Difference between revisions of "Biom-format.org"

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{{Entry
 
{{Entry
|Status=
 
|User level=
 
|Submitted by=Debian import
 
|Computer languages=
 
 
|Name=Biom-format.org
 
|Name=Biom-format.org
|Submitted date=2013-03-20
 
 
|Short description=Biological Observation Matrix (BIOM) format
 
|Short description=Biological Observation Matrix (BIOM) format
|VCS checkout command=
 
 
|Full description=The BIOM file format (canonically pronounced biome) is designed
 
|Full description=The BIOM file format (canonically pronounced biome) is designed
 
to be a general-use format for representing biological sample by
 
to be a general-use format for representing biological sample by
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SEED subsystems, and the counts would correspond to the number of
 
SEED subsystems, and the counts would correspond to the number of
 
times each subsystem is observed in each genome.
 
times each subsystem is observed in each genome.
|Component programs=
 
 
|Homepage URL=http://biom-format.org/
 
|Homepage URL=http://biom-format.org/
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|Accepts cryptocurrency donations=No
 +
|Last review by=Bendikker
 +
|Last review date=2018/03/20
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|Submitted date=2013-03-20
 
|Is GNU=No
 
|Is GNU=No
}}
 
{{Import
 
|Date=2013-03-20
 
|Source=Debian import
 
|Source link=http://packages.debian.org/sid/python-biom-format
 
 
}}
 
}}
 
{{Project license
 
{{Project license
 +
|License=Other
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|License copyright=© © 2010-2012 Greg Caporaso <gregcaporaso@gmail.com>
 +
|License verified by=Debian
 
|License verified date=2013-03-20
 
|License verified date=2013-03-20
|License verified by=Debian
 
|License copyright=© © 2010-2012 Greg Caporaso <gregcaporaso@gmail.com>
 
 
|License=Other
 
 
|License note=License: GPL
 
|License note=License: GPL
  
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}}
 
}}
 
{{Project license
 
{{Project license
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|License=Other
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|License copyright=© © 2012 Andreas Tille <tille@debian.org>
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|License verified by=Debian
 
|License verified date=2013-03-20
 
|License verified date=2013-03-20
|License verified by=Debian
 
|License copyright=© © 2012 Andreas Tille <tille@debian.org>
 
 
|License=Other
 
 
|License note=License: GPL
 
|License note=License: GPL
  
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{{Person
 
{{Person
 
|Real name=Greg Caporaso
 
|Real name=Greg Caporaso
|Resource URL=
 
 
|Role=contact
 
|Role=contact
 
|Email=gregcaporaso@gmail.com
 
|Email=gregcaporaso@gmail.com
 
}}
 
}}
 
{{Resource
 
{{Resource
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|Resource audience=Debian (Ref) (R)
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|Resource URL=https://tracker.debian.org/pkg/python-biom-format
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}}
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{{Resource
 +
|Resource kind=Download
 
|Resource URL=http://biom-format.org/ -> links to Github download
 
|Resource URL=http://biom-format.org/ -> links to Github download
|Resource kind=Download
+
}}
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{{Software category}}
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{{Featured}}
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{{Import
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|Date=2013-03-20
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|Source=Debian import
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|Source link=http://packages.debian.org/sid/python-biom-format
 
}}
 
}}

Revision as of 11:52, 20 March 2018

[edit]

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

Verified by

Verified on

Notes

Verified by

Debian

Verified on

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




Property "Submitted by" (as page type) with input value "{{{Submitted by}}}" contains invalid characters or is incomplete and therefore can cause unexpected results during a query or annotation process.










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


"Debian (Ref) (R)" is not in the list (General, Help, Bug Tracking, Support, Developer) of allowed values for the "Resource audience" property.








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

[[Category:]]



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