[Bioc-devel] Update on SQLite-based annotation data package (prototype available)

Seth Falcon sfalcon at fhcrc.org
Thu Feb 1 16:41:53 CET 2007

Hello all,

We are making progress on converting the annotation data packages to
use SQLite as the backend storage mechanism.

The devel annotation package repository has a prototype of a
SQLite-based annotation data package (hgu95av2db).  If you are running
R-devel, then you should be able to install it via biocLite (sorry,
only source package at this point).

The SQLite-based annotation packages depend on the AnnotationDbi
package which provides an environment-like interface that should be
backwards compatible.  Advanced users can get a connection to the DB
and issue raw SQL queries.  We are also planning to provide more
convenience/accessor functions along the lines of the annotate

Our plan for the upcoming 2.0 release of Bioconductor is to include
both environment-based and SQLite-based annotation packages.

If you maintain a package that makes use of annotation data packages,
it would be good to see if the hgu95av2db prototype will work with
your code (if not, please let us know).

+ seth

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