Add "phenotype" to COB

[matentzn]

fixes #123

Let the war begin.

[wdduncan]

Yes ... I imagine there will be a lot of back forth about this.

@matentzn Are you proposing that by making phenotype a top level class that a particular phenotype may be a characteristic, material entity, or process? This suggests to me that it would be better to define a phenotype of object property (which I mentioned here); e.g.:

• facial tics phenotype of Tourette syndrome
• tumor phenotype of cancer
• discoloration phenotype of rash

[addiehl]

I'm not against the object property approach but I think the inverses should be used here (in a weakened form in some cases):
Tourette syndrome sometimes associated with phenotype facial tics
cancer associated with phenotype tumor (although perhaps cancer disease has basis in tumor might be better although this is a bit chicken and egg)
rash sometimes associated with phenotype discoloration

[matentzn]

This class is intended to group the about 100,000 phenotype classes under UPHENO: https://ols.monarchinitiative.org/ontologies/upheno2/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUPHENO_0001001&viewMode=PreferredRoots&siblings=false

[matentzn]

an alternative would be to avoid the shared "phenotype" term, and use phenotypic effect instead, as @dosumis has been suggesting.

[wdduncan]

@matentzn In UPHENO, phenotype is a type of quality.

Shouldn't it be the same in COB?

[matentzn]

Yes, this is really controversial, and should probably not be in Upheno..

[wdduncan]

There hasn't been any discussion on this in quite a while.
Since the proposed definition for phenotype (or perhaps phenotypic effect) is:

The set of observable characteristics of an individual resulting from the interaction of its genotype with the environment.

Would it be better to define a term for "environment-genotype interaction" (if one doesn't exist) and the define a phenotypes as "output of" that process? This would still encompass a large number of different types of things, but perhaps make the term "phenotype" more palatable?