[BioC] building a new annotation

Hervé Pagès hpages at fhcrc.org
Fri Mar 13 23:14:31 CET 2009

Hi Gabor,

Thanks for writing this document and sharing it. It's amazing that you've
figured out how to make your own AnnDbBimap-based annotation packages using
an entirely new db schema. You've also managed to define maps with a lot of
right attributes (miRNATargetAnnDbBimap and miRNAAnnDbBimap classes) and
to write appropriate "as.list" methods for them. Kudos for that!

Let me just mention that yes you can make multiple inserts with a single
SQL statement with RSQLite by using a "prepared query". See this post
from Seth Falcon on the R-sig-DB mailing list for how to do this:


This will make the "Put the data into the tables" step much much faster!


Gábor Csárdi wrote:
> Dear All, before seeing Hervé's excellent tutorial, I put together a
> page documenting creating an annotation package with a new database
> schema. I am sure it has some flaws, but hopefully not very serious
> ones. I did it mostly for myself, but maybe it is useful for others,
> especially together with Hervé's explanation.
> It is here:
> http://www2.unil.ch/cbg/index.php?title=Building_BioConductor_Annotation_Packages
> Best,
> Gabor
> On Fri, Mar 13, 2009 at 4:47 AM, Hervé Pagès <hpages at fhcrc.org> wrote:
>> Hi Chirag,
> [...]

Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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E-mail: hpages at fhcrc.org
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