[BioC] bovine Annotation package(s)

[Nathan S. Haigh]

Hi Louisa,

Just to clarify with a few things I've learnt in the last week or two regarding the Bioconductor annotation packages/framework.

There are currently two types of annotation packages:
1) Those built by AnnBuilder
2) Those built by SQLForge

The former are the older style annotation packages which I believe are being replaced by the latter. The latter are better as the annotations are
actually stored/distributed in a database format using SQLite and are linked to online resources so are far more extensible than the old flat file
format. However, the latter requires a certain amount of configuration/setup by the bioconductor devs to create a *.db0 package (not distributed with
BioC) for a given organism which are used to generate the "real" annotation package which is distributed with BioC. As a result, if you need an
annotation package for an unsupported organism (I think there are currently 7), you need to ask the devs nicely to build the *.db0 package or you can
use AnnBuilder to build an old-style annotation package.

I have built such a file for the affymatrix bovine chip. However, there are limitations (which I don't yet fully understand) to what packages you can
use to analyse the annotations - not sure it it's because those packages expect the new style *.db annotation packages or not. I need to figure out
exactly what the issue are, but I can send you the package if you like?

Cheers,
Nathan


Quoting Louisa A Rispoli/AS/EXP/UTIA <larispoli at mail.ag.utk.edu>:

> 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                                                            
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> 
> 
> 
> 
> 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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