[Ontology-editors] CC organization question for xps

Tue Nov 18 11:11:01 PST 2008

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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>

-- 
Tanya Berardini
TAIR Curator
www.arabidopsis.org
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