[BioC] advice in building GOALLENTREZID {GO}

[Vladimir Morozov]

 Marc,

I need the "transitive"(direct and "child" term) GO->Enterz mapping.
Where is Entrez mapping in GO.db?

Documentation for package \u2018GO.db\u2019 version 2.0.2
Help Pages
GO 	Bioconductor annotation data package
GOBPANCESTOR 	Annotation of GO Identifiers to their Biological Process
Ancestors
GOBPCHILDREN 	Annotation of GO Identifiers to their Biological Process
Children
GOBPOFFSPRING 	Annotation of GO Identifiers to their Biological Process
Offspring
GOBPPARENTS 	Annotation of GO Identifiers to their Biological Process
Parents
GOCCANCESTOR 	Annotation of GO Identifiers to their Cellular Component
Ancestors
GOCCCHILDREN 	Annotation of GO Identifiers to their Cellular Component
Children
GOCCOFFSPRING 	Annotation of GO Identifiers to their Cellular Component
Offspring
GOCCPARENTS 	Annotation of GO Identifiers to their Cellular Component
Parents
GOMAPCOUNTS 	Number of mapped keys for the maps in package GO.db
GOMFANCESTOR 	Annotation of GO identifiers to their Molecular Function
Ancestors
GOMFCHILDREN 	Annotation of GO Identifiers to their Molecular Function
Children
GOMFOFFSPRING 	Annotation of GO Identifiers to their Molecular Function
Offspring
GOMFPARENTS 	Annotation of GO Identifiers to their Molecular Function
Parents
GOOBSOLETE 	Annotation of GO identifiers by terms defined by Gene
Ontology Consortium and their status are obsolete
GOSYNONYM 	Map from GO synonyms to GO terms
GOTERM 	Annotation of GO Identifiers to GO Terms
GO_dbconn 	Collect information about the package annotation DB
GO_dbfile 	Collect information about the package annotation DB
GO_dbInfo 	Collect information about the package annotation DB
GO_dbschema 	Collect information about the package annotation DB


Thanks


Vladimir 

-----Original Message-----
From: Marc Carlson [mailto:mcarlson at fhcrc.org] 
Sent: Tuesday, April 08, 2008 7:12 PM
To: Vladimir Morozov
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] advice in building GOALLENTREZID {GO}

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