[BioC] building an annotation library from scratch
Marc Carlson
mcarlson at fhcrc.org
Tue Nov 3 19:19:55 CET 2009
Hi Guido,
There is a new vignette that has been contributed to AnnotationDbi, that
you will want to look at soon (it should appear in a day or two). This
vignette will explain in detail how to make custom database schemas.
The vignette will be called "NewSchema". Many thanks to Gabor Csardi
for the nice write-up on this topic.
Marc
Hooiveld, Guido wrote:
> Dear list,
>
> Question for the more knowledgable people:
> A collegue and I would like to create an annotation library based on the
> miRBASE content (for the Affymetrix miRNA array). Luckily miRBASE
> provides a dump of their data in MySQL format
> (ftp://mirbase.org/pub/mirbase/CURRENT/database_files/). We succeeded in
> converting the info into a SQLite format, but are now stuck.
> Based on the BioC vignettes, we do know that we somehow have to use the
> packages AnnotationDbi and SQLForge, but as far as we are able to
> understand the packages use the info available in the corresponding
> organism .db0 packages. However, it is not clear to us how now to
> continue with the mirna.db SQLite file we created.
> Any advice is much appreciated!
>
> Thanks,
> Guido
>
> Code we used to access the conent of mirna.db within R:
>
>
>> conn <- dbConnect("SQLite", dbname = "mirna.db")
>> dbListTables(conn)
>>
> [1] "dead_mirna" "literature_references"
> [3] "mirna" "mirna_2_prefam"
> [5] "mirna_chromosome_build" "mirna_context"
> [7] "mirna_database_links" "mirna_literature_references"
> [9] "mirna_mature" "mirna_pre_mature"
> [11] "mirna_prefam" "mirna_species"
> [13] "mirna_target_links" "mirna_target_url"
> [15] "sqlite_sequence"
>
>> dbListFields(conn, "mirna")
>>
> Error in sqliteFetch(res, n = n, ...) :
> BLOB column handling not implemented
>
>> dbListFields(conn, "dead_mirna")
>>
> [1] "mirna_acc" "mirna_id" "previous_id" "forward_to" "comment"
>
>
>
>
> ------------------------------------------------
> Guido Hooiveld, PhD
> Nutrition, Metabolism & Genomics Group
> Division of Human Nutrition
> Wageningen University
> Biotechnion, Bomenweg 2
> NL-6703 HD Wageningen
> the Netherlands
> tel: (+)31 317 485788
> fax: (+)31 317 483342
> internet: http://nutrigene.4t.com <http://nutrigene.4t.com/>
> email: guido.hooiveld at wur.nl
>
>
>
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>
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