Biom-format.org

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BIOM format

http://biom-format.org/
Biological Observation Matrix (BIOM) format.

The BIOM file format (canonically pronounced biome) is designed to be a general-use format for representing biological sample by observation contingency tables. BIOM is a recognized standard for the Earth Microbiome Project and is a Genomics Standards Consortium candidate project.

The BIOM format is designed for general use in broad areas of comparative -omics. For example, in marker-gene surveys, the primary use of this format is to represent OTU tables: the observations in this case are OTUs and the matrix contains counts corresponding to the number of times each OTU is observed in each sample. With respect to metagenome data, this format would be used to represent metagenome tables: the observations in this case might correspond to SEED subsystems, and the matrix would contain counts corresponding to the number of times each subsystem is observed in each metagenome. Similarly, with respect to genome data, this format may be used to represent a set of genomes: the observations in this case again might correspond to SEED subsystems, and the counts would correspond to the number of times each subsystem is observed in each genome.





Licensing

License

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Notes

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Debian

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20 March 2013




Leaders and contributors

Contact(s)Role
Greg Caporaso contact


Resources and communication

AudienceResource typeURI
Debian (Ref) (R)https://tracker.debian.org/pkg/python-biom-format
VCS Repository Webviewhttps://github.com/biocore/biom-format


Software prerequisites

This entry (in part or in whole) was last reviewed on 30 March 2020.



Entry





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Date 2013-03-20
Source Debian import
Source link http://packages.debian.org/sid/python-biom-format

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