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

  2. More flexible queries.  With the SQLite-based packages, many
     queries that currently require loops over possible many entire
     environments can be accomplished in one statement.  Using some
     simple SQL statements, I've been able to improve the performance
     of the hyperGTest function by 10x.  Focused queries will
     generally be much faster with the SQLite-based packages.

+ seth

sessionInfo()

R version 2.5.0 Under development (unstable) (2007-01-22 r40543)
x86_64-unknown-linux-gnu

locale:
LC_CTYPE=it_IT.UTF-8;LC_NUMERIC=C;LC_TIME=it_IT.UTF-8;LC_COLLATE=it_IT.UTF-8;LC_MONETARY=it_IT.UTF-8;LC_MESSAGES=it_IT.UTF-8;LC_PAPER=it_IT.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=it_IT.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] "tools"     "stats"     "graphics"  "grDevices" "utils"     "datasets"
[7] "methods"   "base"

other attached packages:
   hgu95av2db AnnotationDbi       RSQLite           DBI       Biobase
    "1.13.91"      "0.0.41"      "0.4-19"      "0.1-12"     "1.13.34"
     fortunes
      "1.3-2"
Cheers
 Wolfgang

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

--
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Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber