[Ontology-editors] CC organization question for xps

Wed Nov 19 02:03:44 PST 2008

Hi,

I'm sorry, I'm still not intellectually satisfied, because I don't 
understand the reasoning behind this part:

   > We do NOT make the link between 'cellular component assembly' and
   > 'anatomical structure formation'

If we are saying that any cellular component is a tiny little anatomical 
structure, i.e.

   anatomical structure [some CARO ID, I presume]
   [i] cellular component GO:0005575

then it follows logically that

   anatomical structure formation GO:[0048646 or new ID; see below]
   [i] cellular component assembly GO:0022607

So why don't we want to make this relationship? If it's because the 
existing anatomical structure formation term is_a developmental process, 
we can get around that by either moving or renaming GO:0048646 and adding 
a new term, yielding:

   biological process
   [i] anatomical structure formation (GO:0048646 or GO:new)
   --[i] anatomical structure formation involved in development (GO:new or 
GO:0048646)
   ----[child terms; see below]
   --[i] cellular component assembly GO:0022607

   developmental process
   [i] anatomical structure formation involved in development (GO:new or 
GO:0048646)
   --[all the current formation-of-macroscopic-anatomical-structure 
children of GO:0048646 would go here]

Or we can abandon the notion that a CC is_a anatomical structure (which 
must mean there are some CCs that aren't anatomical structures). I'm not 
sure I feel very strongly whether we keep or drop that idea, but I do 
think that we should either make both statements or neither; it's 
logically inconsistent to have just one.

On Tue, 18 Nov 2008, Tanya Berardini wrote:

> Hello everyone!
>
> After discussing with David this morning, and him dissuading me from
> proposing that not ALL cellular components are anatomical structures
> (fuggedabout FMA), I think I get what he's proposed.
>
> Let me try to restate so that I'm sure I've understood him correctly. We do
> NOT make the link between 'cellular component assembly' and 'anatomical
> structure formation' but instead, we create some new terms (the ones below
> containing the string 'involved in morphogenesis') that allow us to link up
> only those children of 'cellular component organization' that should have
> ties to 'developmental process.'
>
> Now:
>
> cellular process
> --[i]cellular component organization
> ----[i]cellular component assembly
> ----[i]cellular component disassembly
> ----[i]cellular component maintenance
> ----[i]cellular structure morphogenesis
>
> developmental process
> --[i]cellular developmental process
> ----[i]cellular structure morphogenesis
>
> developmental process
> --{several steps}anatomical structure morphogenesis
> ----[i]cellular structure morphogenesis
>
> Future:
>
> cellular process
> --[i]cellular component organization
> ----[i]cellular component assembly
> ------[i]cellular component assembly involved in morphogenesis (GO:new)
> ----[i]cellular component disassembly
> ------[i]cellular component disassembly involved in morphogenesis (GO:new)
> ----[i]cellular component maintenance
> ------[i]cellular component maintenance involved in morphogenesis (GO:new)
> ----[i]cellular component morphogenesis (RENAMED FROM: cellular structure
> morphogenesis)
> ------[p]cellular component assembly involved in morphogenesis (GO:new)
> ------[p]cellular component disassembly involved in morphogenesis (GO:new)
> ------[p]cellular component maintenance involved in morphogenesis (GO:new)
>
> developmental process
> --[i]cellular developmental process
> ----[i]cellular component morphogenesis (RENAMED FROM: cellular structure
> morphogenesis)
>
> developmental process
> --{several steps}anatomical structure morphogenesis
> ----[i]cellular component morphogenesis (RENAMED FROM: cellular structure
> morphogenesis)
> ------[p]cellular component assembly involved in morphogenesis (GO:new)
> ------[p]cellular component disassembly involved in morphogenesis (GO:new)
> ------[p]cellular component maintenance involved in morphogenesis (GO:new)
> ----[i]anatomical structure formation
> ------[i]cellular component assembly involved in morphogenesis (GO:new)
> ----[i]anatomical structure regression
> ------[i]cellular component disassembly involved in morphogenesis (GO:new)
>
>
> How does that grab you?
>
> Tanya
>
>
>
>
> On Tue, Nov 18, 2008 at 6:11 AM, David Hill <dph at informatics.jax.org> 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
>>>>>>
>>>>>>  _______________________________________________
>>>>> Ontology-editors mailing list
>>>>> Ontology-editors at geneontology.org
>>>>> http://fafner.stanford.edu/mailman/listinfo/ontology-editors
>>>>>
>>>>
>>>>
>>>>
>> --
>> David P. Hill, Ph.D.
>> Bioinformatics Scientist: Ontology Development
>> Gene Ontology Consortium
>> The Jackson Laboratory
>> www.geneontology.org
>> www.informatics.jax.org
>>
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>
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