[Ontology-editors] CC organization question for xps

[Midori Harris]

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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