Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2012 Jul 12;1(1):7.
doi: 10.1186/2047-217X-1-7.

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

Daniel McDonald  1 , 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

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

Daniel McDonald et al. Gigascience. .

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.

PubMed Disclaimer

Figures

Figure 1
Figure 1
Growth of the “ome-ome”, or the types of “omic” data, over time based on mentions in Medline abstracts. Chao1 analysis indicates that there may be over 3,000 “omes”: however, given the well-known limitations of such non-parametric extrapolation techniques, we can only wonder how many “omes” remain to be discovered as technological advances usher in a new era of “ome-omics”.
Figure 2
Figure 2
Size of sparse BIOM formatted file versus size of QIIME “classic” OTU Table formatted file, for 60 independent microbiome studies currently stored in the QIIME database at http://www.microbio.me/qiime
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, Mende DR, Li J, Xu J, Li S, Li D, Cao J, Wang B, Liang H, Zheng H, Xie Y, Tap J, Lepage P, Bertalan M, Batto JM, Hansen T, Le Paslier D, Linneberg A, Nielsen HB, Pelletier E, Renault P, Sicheritz-Ponten T, Turner K, Zhu H, Yu C, Li S, Jian M, Zhou Y, Li Y, Zhang X, Li S, Qin N, Yang H, Wang J, Brunak S, Doré J, Guarner F, Kristiansen K, Pedersen O, Parkhill J, Weissenbach J, Weissenbach J, Bork P, Ehrlich SD, Wang J. MetaHIT Consortium. A human gut microbial gene catalogue established by metagenomic sequencing. Nature. 2010;464(7285):59–65. doi: 10.1038/nature08821. - DOI - PMC - PubMed
    1. Reyes A, Haynes M, Hanson N, Angly FE, Heath AC, Rohwer F, Gordon JI. Viruses in the faecal microbiota of monozygotic twins and their mothers. Nature. 2010;466(7304):334–338. doi: 10.1038/nature09199. - DOI - PMC - PubMed
    1. Markowitz VM, Chen IM, Palaniappan K, Chu K, Szeto E, Grechkin Y, Ratner A, Jacob B, Huang J, Williams P, Huntemann M, Anderson I, Mavromatis K, Ivanova NN, Kyrpides NC. IMG: the Integrated Microbial Genomes database and comparative analysis system. Nucleic Acids Res. 2012;40:D115–122. doi: 10.1093/nar/gkr1044. - DOI - PMC - PubMed
    1. Zakrzewski M, Goesmann A, Jaenicke S, Jünemann S, Eikmeyer F, Szczepanowski R, Al-Soud WA, Sørensen S, Pühler A, Schlüter A. Profiling of the metabolically active community from a production-scale biogas plant by means of high-throughput metatranscriptome sequencing. J Biotechnol. 2012;158(4):248–258. doi: 10.1016/j.jbiotec.2012.01.020. - DOI - PubMed
    1. Helbling DE, Ackermann M, Fenner K, Kohler HP, Johnson DR. The activity level of a microbial community function can be predicted from its metatranscriptome. ISME J. 2011;6(4):902–904. - PMC - PubMed