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[Gofriends] linguistic analysis of GO terms -- pigmentation

Jane Lomax jane at
Tue May 18 02:40:08 PDT 2010

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.


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.
> is_a relationship _GO:0043473 :_ _pigmentation:_ The deposition or 
> aggregation of coloring matter in an organism, tissue or cell
> is_a relationship GO:0048066 : developmental pigmentation: The 
> developmental process that results in the deposition of coloring 
> matter in an organism, tissue or cell.   
> is_a relationship _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
Wellcome Trust Genome Campus
Cambridgeshire, UK
CB10 1SD

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

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