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.
Highlights
In recent years, there has been an enormous increase in biological data available from high-throughput studies
On there have been efforts to define data formats that capture all relevant information for an experiment like the Minimum Information About a Microarray Experiment (MIAME) project[1]
The Biological Observation Matrix (BIOM) Format was developed to standardize the storage of observation counts together with all relevant metadata and it is a member project of the GSC3
Summary
There has been an enormous increase in biological data available from high-throughput studies. For the development of web applications that support BIOM data, a corresponding library is currently lacking and would be very useful, since several challenges arise when trying to handle BIOM data. 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. Beside checking and maintaining integrity the biojs-io-biom library implements convenience functions This includes getter and setter for metadata as well as data accessor functions that are agnostic to internal representation (dense or sparse). By including our biojs-io-biom module and the biom-conversion-server into Phinch it was possible to add support for BIOM version 2.1 along with some other improvements[15]. We plan on extending the biom-conversion-server with a light communication API that allows a client to request only the subsets of the full data set that it requires
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