[Go] addition of localization specific process terms ?

[Harold Drabkin]

They are in the sense that they would have the same PMID for both 
annotations.  So, two MF activities for the same reaction but located in 
different component.... The only difference between the two activities 
are that they are done by different proteins. That should not be a 
reason for two terms. Conversely, there are actually proteins that end 
up in both mitochondria and cytoplasm AND do the same activity (some 
AARS's come to mind). In this case 1 activity, 2 component, vs 2 
activities two components. But it's the actual same activity as well as 
protein, so actually there is no difference in the activity, only where 
it is done. 

hjd


Alexander Diehl wrote:
> I agree with Chris.  Co-annotation is insufficient, because the 
> annotations, once entered, are not linked to each other.
>
> -- Alex
>
> Chris Mungall wrote:
>>
>> 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.
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