[Bioc-devel] SQLite databases (was [BioC] getting Locus Link ids from gene symbol])

Francois Pepin fpepin at cs.mcgill.ca
Mon Jun 11 17:18:06 CEST 2007

I would personally very much appreciate something of the sort and I know
several other of my collaborators would also.

My personal favorite was the idea of a by-species package that would
behave just like the chip annotation. To use EntrezID instead of the
probe ids and to have all the xxxGO, xxxENZYME, xxxSYMBOL, etc.

But anything that makes that information easily available would be a
nice addition.

I know biomaRt can do all that, but a lot of people have code that deals
with those annotations and having consistent annotations (processed the
same way) is always useful.


On Mon, 2007-06-11 at 08:52 -0400, Sean Davis wrote:
> Now that RSQLite and DBI are really beginning to merge with Bioconductor
> tools, does it make sense to think about building data sources (SQLite
> databases) as a base for further development?  As an example, might it
> make sense to include all of the data available at the Entrez Gene ftp
> site as a database file?  Does a repository of such database files (and
> possibly supporting files) make sense?  Making such files is pretty
> straightforward, but what makes the most sense for distribution?  A full
> package with accessors, etc?  A simple sqlite file?  Something in between?
> I may be asking questions for which the answers are already
> known/decided, but it would be good to know anyway.
> Thanks,
> Sean
> _______________________________________________
> Bioc-devel at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

More information about the Bioc-devel mailing list