[Go] addition of localization specific process terms ?

[Chris Mungall]

On Mar 4, 2009, at 7:59 AM, 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.

What are your concerns in particular?

>  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.

Good point. By my own argument then there is a good case for composing  
translation-in-mt at annotation time.

Or at least the genetic code component of my argument was on shaky  
foundations, let me have a think and see if there's other reasons,  
because my gut says that mt translation should be precomposed in the  
ontology

>  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.

good point.

> 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!!

I agree that we shouldn't avoid doing the right thing because of the  
weakest tools. I think we should have a plan for how we can support  
tools, but I think we first need to agree roughly on what the right  
thing is..

>
> Jim
>
> =====================================
> Jim Hu
> Associate Professor
> Dept. of Biochemistry and Biophysics
> 2128 TAMU
> Texas A&M Univ.
> College Station, TX 77843-2128
> 979-862-4054
>
>
>