Ankenbrand MJ, Terhoeven N, Hohlfeld S, Förster F, Keller A. biojs-io-biom, a BioJS component for handling data in Biological Observation Matrix (BIOM) format.
F1000Res 2017;
5:2348. [PMID:
28105307 PMCID:
PMC5224677 DOI:
10.12688/f1000research.9618.2]
[Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/09/2017] [Indexed: 11/20/2022] Open
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.
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