joey711/phyloseq — Issue #71: Add support for BIOM format for QIIME / MG-RAST
Author: joey711
Created: 2012-02-13 20:59:54+00:00
State: open
Labels: Feature

The new BIOM format is standard in new versions of QIIME, and is a file-storage format that fits hand-in-glove with the philosophical framework in the phyloseq-package.

http://qiime.org/svn_documentation/documentation/biom_format.html

BIOM format is JSON based, and in general a JSON package in R should be used for dealing with most of the I/O issues. One of the stated reasons for the switch by QIIME was to facilitate export / IO with the MG-RAST server, also a good goal for the phyloseq-package (although, full-fledge interaction with MG-RAST would definitely be a separate "Issue" for this package).

This should be given high priority, as it will greatly increase the utility and timeliness of this package.