[Ontology-editors] CC organization question for xps

[David Hill]

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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-- 
David P. Hill, Ph.D.
Bioinformatics Scientist: Ontology Development
Gene Ontology Consortium
The Jackson Laboratory
www.geneontology.org
www.informatics.jax.org