[BioC] advice in building GOALLENTREZID {GO}

[Robert Gentleman]

Vladimir Morozov wrote:
> Now I got it! Thanks
> 
> Can you provide the code to build GO{BP|MF|CC}OFFSPRING
> I probably want to update it more often than biannually

   Yes, but if you do, and you want to use any other annotation, you 
must also build that.  The annotation packages are inter-connected in 
non-trivial ways (many depending on GO), so mixing and matching is not a 
simple process, which is pretty much why we don't do it more often.

  best wishes
    Robert

> 
> Thanks
> Vlad
> 
>  
> 
> -----Original Message-----
> From: Marc Carlson [mailto:mcarlson at fhcrc.org] 
> Sent: Wednesday, April 09, 2008 11:57 AM
> To: Vladimir Morozov
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] advice in building GOALLENTREZID {GO}
> 
> Vladimir Morozov wrote:
>>  Marc,
>>
>> I need the "transitive"(direct and "child" term) GO->Enterz mapping.
>> Where is Entrez mapping in GO.db?
>>
>>   
> 
> Yes those maps were deliberately not put into the newer GO.db package.  
> Instead you can now find this information in the organism based packages
> as I described in my previous post. 
> 
> In short, you need to look at the org.Xx.eg.db package for your species,
> where Xx is the genus and species 1st letter (Homo sapiens becomes Hs,
> Mus musculus becomes Mm etc.).
> 
> Then you need to look at the  org.Hs.egGO2ALLEGS and the org.Hs.egGO2EG
> mappings that the package contains (continuing the human example).
> 
> The problem with having that data in GO was that it munges together GO
> to entrez gene ID associations from several different organisms at the
> same time.  Entrez gene IDs are unique, so what we had before with these
> maps inside of GO is not really wrong, but we fear that someone could
> potentially become confused by this, and we want to help steer you guys
> towards getting the correct answers whenever possible.  Plus, this map
> was already really huge and needed to be split up in order to prevent
> future versions of the GO package from swelling up into a "GOjira" 
> package.  ;)
> 
> Hope this helps,
> 
> 
>     Marc
> 
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-- 
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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PO Box 19024
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206-667-7700
rgentlem at fhcrc.org