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

Seth Falcon 
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
package.

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

Thread (6 messages)

Seth Falcon Update on SQLite-based annotation data package (prototype available) Feb 1 Wolfgang Huber Update on SQLite-based annotation data package (prototype available) Feb 1 Seth Falcon Update on SQLite-based annotation data package (prototype available) Feb 1 Vincent Carey Update on SQLite-based annotation data package (prototype available) Feb 1 Seth Falcon Update on SQLite-based annotation data package (prototype available) Feb 1 Laurent Gautier Update on SQLite-based annotation data package (prototype available) Feb 1