[Go] addition of localization specific process terms ?

[Chris Mungall]

On Mar 4, 2009, at 8:11 AM, 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".

By this line of argument, there is a reasonable case for not pre- 
composing a P-in-C term. However, I would not counsel any over-hasty  
obsoletion, and I would far prefer we err on the side of over-pre- 
composing until everyone is familiar with composing at annotation time.

>
> It makes more sense in this case to annotate concurrently.

Or even better: co-annotate, AND fill in the CC in col17 of the BP  
annotation.

>  I'd find genes annotated by asking for genes annotated to  
> mitochondria AND tRNA aminoacylation and look at what I get.

Remember, a gene co-annotated to mt and tRNA aminoacylation does *not*  
conclusively state that its gene product ever participates in this  
process in the mt. It may do one thing in the mt, and do it's tRNA  
aminoacylation somewhere else.

If you want to conclusively state that the gene product of gene G  
performs RNA aminoacylation in the mt, the you co-annotated *and* fill  
in mt in the annotation xp.

> 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?

I'm not sure I follow, but I think I disagree

>
> 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
>>
>>
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>
>