The 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. We are currently seeking recognition of the BIOM format by the Genomics Standards Consortium.

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.

There are two components to the BIOM project: first is definition of the BIOM format, and second is development of support objects in multiple programming languages to support the use of BIOM in diverse bioinformatics applications. A 1.0 release of the biom-format project will coincide with publication of a manuscript describing the project.

Contents¶

BIOM Documentation
- The biom file format
- biom-format Table objects
  - biom-format table_factory method
  - Description of available Table objects

BIOM version¶

The latest official version of the biom-format project and file format is 0.9.1.

The biom-format project and file format version are always the same. Official versions contain three integers in the following format: major-version.incremental-version.minor-version. When -dev is appended to the end of a version string that indicates a development (or between-release version). For example, 1.0.0-dev would refer to the development version following the 1.0.0 official release.

Installing the BIOM project¶

To install the BIOM project, you can download the release version biom-format-0.9.1, or work with the development version. Generally we recommend working with the release version as it will be more stable, but if you want access to the latest features (and can tolerate some instability) you should work with the development version.

To pull the development version from our svn repository, first cd to the directory where you’d like to install the code. We’ll call this $HOME/code:

cd $HOME/code

To install the release version, download from biom-format-0.9.1, and then run tar -xvzf on the resulting file to unzip it. To install the development version, run the following command:

svn checkout svn://svn.code.sf.net/p/biom-format/code/trunk biom-format

To install (either the development or release version), follow these steps:

echo "export PYTHONPATH=$HOME/code/biom-format/python-code/:$PYTHONPATH" >> $HOME/.bashrc
echo "export PATH=$HOME/code/biom-format/scripts/:$PATH" >> $HOME/.bashrc
source $HOME/.bashrc

You should then have access to the biom-format project. You can test this by running the following command:

python -c "from biom import __version__; print __version__"

You should see the current version of the biom-format project.

Next you can run:

which convert_biom.py

You should get $HOME/code/biom-format/scripts/convert_biom.py printed to your screen if it is installed correctly.

Citing the BIOM project¶

While our manuscript is under review you can cite the BIOM project with this URL: http://www.biom-format.org.

Development team¶

The biom-format project was conceived of and developed by the QIIME, MG-RAST, and VAMPS development groups to support interoperability of our software packages. If you have questions about the biom-format project you can contact gregcaporaso@gmail.com.