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

ABSTRACT: 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.

SUBMITTER: Ankenbrand MJ

PROVIDER: S-EPMC5224677 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

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

Ankenbrand Markus J MJ Terhoeven Niklas N Hohlfeld Sonja S Förster Frank F Keller Alexander A

F1000Research 20160920

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, modifi ...[more]

PMID: 28105307

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The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome.

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