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

[Vincent Carey 525-2265]

>
>   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.

do we need a sql tutorial doc (i know there are plenty on the
web but perhaps some that are focused on the types of queries to
be used here?)  helper code that 'translates' R-like actions to
SQL may be feasible for some of the more common tasks.

>
> + 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
> >>
> >> _______________________________________________
> >> Bioc-devel at stat.math.ethz.ch mailing list
> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
> >
> > --
> > ------------------------------------------------------------------
> > Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber
>
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