[BioC] advice in building GOALLENTREZID {GO}

[Marc Carlson]

Vladimir Morozov wrote:
> Hi,
>  
> Can somebody advice in building GOALLENTREZID {GO}
>  
> 'GO' package description tells:
> The annotation package was built using a downloadable R package -
> AnnBuilder (download and build your own) from www.bioconductor.org
> <http://www.bioconductor.org/>  using the following public data sources:
> Entrez Gene:ftp://ftp.ncbi.nlm.nih.gov/gene/DATA. Built: Source data
> downloaded from Entrez Gene on Wed Aug 29 09:09:16 2007
>  
> Gene
> Ontology:ftp://ftp.geneontology.org/pub/go/godatabase/archive/latest.
> Built: Build Information not available 
>  
>  
> AnnBuilder function:
> GOPkgBuilder(pkgName, pkgPath, filename, version, author, lazyLoad=TRUE)
> requires the GO ontology structure file (filename argument) 
> But how does it get Entrez mapping?
>  
>  
> Kind of related question, is the GO package supposed to be updated. I
> see the old package version number in the Bioconductor development
> version
>  
>  
> Thanks
> Vlad
>  
>   

Hi Vlad,

I recommend that you NOT use the GOALLENTREZID field from GO.   There is 
nothing really "wrong" with it, but it's the old way of doing things.  
The old annotation packages are going to go away soon.

Instead I would get the appropriate organism based package and use the 
appropriate map from there. 

So for example if you were using human, you would want the org.Hs.eg.db 
package and would want to use the mapping in the org.Hs.egGO2ALLEGS field. 

Also, you probably want to switch over to the newer GO.db package 
instead of the old style GO package.  we plan to deprecate the older GO 
package imminently.  ;)


    Marc