[Annotation] cellular processes - renaming some terms

[Suzanna Lewis]

On Aug 21, 2008, at 9:09 AM, Midori Harris wrote:

> Renaming makes the string consistent with the definition implied by  
> the parents. The text of the natural-language definition may also  
> have to be made more explicit in some (perhaps all) of these cases,  
> but the 'cellular metabolic process' parent is what leads us to  
> suggest that the terms are intended to represent cellular processes.

?
The parentage is all that should be necessary. These are children of  
"cellular metabolic process" therefore they are all different types of  
this parent.

>
> If there are annotations not compatible with the 'cellular' parent,  
> that would make the case that the term should be moved instead.

Yes, this should be checked.

>
>
> This approach has been taken in other areas, and is consistent with  
> the GOC's agreement to take paths and annotations into account when  
> the intended meaning of a term has to be determined.

Exactly. It is the paths and location within the graph that properly  
indicates the meaning of a term. NOT the string.

So my question remains, and changing the string for these terms  
doesn't solve anything.

>
>
> m
>
> On Thu, 21 Aug 2008, Suzanna Lewis wrote:
>
>> Sorry,
>>
>> I don't see how renaming constitutes a solution.
>>
>> The question in the SF item does not appear to be a question about  
>> the name, but simply whether or not they really belong under  
>> cellular. Depending on how they are defined they could be either  
>> cellular or at the level of an organ (e.g. the liver). Either the  
>> definitions must be augmented to more clearly reflect that they are  
>> limited to cellular (and if needed corresponding terms added under  
>> organismal) or they must be moved so that they aren't logically  
>> limited to merely cellular. The definitions do seem to indicate  
>> these are at the biochemical level, so it doesn't seem to be a big  
>> deal.
>>
>> Changing the string solves nothing (and besides, we do want to keep  
>> the strings as close to natural language as possible).
>>
>> -S
>>
>> On Aug 21, 2008, at 5:24 AM, Midori Harris wrote:
>>
>>> Dear annotators,
>>> To handle the question posed in SF 2034990, we propose to rename  
>>> some terms to be consistent with their parentage. All of these  
>>> terms are is_a children of "cellular metabolic process" (GO: 
>>> 0044237):
>>> GO:0006066 : alcohol metabolic process
>>> GO:0006081 : aldehyde metabolic process
>>> GO:0043446 : alkane metabolic process
>>> GO:0043449 : alkene metabolic process
>>> GO:0043452 : alkyne metabolic process
>>> GO:0043603 : amide metabolic process
>>> GO:0009308 : amine metabolic process
>>> GO:0006519 : amino acid and derivative metabolic process
>>> GO:0006725 : aromatic compound metabolic process
>>> GO:0042445 : hormone metabolic process
>>> GO:0046950 : ketone body metabolic process
>>> GO:0042180 : ketone metabolic process
>>> GO:0043094 : metabolic compound salvage
>>> We'd like to add the word "cellular" to each of these term names  
>>> (e.g. GO:0006066 would become "cellular alcohol metabolic  
>>> process", because these terms are already implicitly cellular  
>>> processes. For any of these processes that occur at a  
>>> multicellular level, we can add a new term.
>>> Would this change pose a problem for any existing annotations? If  
>>> so, please let me know within about a week; any terms that  
>>> shouldn't be renamed to "cellular ..." can be moved out from under  
>>> "cellular metabolic process".
>>> Also shout if you have any questions.
>>> Thanks,
>>> Midori
>>> _______________________________________________
>>> Annotation mailing list
>>> Annotation at geneontology.org
>>> http://fafner.stanford.edu/mailman/listinfo/annotation
>>
>