[Go] addition of localization specific process terms ?

Wed Mar 4 05:31:09 PST 2009

Forebrain is an anatomy term, e.g.

http://www.informatics.jax.org/searches/AMA.cgi?id=MA:0000170
http://zfin.org/action/anatomy/term-detail?anatomyItem.zdbID=ZDB-ANAT-010921-534
http://fme.biostr.washington.edu:8089/FME/body.jsp?sel=Forebrain&selID=1686

The principle holds for processes that occur in specific cellular 
components.

m

On Wed, 4 Mar 2009, Ruth Lovering wrote:

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