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 it's usefulness by two applications that already use this component. Availability: https://github.com/molbiodiv/biojs-io-biom, https://dx.doi.org/10.5281/zenodo.61698.
Highlights
In recent years, there has been an enormous increase in biological data available from high-throughput studies
It is implemented using latest web technologies, well tested and well documented. It provides a unified interface and abstracts from details like version or internal data representation. It will facilitate the development of web applications that rely on the Biological Observation Matrix (BIOM) format
Ankenbrand et al provide a javascript library to interact with the microbial consortia BIOM format version 1 class
Summary
There has been an enormous increase in biological data available from high-throughput studies. We present biojs-io-biom, a JavaScript module that provides a unified interface to read, modify, and write BIOM data It can be readily used as a library by applications that need to handle BIOM data for import or export directly in the browser. The popular BIOM visualization tool Phinch[7] has been forked and extended with new features, in particular support for BIOM version 2 by integrating biojs-io-biom[13]. This fork is available as Blackbird via https:// github.com/molbiodiv/Blackbird. In order to do that for large datasets sophisticated, accession functions capitalizing on the sparse data representation have to be implemented
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