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the biological observation matrix (biom) format or how i learned to stop worrying and love the ome-ome生物观测矩阵(biom)格式或者我如何学会停止忧虑,爱ome-ome
McDonald et al. GigaScience 2012, 1:7
/content/1/1/7
TECHNICAL NOTE Open Access
The Biological Observation Matrix (BIOM) format
or: how I learned to stop worrying and love the
ome-ome
1† 2† 3 4 2 2
Daniel McDonald , Jose C Clemente , Justin Kuczynski , Jai Ram Rideout , Jesse Stombaugh , Doug Wendel ,
5 6 6 5 1,2,7 4,5*
Andreas Wilke , Susan Huse , John Hufnagle , Folker Meyer , Rob Knight and J Gregory Caporaso
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 translat
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