[Go] addition of localization specific process terms ?

[Jim Hu]

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