank
Keller, Alexander
biojs-io-biom, a BioJS component for handling data in Biological Observation Matrix (BIOM) format
title biojs-io-biom, a BioJS component for handling data in Biological Observation Matrix (BIOM) format
title_full biojs-io-biom, a BioJS component for handling data in Biological Observation Matrix (BIOM) format
title_fullStr biojs-io-biom, a BioJS component for handling data in Biological Observation Matrix (BIOM) format
title_full_unstemmed biojs-io-biom, a BioJS component for handling data in Biological Observation Matrix (BIOM) format
title_short biojs-io-biom, a BioJS component for handling data in Biological Observation Matrix (BIOM) format
title_sort biojs-io-biom, a biojs component for handling data in biological observation matrix (biom) format
topic Software Tool Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5224677/
https://www.ncbi.nlm.nih.gov/pubmed/28105307
http://dx.doi.org/10.12688/f1000research.9618.2
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