[BioC] building an annotation library from scratch

[James F. Reid]

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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