[BioC] bovine Annotation package(s)

Marc Carlson mcarlson at fhcrc.org
Wed Jul 16 19:19:53 CEST 2008

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.


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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