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[Gofriends] linguistic analysis of GO terms -- pigmentation

David Osumi-Sutherland djs93 at
Sun May 16 12:57:28 PDT 2010

Hi Colleen,

On 14 May 2010, at 04:00, 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?

Is the distinction being made?  One important thing to note about  
ontologies (certainly those expressed in OBO and OWL) is that they  
follow an open world assumption.  One result of this is that classes  
that are not declared to be disjoint (non overlapping) should not be  
assumed to be.   Note - I doubt you will be able figure out whether  
two classes are disjoint by linguistic analysis.  This would require  
analyzing the structure of the ontology itself.

- David

> 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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David Osumi-Sutherland, PhD
Ontologist / Curator
Virtual Fly Brain / FlyBase
Department of Genetics
University of Cambridge
Downing Street
Cambridge, CB2 3EH
+44 (0)1223 333 963

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