[Go] addition of localization specific process terms ?

[Ruth Lovering]

I agree with this sentiment, however I maybe missed something about  
the creation of 'forebrain' as a C term, I think forebrain would end  
up being within a new ontology ie tissue/cell type term, not component  
term

Ruth


On 4 Mar 2009, at 12:34, Judith Blake wrote:

> I agree with having ‘P that occurs_in C’ terms and I think some of  
> this discussion, or similar, is being discussed by David et al.  for  
> discussion at the upcoming GOC meeting.
> David, btw, hopes to back at work next week.
>
> The emphasis needs to be on those cases that can be generalized to  
> some extent...as in ‘translation in the forebrain’ where each term  
> ‘translation’ and ‘forebrain’ has xref (parents in the case of  
> translation?).  This will facilitate alignment of ontologies and the  
> maintenance of consistent logical definition of the terms.
>
> These new terms will be particularly important when we get to  
> annotating microRNAs that function in the ‘regulation of translation  
> in the forebrain’ or ‘regulation...in a specific celltype’.
>
> I think these are necessary extensions of the GO to represent  
> biology.  One of the ‘issues’ with GO at the moment, when I look at  
> the literature and attend seminars, is that the GO doesn’t yet  
> include the necessary granularity to accommodate this level of  
> knowledge.
>
> Judy
>
>
> On 3/3/09 6:57 PM, "Chris Mungall" <cjm at berkeleybop.org> 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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