[Go] addition of localization specific process terms ?

[Alexander Diehl]

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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-- 
Alexander D. Diehl, Ph.D.
Senior Scientific Curator
Mouse Genome Informatics
The Jackson Laboratory
600 Main Street
Bar Harbor, ME  04609

email:  adiehl at informatics.jax.org
work:  +1 (207) 288-6427
fax:  +1 (207) 288-6131