The biological observation matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome

McDonald, Daniel and Clemente, Jose C. and Kuczynski, Justin and Rideout, Jai Ram and Stombaugh, Jesse and Wendel, Doug and Wilke, Andreas and Huse, Susan and Hufnagle, John and Meyer, Folker and Knight, Rob and Caporaso, J. Gregory (2012) The biological observation matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome. GigaScience, 1 (1). p. 7. ISSN 2047-217X

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Abstract

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.

Item Type:	Article
Publisher’s Statement:	Creative Commons Attribution License.
ID number or DOI:	10.1186/2047-217X-1-7
Keywords:	BIOM; Comparative genomics; Metagenomics; MG-RAST; microbial ecology; QIIME; VAMPS
Subjects:	Q Science > Q Science (General) Q Science > QH Natural history > QH301 Biology
NAU Depositing Author Academic Status:	Faculty/Staff
Department/Unit:	College of Engineering, Forestry, and Natural Science > Electrical Engineering and Computer Science
Date Deposited:	07 Oct 2015 18:44
URI:	http://openknowledge.nau.edu/id/eprint/699

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