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@wur.nl 



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