Three question on phenotype

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1. Does phenotype include behavioral phenotype (e.g. gross motor skill). I 
would advocate this.

2. Clinical phenotype and disease phenotype are siblings, yet the definitions 
read as follows:

"A clinically abnormal phenotype."
"A clinically abnormal phenotype that is characteristic of a single disease."

This looks like disease phenotype ought to be a subtype to clinical phenotype. 
Please, either change the definitions or make disease phenotype a subtype to 
clinical phenotype.

3. Where do normal phenotypes go? I presume they are just subtypes of 
phenotype. If so, then I hope we agree that both clinical and disease phenotype 
should get a formal definition.

Original issue reported on code.google.com by MBrochhausen@gmail.com on 6 Feb 2011 at 3:38

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In regards to item 2, I agree that a fix is required. I believe 'disease 
phenotype' should be a subtype of 'clinical phenotype'. Not only according to 
our current definition, but it seems intuitively as well, any instance of a 
'disease phenotype' will also be an instance of a 'clinical phenotype'. 
Conversely, an instance of a 'clinical phenotype' will not always be a 'disease 
phenotype'. Can anyone think of a reason not to make this change?

This issue has been raised in a couple of different threads, but no discussion 
has resulted such that a resolution could be achieved. As was pointed out, if 
the current hierarchy is to be maintained, then either the definitions should 
change or an elucidation should be provided to show why some phenotypes that 
are characteristic of a disease will not also be clinical phenotypes. 

Mark J

Original comment by mpjens@gmail.com on 19 Feb 2012 at 10:03

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Is a plant disease phenotype a clinical phenotype?

Original comment by cmung...@gmail.com on 19 Feb 2012 at 10:41

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I think, Mathias and Mark propose a valid solution with the definitions as they 
are currently written.

Chris M: 

Two points: (1) OGMS does not try to further elaborate the word 'clinically', 
(2) OGMS currently considers only human organisms in-scope for being the 
subject of care (but, currently, this is tacit and only amounts to a warning to 
be careful when dealing with domains like veterinary medicine and plant 
infectious diseases).

If you are taking a broad reading of 'clinically', I don't see any reason to 
block the inference that a plant disease phenotype is a clinical phenotype. As 
long as you have some reference for the canonical anatomy and physiology for 
the plant in question, you can describe clinically abnormal phenotypes.

Original comment by albertgo...@gmail.com on 20 Feb 2012 at 3:06

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Ig OGMS is restricted to humans it should not attempt to define "disease 
phenotype", it should import this from elsewhere. It could optionally subclass 
it - e.g. "human disease phenotype"

Original comment by cmung...@gmail.com on 20 Feb 2012 at 4:37

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Chris M, could you provide some reasons that if a 'disease phenotype' is_a 
'clinical phenotype', according to the current definitions and elucidations, it 
would not apply to non-human organisms? My understanding of the the way in 
which "disease" is used outside the human domain is limited, but at first gloss 
it seems a plant that is diseased would be characterized by a clinically 
abnormal phenotype. If a disease specific to (say) a type of fern is being 
researched or treated by the requisite experts, then doesn't this fit current 
usage in OGMS? I contend the mere fact it is considered a condition that 
deviates from the canonical and requires treatment so as to restore "normal" 
functioning makes it clinically abnormal. 

As an aside, I agree that a future action item (at least for discussion) in 
OGMS development is the incorporation of external references to related or 
equivalent terms in other ontologies. I am less certain we should be outright 
importing (via MIREOT?) something as basic as 'phenotype' or 'disease 
phenotype'.

Original comment by mpjens@gmail.com on 21 Feb 2012 at 5:40

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Not all disease phenotypes are treated. Treatments are a relatively recent 
innovation but there have been disease phenotypes for a while.

Original comment by cmung...@gmail.com on 21 Feb 2012 at 9:05