phenotype definition unsatisfactory

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By the definition of phenotype, what about an individual isn't one?

Original issue reported on code.google.com by alanruttenberg@gmail.com on 4 Sep 2009 at 11:14

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Original comment by alanruttenberg@gmail.com on 4 Sep 2009 at 11:16

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Issue from Melanie Courtot:
> 1.a. clinical phenotype
> definition reads "A clinically abnormal phenotype." which doesn't match the
> label and is circular.

Original comment by albertgo...@gmail.com on 5 Jan 2010 at 7:13

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Issue from Melanie Courtot:
> 1.b. disease phenotype
> definition reads "A clinically abnormal phenotype that is characteristic of
> a single disease." Per this definition it should be a subclass and not
> sibling of clinical phenotype.

Original comment by albertgo...@gmail.com on 5 Jan 2010 at 7:14

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'clinical phenotype' is still defined as "A clinically abnormal phenotype."
I think this definition is good.

The definition of 'disease phenotype' is "A clinically abnormal phenotype that 
is characteristic of a single disease."
This definition is also good.

The problem is that disease phenotype is a sister class of clinical phenotype.  
Based on the definitions of these classes, either disease phenotype should be 
made a child of clinical phenotype or the definition of one or both classes 
should be changed to make it clear that this proposed change would be 
inappropriate.

Original comment by Alexande...@gmail.com on 12 Jun 2012 at 3:25

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Two concerns are being expressed: (a) whether the OGMS definition of 
'phenotype' and its children is satisfactory (related is whether 'phenotype' 
should be imported from or referenced to PATO); (b) given the current 
definitions, logic dictates that 'disease phenotype' be a child of 'clinical 
phenotype'.

Melanie's second comment (#3) and Alex's recent comment (#4) directly relate to 
(b), which is also being discussed in this thread: 

http://code.google.com/p/ogms/issues/detail?id=62

First, for clarity and to avoid duplication, I recommend these two threads be 
combined, and one closed. Second, I recommend that 'disease phenotype' be made 
a child of 'clinical phenotype' and discussion continue as to whether 
definitions need to be changed.
-
Mark

Original comment by mpjens@gmail.com on 12 Jun 2012 at 6:30