[BioC] bovine Annotation package(s)

[Louisa A Rispoli/AS/EXP/UTIA]

Marc-

I was wondering how it was going with building a bovine annotation
database? I have been reading through the vignette for AnnBuilder and not
sure that I have the skills for building the bovine.


Is there something else that I need to be reading to assist? Thanks

Louisa Rispoli

"If we knew what we were doing, it wouldn't be called Research." - Albert
Einstein

Louisa Rispoli, Ph.D. Reproductive Physiology
Department of Animal Science
University of Tennessee, Knoxville
A105 Johnson Animal Research and Teaching Unit
1750 Alcoa Highway
Knoxville, TN 37920
phone:(865) 946-1874
fax:(865) 946-1010
email: lrispoli at utk.edu




                                                                           
             Marc Carlson                                                  
             <mcarlson at fhcrc.o                                             
             rg>                                                        To 
             Sent by:                  Sean Davis <sdavis2 at mail.nih.gov>   
             bioconductor-boun                                          cc 
             ces at stat.math.eth         Nathan.Watson-Haigh at csiro.au,       
             z.ch                      bioconductor at stat.math.ethz.ch      
                                                                   Subject 
                                       Re: [BioC] bovine Annotation        
             07/16/2008 01:21          package(s)                          
             PM                                                            
                                                                           
                                                                           
                                                                           
                                                                           
                                                                           




Hi Nathan,

What Sean says is true.  However, I have not yet made a bovine.db0
database, so it is not yet possible to make .db annotation packages for
bovines.  However, if you would be willing to work with me a little bit,
I would be willing to look into it.  Lets take this off line and explore
it a little bit.  In the meantime part of the reason that AnnBuilder is
still alive is because of odd corner cases like this one where someone
needs support for an unusual organism.  So you should be able to use
AnnBuilder in the interim.

    Marc




Sean Davis wrote:
> On Tue, Jul 15, 2008 at 8:08 PM,  <Nathan.Watson-Haigh at csiro.au> wrote:
>
>> I'd like to be able to conduct metadata analyses on things such as GO
>> with data I have from an Affymetrix bovine chip. I've not done this on
>> other arrays, so I'm not sure what is needed to do this.
>>
>> I saw that there were no bovine or bovine.db packages available, so I
>> used AnnBuilder to create a bovine package from the GenBank IDs provided
>> by Affymetrix. My question/confusion is what's the *.db packages for, do
>> I need one for the bovine chip, and how would I make one?
>>
>
> The *.db packages are the new standard for annotation packages.  Have
> a look at how to create one by looking at the AnnotationDbi package
> and, specifically, the SQLForge vignette.
>
> Sean
>
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