Entering edit mode
James F. Reid
▴
610
@james-f-reid-3148
Last seen 10.2 years ago
Hi Guido,
you could create a file containing the microRNA ID and it's
corresponding Gene ID (NCBI) and then use SQLForge to create a custom
annotation package which would use an organism .db0 package.
HTH,
J.
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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