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[Gofriends] linguistic analysis of GO terms -- pigmentation

Jane Lomax jane at ebi.ac.uk
Tue May 18 13:54:00 PDT 2010


Hi Colleen - yes, your new definitions are pretty accurate.

I don't *think* there is a distinct process of depositing pigment within a 
cell - the problem is that deposition isn't defined - is it just does it 
mean the depositing of pigment only at a tissue level? Or would it also 
apply, say, to a situation where pigment was transported to a particular 
organelle within a cell (I have no idea whether the latter happens in 
nature btw - getting rather out of my depth with the biology here!)

Anyone who knows more about the biology should please jump in!

Jane



On Tue, 18 May 2010, Colleen E Crangle, Phd wrote:

> How interesting. Thanks, Jane. This is beginning to make sense. Do the following revised definitions capture what you're saying?
>
>  GO:0043473 : pigmentation: The deposition or aggregation of coloring matter in an organism, tissue or cell
>          GO:0048066 : developmental pigmentation: The developmental process that involves the movement of pigment-containing cells to deposit coloring matter within a tissue or organism.
>                  GO:0048067 : cuticle pigmentation: Establishment of a pattern of pigment in the cuticle of an organism.
>                  GO:0048069 : eye pigmentation: Establishment of a pattern of pigment in the eye of an organism.
>                  GO:0048071 : sex-specific pigmentation: Establishment of a pattern of pigment in one sex that is not observed in the other sex.
>          GO:0043476 : pigment accumulation: The aggregation of coloring matter in a pigment-containing cell that is in particular tissue or a particular part of an organism, occurring in response to some external stimulus.
>
> And one other clarification. Commenting on the old definition "The developmental process that results in the deposition of coloring matter in an organism, tissue or cell" you say for a cell this process wouldn't be developmental.
>
> My question: Is there a distinct process that involves depositing coloring matter in a cell? As opposed to 1) pigment accumulating in a pigment-containing cell and 2) pigment-containing cells moving.
>
> Colleen
>
>
> ----- Original Message -----
> From: "Jane Lomax" <jane at ebi.ac.uk>
> To: "Colleen E Crangle, Phd" <crangle at stanford.edu>
> Cc: <gofriends at genome.stanford.edu>
> Sent: Tuesday, May 18, 2010 12:53 PM
> Subject: Re: [Gofriends] linguistic analysis of GO terms -- pigmentation
>
>
>> Hi again Colleen - apologies, upon closer examination this turned out to
>> be more complicated than it looks.
>>
>> So it looks like the 'pigment accumulation' term is supposed to describe
>> the aggregation of pigment within a pigment-containing cell - note that
>> the definition is rather misleading here becuase it talks about accumulation
>> 'in an organism, tissue or cell' when in fact the accumulation within a
>> tissue or organism is just the result of the accumulation within
>> individual cells - more like a phenotypic observation.
>>
>> The developmental pigmentation term describes the movement of the
>> pigment-containing cells themsleves to deposit pigment within a tissue or
>> organism (note that the definition here is misleading too: "The
>> developmental process that results in the deposition of coloring matter in
>> an organism, tissue or cell." - for a cell this process wouldn't be
>> developmental).
>>
>> So in summary, the defintions of these terms could do with looking at, but
>> in fact I think you are right, the distinction is being made bewteen
>> pigment deposition (developmental) and pigment accumulation
>> (physiological). I'm not entirely sure they warrant a common parent term
>> to be honest, as they don't really have much in common other that they
>> involve pigment.
>>
>> Jane
>>
>> On Tue, 18 May 2010, Colleen E Crangle, Phd wrote:
>>
>>> Hi Jane,
>>>
>>> Thanks for the clarification. Is an intended distinction being made
>>> between pigment aggregation and pigment deposition? Most of the time
>>> pigmentation-related terms in the ontology include the phrase
>>> "deposition or aggregation of coloring matter."
>>>
>>> Colleen
>>>  ----- Original Message -----
>>>  From: Jane Lomax
>>>  To: Colleen E Crangle, Phd
>>>  Cc: gofriends at genome.stanford.edu
>>>  Sent: Tuesday, May 18, 2010 2:40 AM
>>>  Subject: Re: [Gofriends] linguistic analysis of GO terms -- pigmentation
>>>
>>>
>>>  Hi Colleen - David is absolutely right - no such distinction is being
>>> made. I would say developmental pigmentation almost certainly involves
>>> some pigment aggregation, although this isn't stated in the ontology.
>>>
>>>  Jane
>>>
>>>  Colleen E Crangle, Phd wrote:
>>>    Dear GO friends,
>>>
>>>    I'm doing a linguistic analysis of biological process terms in GO and, as a non-biologist, have encountered a puzzle in some terms related to pigmentation.
>>>     GO:0043473 : pigmentation: The deposition or aggregation of coloring matter in an organism, tissue or cell
>>>
>>>     GO:0048066 : developmental pigmentation: The developmental process that results in the deposition of coloring matter in an organism, tissue or cell.
>>>
>>>     GO:0043476 : pigment accumulation: The aggregation of coloring matter in a particular location in an organism, tissue or cell, occurring in response to some external stimulus.
>>>
>>>
>>>    Pigment accumulation, a process that is in response to some external stimulus, is differentiated from developmental pigmentation, driven presumably by internal cues. These processes, however, are further differentiated by coloring matter being aggregated in the first and deposited, not aggregated, in the second.  Depositing and aggregating coloring matter differ in their verbal aspect--this is what interests me here.
>>>
>>>    So my question is: Is it really not possible for pigment aggregation to play any role in developmental pigmentation or for pigment deposition to play any role in response to external stimuli? Is this distinction intended?
>>>
>>>    The subtype processes under developmental pigmentation (cuticle, eye, and sex-specific pigmentation) give no clue and have their own aspectual problems.
>>>
>>>    I'd appreciate any thoughts.
>>>
>>>    Colleen
>>> ----------------------------------------------------------------------------
>>> _______________________________________________
>>> Gofriends mailing list
>>> Gofriends at geneontology.org
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>>>
>>>
>>>
>>
>> --
>> Dr Jane Lomax
>> GO Editorial Office
>> EMBL-EBI
>> Wellcome Trust Genome Campus
>> Hinxton
>> Cambridgeshire, UK
>> CB10 1SD
>>
>> p: +44 1223 492516
>> f: +44 1223 494468
>> _______________________________________________
>> Gofriends mailing list
>> Gofriends at geneontology.org
>> http://fafner.stanford.edu/mailman/listinfo/gofriends
>>

-- 
Dr Jane Lomax
GO Editorial Office
EMBL-EBI
Wellcome Trust Genome Campus
Hinxton
Cambridgeshire, UK
CB10 1SD

p: +44 1223 492516
f: +44 1223 494468



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