[BioC] advice in building GOALLENTREZID {GO}

[Marc Carlson]

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