[Annotation] cellular processes - renaming some terms

[Midori Harris]

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.

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

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.

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
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>