[Go] addition of localization specific process terms ?

[Chris Mungall]

On Mar 4, 2009, at 9:34 AM, Harold Drabkin wrote:

> Valerie Wood wrote:
>> I agree that the aa specific tRNA aminoacylation process terms are  
>> excessively granular (although I have used them), as they are  
>> equivalent to the function terms. I still think we need terms for  
>> mitochondrial tRNA aminoacylation because, although the process is  
>> the same (and sometimes the gene products involved) the process has  
>> different target genes and hence different biological consequences  
>> (and phenotypes).
>
> I really think these are annotation issues, not ontology issues. You  
> are saying that the gene products involved are different. But we are  
> still talking about translation. We do not, and should not, have  
> things like "translation of x protein", translation of y protein";  
> It's still translation. Different 'targets"; same process.  The  
> ontology can be used to describe the overall biology of all sorts of  
> different proteins.
>>
>> For your simple search, (i.e to retrieve genes involved in  
>> mitochondrial amino acylation) a combination of mitochondria and  
>> tRNA aminoacylation would work fine.
>> However this is not the major use of GO. Increasingly GO is used  
>> for hypothesis generating exercises with a complete gene set, these  
>> combination searches are not helpful, you need to be able to look  
>> for enrichment at the level of process, none of the enrichment  
>> tools (including the one in AmiGO) can perform these inter ontology  
>> analyses.
>>
>> In a genome wide set you would not be able to detect  (for example)  
>> that the set of essential genes in S. cerevisiae is enriched for  
>> translation components BUT not for mitochondrial translation  
>> components, but that in pombe the mitochondrial translation  
>> components are also essential (this is a real example).
>
> Why not? If the user understands the GO properly, they would set up  
> the scan to return things annotated to both the component and the  
> process. You will see overlap in gene products that appear enriched  
> to "mitochondria" and "translation" annotations.

See my original email. co-annotation is insufficient.