[Go] addition of localization specific process terms ?

[Harold Drabkin]

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.


>
> Val
>
>
> Harold Drabkin wrote:
>
>> Yes, and one rule of thumb was to think about whether the actual 
>> process is different rather than where it is.
>> In Jim's example, the processing of tRNA charging (actually one 
>> enzyme) is the same whether it is in the mitochondria or chloroplast: 
>> amino acid gets activated with ATP, then transfer of the AA from 
>> AA-AMP to tRNA (all with one enzyme). The only time this process is 
>> "different" is in the caseswhere, for example, there is not a gln RS, 
>> but you can get gln-tRNA by first making a glu-tRNA, then amination 
>> (by a separate gene_product)  to gln-tRNA. However, the first step 
>> (the making of glu-tRNA, the "charging" is STILL the same".
>>
>> It makes more sense in this case to annotate concurrently.  I'd find 
>> genes annotated by asking for genes annotated to mitochondria AND 
>> tRNA aminoacylation and look at what I get. A single term for each 
>> and every process that takes into account where it is kind of defeats 
>> the purpose of having the three ontologies I would think?
>>
>>
>>
>> Jim Hu wrote:
>>
>>> On Mar 4, 2009, at 2:38 AM, Valerie Wood wrote:
>>>
>>>> Because of all of the arguments in favour  mentioned by Karen and 
>>>> Chris I  thought it was always necessary and required for curators 
>>>> to make the more granular annotation in these cases. We decided 
>>>> long ago that proliferation of the ontology was not an issue when 
>>>> pitched against accurate capture of biology, and  I wasn't aware 
>>>> that it was ever GO philosophy not to capture compartment specific 
>>>> processes in this way.
>>>
>>>
>>> I wasn't involved in GO when this was decided, but as someone who 
>>> does stuff on the software side as well as the annotation side, I 
>>> think proliferation of the ontology should be an issue that is not 
>>> dismissed so lightly.  I just posted a similar concern on the SF 
>>> item on children of protein folding, and I've taken that position on 
>>> the binding terms as well.
>>>
>>> The number of components where translation occurs is much smaller 
>>> than the number of ligands for binding or proteins for folding.  But 
>>> translation has lots of children.  I see that there is already 
>>> proliferation of mitochondrial child terms among these, including 20 
>>> terms for tRNA charging.  There are other child branches that don't 
>>> have precomposed mitochondrial child terms.  If it was up to me, I'd 
>>> obsolete things like 
>>> GO:0070143_!_mitochondrial_alanyl-tRNA_aminoacylation rather than 
>>> making more children for everything else.
>>>
>>> This strikes me as being way too much like adding back sensu terms.
>>>
>>> <snip>
>>>
>>>>> However, mitochondrial translation is fundamentally different 
>>>>> from  nuclear translation because a different genetic code is used.
>>>>
>>>
>>> But is this a fundamental difference?  Codon reassignments have 
>>> occurred many times across a variety of species.  This includes 
>>> prokaryotes and cytosolic eukaryotic systems as well as 
>>> mitochondria.  And not all mitochondria use the same noncanonical 
>>> code.  See:
>>>
>>>     http://www.nature.com/nrg/journal/v2/n1/full/nrg0101_049a.html
>>>
>>> Just look at Figure 2 if you don't want to read the whole thing.  
>>> And that's just taking Chris' instance of what is supposed to be a 
>>> clear cut example.  Is translation in the silkworm silk gland 
>>> fundamentally different enough?  In that case, specialized tRNA 
>>> genes are overexpressed to deal with the massive use of alanine in 
>>> the silk protein.
>>>
>>> I find the argument that one can't do an AND with some tools to be 
>>> more of an argument to improve the tools than an argument to do 
>>> extensive precomposition.  If we have to build GO practice around 
>>> the weakest tools, then we should also do explicit annotation all 
>>> the way up to root for every term, to handle tools that don't use 
>>> the true path rule.  I'm NOT advocating that!!
>>>
>>> Jim
>>>
>>> =====================================
>>> Jim Hu
>>> Associate Professor
>>> Dept. of Biochemistry and Biophysics
>>> 2128 TAMU
>>> Texas A&M Univ.
>>> College Station, TX 77843-2128
>>> 979-862-4054
>>>
>>>
>>> _______________________________________________
>>> Go mailing list
>>> Go at geneontology.org
>>> http://fafner.stanford.edu/mailman/listinfo/go
>>
>>
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