title: The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome.
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.
  
  
  RESULTS
  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.
authors.affiliation: Department of Computer Science, Northern Arizona University, Flagstaff, AZ, USA. gregcaporaso@gmail.com.
authors.forename: Daniel
authors.initials: D
authors.lastname: McDonald
authors.forename: Jose C
authors.initials: JC
authors.lastname: Clemente
authors.forename: Justin
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authors.lastname: Kuczynski
authors.forename: Jai Ram
authors.initials: JR
authors.lastname: Rideout
authors.forename: Jesse
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authors.lastname: Stombaugh
authors.forename: Doug
authors.initials: D
authors.lastname: Wendel
authors.forename: Andreas
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authors.lastname: Wilke
authors.forename: Susan
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authors.lastname: Huse
authors.forename: John
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authors.lastname: Hufnagle
authors.forename: Folker
authors.initials: F
authors.lastname: Meyer
authors.forename: Rob
authors.initials: R
authors.lastname: Knight
authors.forename: J Gregory
authors.initials: JG
authors.lastname: Caporaso