[Go] addition of localization specific process terms ?

[Chris Mungall]

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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