[BioC] building a new annotation

Marc Carlson mcarlson at fhcrc.org
Thu Mar 12 18:38:19 CET 2009

Hi Chirag,

If you are building this to a custom database that you already have in
hand the you cannot use SQLforge because that will try to make a
customized database for you.  And AnnBuilder is gone now (and would not
have helped you here anyways).  Instead, you might want to look closely
at the code in AnnotationDbi which defines several types of databases
along with the mappings to represent the underlying DB data in R using
an L2Rchain structure.  Access to these structures outside the domain of
AnnotationDbi is planned to be made more accessible in the future. 
Alternatively, (depending completely upon what kind of access you want
to provide to your users), you could also  pretty easily just write some
simple accessors to talk to this database.  Direct access to SQLite
databases is pretty straightforward from R using the RSQlite and DBI
packages.  There are some examples of this in the AnnotationDbi vignette
of this direct style of access that you can look at here.


If you have further questions please let me know,


Chirag Patel wrote:
> Hello,
> I would like to build a new annotation using data from the CTD
> (http://ctd.mdibl.org).
> This data contains in sqlite DB a main table with the schema:
> entrez_gene_id, chemical_id, relation_id, and pubmed_citation_id.
> Relation_id is a internal id I use to manage relations between the
> chemical and genes.  Chemical_id is an id used by the CTD to identify
> chemicals.
> How may I best do this using the tools available on bioconductor?-- I
> was thinking of using AnnBuilder or AnnotationDbi, but am unsure if
> this is the right way to go; this is a first time building a package
> or an annotation.
> Any help would be much appreciated,
> Chirag
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