[Gofriends] linguistic analysis of GO terms -- pigmentation

[Jane Lomax]

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