[BioC] GO

[Marc Carlson]

Salim Charaniya wrote:
> Hello,
>
> I have a question about GO annotations. I am trying to use the GOSim package
> to explore functional similarities between genes. I am working with the
> bacterial species Streptomcyes coelicolor. I cannot retrieve the GO
> annotations for the genes using the command - getGOInfo (The command returns
> an empty list). GOSim uses the GO package to retrieve the annotations of
> genes using Entrez gene IDs. 
>
> The GO annotations for this organism are available on Sanger website
> (http://streptomyces.org.uk/GO/index.html). 
>
> Is there a way to link the Entrez gene IDs of this organism to the GOs?
>
>  
>
> Thank you,
>
> Salim
>
>  
>
>  
>
> ----------------------------------------------------------------------------
> --------
>
> Salim Charaniya
>
> PhD candidate
>
> Department of Chemical Engineering and Materials Science
>
> University of Minnesota, Minneapolis
>
> Email: salim at cems.umn.edu
>
> Phone: (612) 625-3051
>
> ----------------------------------------------------------------------------
> --------
>
>  
>
>
> 	[[alternative HTML version deleted]]
>
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>   

Hi,

The latest GO package is meant to hold all the information about the
latest version of the GO ontology.  The GO package itself does not
contain any entrez gene IDs however.  Those IDs are normally found as
mappings in other organism specific or platform specific packages.  So I
think that what you are going to be missing (if you need a map of go
terms that are paired with entrez gene IDs) is a "go term to entrez gene
ID" mapping for your organism.  Nobody has to my knowledge made an
annotation package for this species yet. 

So your options are going to be to either 1) try to use the AnnBuilder
package to just make an annotation package for this critter or 2) figure
out what maps you are missing and just make those on the fly in R from
the annotations you found at the sanger.

Hopefully this will help you get started,


    Marc