The Biological Observation Matrix (BIOM) Format Or: How I Learned to Stop Worrying and Love the Ome-ome

Overview

Journal Gigascience

Publisher Oxford University Press

Specialties Biology
Genetics

Date 2013 Apr 17

PMID 23587224

Citations 388

Authors

Daniel McDonald

Jose C Clemente

Justin Kuczynski

Jai Ram Rideout

Jesse Stombaugh

Doug Wendel

Andreas Wilke

Susan Huse

John Hufnagle

Folker Meyer

Rob Knight

J Gregory Caporaso

Affiliations

Soon will be listed here.

Abstract

Background: We present the Biological Observation Matrix (BIOM, pronounced "biome") format: a JSON-based file format for representing arbitrary observation by sample contingency tables with associated sample and observation metadata. As the number of categories of comparative omics data types (collectively, the "ome-ome") grows rapidly, a general format to represent and archive this data will facilitate the interoperability of existing bioinformatics tools and future meta-analyses.

Findings: The BIOM file format is supported by an independent open-source software project (the biom-format project), which initially contains Python objects that support the use and manipulation of BIOM data in Python programs, and is intended to be an open development effort where developers can submit implementations of these objects in other programming languages.

Conclusions: The BIOM file format and the biom-format project are steps toward reducing the "bioinformatics bottleneck" that is currently being experienced in diverse areas of biological sciences, and will help us move toward the next phase of comparative omics where basic science is translated into clinical and environmental applications. The BIOM file format is currently recognized as an Earth Microbiome Project Standard, and as a Candidate Standard by the Genomic Standards Consortium.

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