[BioC] Finding GO leaf nodes for an ontology - which package?

[John Zhang]

>
>Thanks for the reply. I tried the following:
>
>t("GO:0008150", GOBPCHILDREN)
>> length(g1)
>[1] 12
>> g1
> [1] "GO:0050789" "GO:0050896" "GO:0009987" "GO:0016032"
> [5] "GO:0043473" "GO:0019952" "GO:0000003" "GO:0000004"
> [9] "GO:0040007" "GO:0007275" "GO:0007582" "GO:0051704"
>
>
>So, starting with the root node for biological process, I would want to get 
only the outermost leaf nodes (and not any intermediate nodes in the graph). 
>
>The above code would appear to give the direct children of the root node (is 
that correct?).

That is right. GOBPOFFSPRING will give you all the children nodes but the node 
structure is not preserved and there is no way to figure out which ones are the 
outmost. 

You may need to travel through all the children nodes you get from the CHILDREN 
environment to get down to the outmost leaf nodes.


>
>many thanks
>
>John Zhang <jzhang at jimmy.harvard.edu> wrote: 
>>
>>I was trying to list all the leaf nodes for a particular ontology. For this, I 
>was using the GOstats:
>>
>>g1 <- oneGOGraph("GO:0003674", GOMFCHILDREN)
>>g2 <- GOleaves(g1)
>>
>>Hopefully, this would give me a list of all the leaf nodes for the molecular 
>function ontology. But this is taking too long to execute.
>>
>>Is there a similar function in some other package that would be quicker?
>
>Just for the GO ids:
>
>>library(GO)
>>leafGOs <- get("GO:0003674", GOMFCHILDREN)
>
>
>
>>
>>thanks!
>>
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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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Jianhua Zhang
Department of Medical Oncology
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084