Biom-format.org

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Biom-format.org

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.


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Licensing

LicenseVerified byVerified onNotes
OtherDebian20 March 2013
License: GPL

This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this package; if not, write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA

On Debian systems, the full text of the GNU General Public License version 2 can be found in the file `/usr/share/common-

licenses/GPL-2'.



Leaders and contributors

Contact(s)Role
Greg Caporaso contact


Resources and communication

AudienceResource typeURI
Downloadhttp://biom-format.org/ -> links to Github download


Software prerequisites



Entry



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

[[Category:]]








"contact" is not in the list (Maintainer, Contributor, Developer, Sponsor, Unknown) of allowed values for the "Role" property.






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