[Go] addition of localization specific process terms ?

[Karen Christie]

I don't think you can necessarily count on the P and C annotations always 
being made from the same paper. Certainly for cerevisiae, I see genes 
where the localization may be shown in one paper and subsequent papers 
build on that to show process, but may or may not duplicate the 
experimental demonstration of localization in a way that can be annotated.

However, if the problem is that "co-annotation is insufficient, because 
the annotations, once entered, are not linked to each other", then 
possibly there are other solutions than creating all possible 
localization-specific P terms. In Chris's original email, he wrote this:

   1. post-compose
         http://wiki.geneontology.org/index.php/Annotation_Cross_Products
         - annotate to P and C as normal, using two annotations
         - in the annotation for P, put "occurs_in(C)" in col17

However, we don't currently explicitly link a P annotation with a C term 
in the way that he writes in his summary of the post-compose approach.

I can see advantages and disadvantages of both approaches, either
pre-composing or post-composing. However, right now, it seems that we
are kind of half and half, where we have created localization-specific
process terms for some things, but not for lots of others.  A big
problem with this half and half situation for me, as an annotater and
ontology developer, is that it is not clear when it is, or is not,
appropriate to ask for a new localization-specific process terms.

If we are on the path of fully instantiating all possible 
localization-specific process terms, we will have a vast expansion of the 
number of terms. Even currently, it's not just the term "mitochondrial 
translation", but the children under that term already duplicate whole 
sections of the children of "translation", and then there are things we 
don't even have localization-specific P terms for, like the mitochondrial 
specific proteases that initiated the discussion...

-Karen




On Wed, 4 Mar 2009, 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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>> 
>
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