[Go] addition of localization specific process terms ?

[Judith Blake]

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
>
> _______________________________________________
> Go mailing list
> Go at geneontology.org
> http://fafner.stanford.edu/mailman/listinfo/go
>

_______________________________________________
Go mailing list
Go at geneontology.org
http://fafner.stanford.edu/mailman/listinfo/go

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://fafner.stanford.edu/pipermail/go/attachments/20090304/b1c920d7/attachment-0001.html>