[Ontology-editors] CC organization question for xps

[Midori Harris]

It sounds good to me, but what with my yeastie-beastie background I'm 
perhaps not the best person to comment on the bigger-than-cellular 
phenomena.

Whatever we do will have consequences for the xp set I've been looking at.
m

On Tue, 18 Nov 2008, David Hill wrote:

> We could change the existing terms to be for example 'anatomical structure 
> formation involved in morphogenesis'. Can anyone think of a non-cellular 
> component that would not fall under this category? If not, then the cellular 
> component terms can live outside this part of the graph and have specific 
> children that live under 'involved in morphogenesis terms'.
>
>
>
> Midori Harris wrote:
>> Yup, I think we're converging on a revised model nicely here.
>> 
>> We do still have to consider whether anatomical structure formation can 
>> still stay under developmental process, in light of our emerging agreement 
>> that cellular component assembly is sometimes -- but not always -- 
>> developmental, and we haven't questioned (second-guessed) our decision that 
>> a CC is_a anatomical structure. The implication is that anatomical 
>> structure formation is not always developmental, and we need new terms.
>> 
>> m
>> 
>> On Tue, 18 Nov 2008, David Hill wrote:
>> 
>>> Tanya talked to me about this issue yesterday. I share her concerns and I 
>>> think that this is why we have a term for cellular structure morphogenesis 
>>> [GO:0032989] 
>>> <http://www.informatics.jax.org/searches/GO.cgi?id=GO:0032989#top> and a 
>>> term for cellular component organization [GO:0016043] 
>>> <http://www.informatics.jax.org/searches/GO.cgi?id=GO:0016043#top> in the 
>>> first place. The morphogenesis term is a developmental process. I think 
>>> the key distinguishing factor is that development is a progression of the 
>>> cell over time, from an immature state to a mature state if you will. Some 
>>> of the terms that Tanya points out don't reflect that. They are things 
>>> that happen in a cell as just part of its routine being. I think actin 
>>> cortical patch formation would certainly work for this. So the bottom line 
>>> is, I take back what I suggested yesterday.
>>> 
>>> I do think that in some cases the assembly of a cellular component is in 
>>> fact a developmental process. It's when it also is part of the progression 
>>> of the cell over time from a less mature to a more mature state. I know 
>>> it's a fine line, but it's certainly a line. Hey, that's why we work as a 
>>> team!
>>> 
>>> David
>>> 
>>> Midori Harris wrote:
>>>> Well, it's pretty much consistent with what I alluded to much more 
>>>> briefly in my last contribution to this thread, so I'm also keen to hear 
>>>> what David and Tanya have to say about it.
>>>> 
>>>> m
>>>> 
>>>> On Tue, 18 Nov 2008, Jennifer Deegan (nee Clark) wrote:
>>>> 
>>>>> Hi Tanya,
>>>>> 
>>>>> Are you saying that you don't feel that the process by which subcellular 
>>>>> components are generated should really be is_a to developmental process? 
>>>>> I feel this, but I'm not sure whether I have missed some intention you 
>>>>> had in making this graph, as the developmental process def currently 
>>>>> does include subcellular structures:
>>>>> 
>>>>> def:A biological process whose specific outcome is the progression of an 
>>>>> integrated living unit: an anatomical structure (which may be a 
>>>>> subcellular structure, cell, tissue, or organ), or organism over time 
>>>>> from an initial condition to a later condition.
>>>>> 
>>>>> To my mind it would make more sense somehow to distinguish between the 
>>>>> kind of multicellular structures that undergo classical developmental 
>>>>> processes, and the subcellular structures that are generated in 
>>>>> different ways. If my understanding is correct then I think maybe the 
>>>>> answer is just to do something like this:
>>>>> 
>>>>> [i]anatomical structure generation (renamed from anatomical structure 
>>>>> dev)
>>>>> ---[i]multicellular structure development (classical organ and tissue 
>>>>> and larger scale developmental processes)
>>>>> ---[i]cell development (to include things like cell differentiation as 
>>>>> now)
>>>>> ---[i]subcellular structure generation
>>>>> 
>>>>> [i]developmental process
>>>>> ---[i]multicellular structure development (classical developmental 
>>>>> processes)
>>>>> ---[i]cell development (to include things like cell differentiation)
>>>>> 
>>>>> This would take CC assembly out of under development, but keep it under 
>>>>> anatomical structure generation. It would also avoid massive 
>>>>> rearrangements of the development/morphogenesis structures that were so 
>>>>> carefully put together before. Does that make sense or have I missed 
>>>>> something?
>>>>> 
>>>>> Thanks,
>>>>> 
>>>>> Jen
>>>>> 
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>>> 
>
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