[Annotation] cellular processes - renaming some terms

[Suzanna Lewis]

Understood, but the first message seemed to imply that the renaming  
actually fixed the underlying logical problem.

Axiom 1: Names should be as close to what a biologist would use in  
natural language
Axiom 2: Names should be clearly indicative of their intended meaning  
(as possible)

And sometimes these 2 axioms are in tension.

In this particular case however their is a second, and more  
fundamental, problem to be solved.

Either corresponding terms are needed under organismal, or they are  
not. That is the question to be answered. (and this is what prompted  
my 1st e-mail, because merely renaming doesn't address this nub)

-S

On Aug 21, 2008, at 9:24 AM, D'Eustachio, Peter wrote:

> "Doesn't change anything" except in the sense that it forces the  
> issue.
> To the extent that these terms have been (incorrectly) attached to
> processes that intrinsically involve multiple cells or tissues (or,
> possibly, multiple individual organisms in a symbiotic community), the
> change makes the error explicitly visible. The name change is formally
> redundant in that the information is already present in parents of  
> these
> terms but for those of us who tend to find appropriate-looking terms  
> by
> browsing through the leaves of the ontology and ignoring the branches
> they're attached to, this looks like a feature, not a bug.
>
> Peter
>
> -----Original Message-----
> From: annotation-bounces at genome.stanford.edu
> [mailto:annotation-bounces at genome.stanford.edu] On Behalf Of Suzanna
> Lewis
> Sent: Thursday, August 21, 2008 12:16 PM
> To: Midori Harris
> Cc: GO Annotation list
> Subject: Re: [Annotation] cellular processes - renaming some terms
>
>
> 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
>>>
>>
>
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