[BioC] GO package

[Marc Carlson]

Salim Charaniya wrote:
> Hi,
>
> I have a question about the annotation package GO. Currently I am trying to
> use the package GOSim (developed by Holger Fröhlich), which requires the GO
> package. My organism of interest is a bacterial species Streptomyces
> coelicolor. The GO annotations for this antibiotics-producing organism are
> available from Sanger center website
> (http://streptomyces.org.uk/GO/index.html). However, I don't think these
> annotations are part of the GO database/package. The Entrez geneIDs for this
> organism are not linked to their GO annotations. More importantly (for me),
> GOSim has the information content of each GO term based on the number of
> genes that have been annotated with that particular GO term. Hence,
> modifying the gene/GO database can change the information content of the GO
> terms. Is it possible to add the GO annotations of this microorganism to the
> GO package? (Perhaps in a new release in the future?)
>
>  
>
> Thanks,
>
> 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
>
> ----------------------------------------------------------------------------
> --------
>
>
>
>
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>
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Hi Salim,

I really appreciate your interest in these packages, but presently the
annotation packages are heading in another direction entirely than what
you propose.  The GO package is already shedding its Entrez Gene ID map
as this map is simply too enormous to keep inside the GO package any
longer (these are already absent from the GO.db package).  Instead, you
can find mappings with this kind of data inside of the appropriate
organism based packages.  I would reccomend that you have a look at the
org.Hs.eg.db package for an example of this.

In spite of this, I think there is still a chance that we might still be
able to help you eventually.  We are looking at our supported organism
packages and we are already looking into ways to add more supported
organisms.  Right now, the process is a little bit challenging to add a
new organism, but over time we aim to fix that so that we hope that we
can accommodate more different model organisms as data resources become
available.  So if you are willing to help us locate the data resources
for your organism of interest, and to be a little bit patient then we
can consider adding this in the future. 


    Marc