Hi Eric,

At 1st your questions confused me because the GO.sqlite package does not 
actually record the information that you appear to think it does.  That 
is, the GO.sqlite db is really only for storing information about the GO 
hierarchy itself.  It does not actually know anything about which terms 
are associated with which genes (or whether the association was IEA or 
something else).  That kind of information (gene to GO term 
associations) is actually stored in the database from your 'org.Bt.eg.db 
package'.

And you have several options for rebuilding that DB if you need a 
different one.  The most 'hands on' way to rebuild it, is to use the 
makeOrgPackage() function from the AnnotationForge package. That 
function will allow you to make an organism package (with populated 
database etc.) from a set of data.frames objects.  Using that, you could 
easily supply your own preferred GO information for Bovine and be as 
liberal as you feel is appropriate.

Hope that clarifies things, please let me know if you have more questions!


  Marc



On 07/22/2014 08:31 AM, Eric Fournier wrote:
> Hello,
>
> I am performing GO term enrichment analysis in my organism of interest (bos taurus) using the org.Bt.eg.db and GO.db package. However, since the GO.db package uses the "lite" version of the Gene Onthology database, all IEA (Inferred from Electronic Annotation) terms are absent. In cattle, this makes the annotation pretty barren (Over 60% of my genes have no GO annotation at all). Therefore, I am looking for ways to rebuild the GO.sqlite file used by GO.db using the full GO database. However I cannot find any indication on how to do so, either from the package source (where the file is already packaged) or from its manual. Could anyone point me in the right direction?
>
> Thank you,
> ________________________________________________________
> Eric Fournier, B. Sc.
> Research Assistant in Bioinformatics
> Université Laval, Qc, Canada
> eric.fournier.4@ulaval.ca
> 418-656-2131 x 11465
>
>
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