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[Gofriends] linguistic analysis of GO terms -- pigmentation

Jane Lomax jane at ebi.ac.uk
Wed May 19 05:04:42 PDT 2010


I don't think that those papers are describing the disruption of a 
normal pigment deposition process:

Pigmentary glaucoma results when deposition of excessive pigment in the 
trabecular meshwork (as a result of liberation of pigment from the 
posterior iris epithelial surface in response to rubbing against the 
lens zonules) causes elevated intraocular pressure and subsequent optic 
disc damage

So basically bits of pigment shear away from the iris and prevent the 
eye being able to regulate its pressure. The pigment itself was laid 
down during development...

Jane

Colleen E Crangle, Phd wrote:
> They were interesting videos anyway!
>
> I have come across references that seem to me to present pigment 
> deposition as a distinct process -- when there is abnormal ocular 
> pigmentation associated with glaucoma, for instance. So here we would 
> have pigment deposition that is not developmental?
>
> ----- Original Message ----- From: "John Matese" 
> <jcmatese at genomics.princeton.edu>
> To: "Jane Lomax" <jane at ebi.ac.uk>
> Cc: "Colleen E Crangle, Phd" <crangle at stanford.edu>; 
> <gofriends at genome.stanford.edu>
> Sent: Tuesday, May 18, 2010 2:10 PM
> Subject: Re: [Gofriends] linguistic analysis of GO terms -- pigmentation
>
>
>> 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
>>
>>
>>
>>
>>


-- 
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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