[Ontology-editors] CC organization question for xps

[David Hill]

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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>>
>>

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