[BioC] advice in building GOALLENTREZID {GO}

[Vladimir Morozov]

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

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