[Gofriends] linguistic analysis of GO terms -- pigmentation

[John Matese]

Hi Jane and Colleen,

I am not certain if this in entirely diversionary, but the first thing  
this discussion made me think of was chromatophores.

http://www.youtube.com/watch?v=URrXDJy1SGk
http://www.youtube.com/watch?v=GwQ3kYVE9wo

So moving pigment around within a cell might be a process, but that  
may be different than "depositing pigment within a cell"?

-John


On May 18, 2010, at 4:54 PM, Jane Lomax wrote:

> 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
>>>> 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
>>> _______________________________________________
>>> 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
> _______________________________________________
> Gofriends mailing list
> Gofriends at geneontology.org
> http://fafner.stanford.edu/mailman/listinfo/gofriends