[Annotation] cellular processes - renaming some terms

[Midori Harris]

On Thu, 21 Aug 2008, Suzanna Lewis wrote:

>
> 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.

My enquiry is meant to ensure that the terms have been used correctly. If 
not, our current policies dictate that they should be moved rather than 
made obsolete.

>
>> 
>> 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.

Renaming will help annotators avoid errors in the future. Also, for at 
least some of the terms in question, a new organismal-level term will be 
required, and in those cases renaming the existing term will be essential 
to avoid a string conflict (name redundancy).

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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>>>> Annotation at geneontology.org
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>>> 
>