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[Gofriends] linguistic analysis of GO terms -- pigmentation

Crangle at Converspeech crangle at converspeech.com
Wed May 19 08:27:14 PDT 2010


I see. It's a lot more complicated than first appears/

----- 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: Wednesday, May 19, 2010 5:04 AM
Subject: Re: [Gofriends] linguistic analysis of GO terms -- pigmentation


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





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