The Biological Observation Matrix (BIOM) format or

How I learned to stop worrying and love the ome-ome

Daniel McDonald, Jose C. Clemente, Justin Kuczynski, Jai R. Rideout, Jesse Stombaugh, Doug Wendel, Andreas Wilke, Susan Huse, John Hufnagle, Folker Meyer, Rob Knight, James G Caporaso

Research output: Contribution to journalArticle

249 Citations (Scopus)

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.

Original languageEnglish (US)
Article number7
JournalGigaScience
Volume464
Issue number1
DOIs
StatePublished - Jul 12 2012

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Love
Observation
Bioinformatics
Boidae
Metadata
Interoperability
Computer programming languages
Computational Biology
Earth (planet)
Programming Languages
Biological Science Disciplines
Microbiota
Ecosystem
Meta-Analysis
Software

Keywords

  • BIOM
  • Comparative genomics
  • Metagenomics
  • MG-RAST
  • Microbial ecology
  • QIIME
  • VAMPS

ASJC Scopus subject areas

  • Health Informatics
  • Computer Science Applications

Cite this

The Biological Observation Matrix (BIOM) format or : How I learned to stop worrying and love the ome-ome. / McDonald, Daniel; Clemente, Jose C.; Kuczynski, Justin; Rideout, Jai R.; Stombaugh, Jesse; Wendel, Doug; Wilke, Andreas; Huse, Susan; Hufnagle, John; Meyer, Folker; Knight, Rob; Caporaso, James G.

In: GigaScience, Vol. 464, No. 1, 7, 12.07.2012.

Research output: Contribution to journalArticle

McDonald, D, Clemente, JC, Kuczynski, J, Rideout, JR, Stombaugh, J, Wendel, D, Wilke, A, Huse, S, Hufnagle, J, Meyer, F, Knight, R & Caporaso, JG 2012, 'The Biological Observation Matrix (BIOM) format or: How I learned to stop worrying and love the ome-ome', GigaScience, vol. 464, no. 1, 7. https://doi.org/10.1186/2047-217X-1-7
McDonald D, Clemente JC, Kuczynski J, Rideout JR, Stombaugh J, Wendel D et al. The Biological Observation Matrix (BIOM) format or: How I learned to stop worrying and love the ome-ome. GigaScience. 2012 Jul 12;464(1). 7. https://doi.org/10.1186/2047-217X-1-7
McDonald, Daniel ; Clemente, Jose C. ; Kuczynski, Justin ; Rideout, Jai R. ; Stombaugh, Jesse ; Wendel, Doug ; Wilke, Andreas ; Huse, Susan ; Hufnagle, John ; Meyer, Folker ; Knight, Rob ; Caporaso, James G. / The Biological Observation Matrix (BIOM) format or : How I learned to stop worrying and love the ome-ome. In: GigaScience. 2012 ; Vol. 464, No. 1.
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