Dear John,
 
 Thank you very much for your reply. I would like to know, how to get GOID from gene name? Is it possible using BioC or I have to do it explicitely?
 
 Regards,
 Kaustubh

John Zhang <jzhang@jimmy.harvard.edu> wrote: 
> How can I use Gene Ontology in BioC? Is there any tutorial or manual 
available? Especially how can I construct (extract) a tree if I have a gene name 
(e.g. RAD52)

GO() lists all the environments of the GO package.
?environment name gives you the description of the environment of interest with 
some example code.

For the thing you would like to do you may try to get the Gene id for the gene 
(e. g. 19365) and then do the following:

> goids <- get("19365", GOLOCUSID2GO)

You will get a few goids the gene maps to. Suppose we are interested in 
GO:0005515 that belongs to MF.

> get("GO:0005515", GOMFPARENTS) # Get the direct parents 
> get("GO:0005515", GOMFCHILDREN) # Get the direct children
> get("GO:0005515", GOMFANCESTOR) # Get the parents and grand parents ...
> get("GO:0005515", GOMFOFFSPRING) # Get the children and grand children ...

The above do not give you enough to construct a GO tree but you can always 
search the Gene Ontology web site for a tree.



> 
> Thanks and regards,
> Kaustubh
> 
>
>  
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Jianhua Zhang
Department of Medical Oncology
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084




			
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