[Go] addition of localization specific process terms ?

[Alexander Diehl]

Without rereading a particular paper, there's no proof that two 
annotations derive from the same experiment, which defeats the point of 
doing the annotation in the first place.

I'm not for a wild proliferation of terms, but compound terms often 
simplify annotation and provide richer meaning to microarray analysis 
based on GO annotation.

-- Alex


Harold Drabkin wrote:
> 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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>>
>>
>


-- 
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