[Go] addition of localization specific process terms ?

[Valerie Wood]

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.

Another 'for' arguement is that, the more specific terms can have 
additional parentage. For example, mitochondrial DNA replication, can 
have parents to mitochondrial genome maintenance and mitochondrial 
organization, which would not be possible if there was no mitochondrial 
replication term. This would make lots more work as you would need to 
make concurrent annotations to 
'mitochondrial genome maintenance' and 'DNA replication". 

I spoke to Midori about after the meeting and apparently  the terms 
which it was agreed to purge from GO for this reason (very early in GO) 
were those  which combined Component and Function (not Process), so this 
may be the source of the confusion. Apparently some  mitochondrial 
processes got purged  at the same time (i.e mitochondrial translation), 
but these were subsequently added back.

Val



Chris Mungall wrote:

>
> First, just to emphasize an important point:
>
> An annotation to a term "P that occurs_in C" carries *more*  
> information than two independent annotations to P and C. This can be  
> seen if we have 4 annotations, to P1, P2, C1 and C2. Currently we 
> have  no way of knowing if this means that P1 occurs_in C1 or C2 or 
> neither  or both, and similarly for P2.
>
> Thus we need a way to annotate to "P that occurs_in C" if we are to  
> begin to fully capture the biology. There are two options
>
> 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
>
> 2. pre-compose: create a term "P that occurs_in C"
>     (and optionally for now, but required in the future, add the XP  
> definition[*])
>
> So your question is: how do we know when to choose 1 vs 2?
>
> My own personal guideline is whether or not the location of P is an  
> 'accidental' property of P, or something fundemental.
>
> For example: translation in the forebrain is (I am guessing) not  
> fundamentally different from translation in the midbrain. The 
> cellular  machinery goes through roughly the same sequence of steps 
> using the  same materials. You can imagine 'transplanting' the 
> process. There's  not much you would say in the definition of this 
> term other than -  translation that occurs in the forebrain.
>
> However, mitochondrial translation is fundamentally different from  
> nuclear translation because a different genetic code is used.
>
> This argues strongly for "forebrain translation" being annotated by  
> composing the description at annotation time (annotation xp), and  
> mitochondrial translation being pre-composed in the ontology (and  
> logically defined in bp_xp_cc).
>
> Of course, I deliberately chose a clear cut example. Other cases will  
> be more difficult. But this isn't a worry, because the two methods 
> are  logically equivalent, so long as we keep bp_xp_cc up to date, and 
> are  clear about which relations to use.
>
> Cheers
> Chris
>
> [*] see 
> http://wiki.geneontology.org/index.php/XP:biological_process_xp_cellular_component 
>
>
> On Mar 3, 2009, at 3:16 PM, Karen Christie wrote:
>
>> Hi,
>>
>> In last week's Reference Genomes annotation jamboree, a question came
>> up about whether/when it is appropriate to add localization specific
>> process terms. We'd like clarification of the GOC's current practice
>> on this issue. More details are below.
>>
>> thanks,
>>
>> -Karen
>>
>>
>>
>> We were discussing the appropriate process terms for the LONP1 group
>> of genes, which are involved in proteolysis of proteins in the
>> mitochondrial matrix. The question came up regarding whether it would
>> be appropriate to have a specific term for mitochondrial proteolysis,
>> considering that we already have terms like:
>>
>> - ER-associated protein catabolic process (GO:0030433)
>> - mitochondrial translation (GO:0032543)
>>
>> At one time, the philosophy on this was to have one term representing
>> the basic process, and to indicate localizations using the component
>> annotations. However, more recently, terms such as the two listed
>> above have been added to GO.
>>
>>
>> Arguments in favor of localization specific process terms included:
>>
>> -- 1. the fact that a different set of genes is involved in a given
>> "process", e.g. mitochondrial translation versus cytoplasmic
>> translation
>>
>> -- 2. being able to look for terms enriched in a process such as
>> "mitochondrial translation", without having to also use a component
>> term to narrow the search to the mitochondrial genes (this is
>> apparently not possible in many tools)
>>
>>
>> Arguments against having localization specific process terms included:
>>
>> -- 1. unnecessary proliferation of terms in the ontology, since the
>> localization can be obtained via the component annotations
>>
>>
>> So, for going forwards, we'd like clarification of when it is or is
>> not appropriate to request localization specific process terms and on
>> the guiding principles for deciding when/if such terms are  appropriate.
>>
>> thanks,
>>
>> -Karen
>>
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>
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>
>



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