Re: [Obo-discuss] Alternative to "NCBI" taxonomy

[Wacek K. <Wac...@id...>]

Richard Biehl wrote:
> Phil,
>
> I think I see the distinction you're aiming at, so let me see if I can piece 
> it together step by step:
>
> THIRD, the sets of the above taxon that form types....
>
> Animal is a class.
> Animal is_instance_of Kingdom where Kingdom.name = "Animalia"
> Chordate is a class.
> Chordate is_instance_of Phylum where Phylum.name = "Chordata"
> Chordate is_subset_of Animal.
> Vertebrate is a class.
> Vertebrate is_instance_of Subphylum where Subphylum.name = "Vertebrata"
> Vertebrate is_subset_of Chordate.
> Mammal is a class.
> Mammal is_instance_of Class where Class.name = "Mammalia"
> Mammal is_subset_of Vertebrate.
> Cow is a class.
> Cow is_instance_of Species where Species.name = "Cow"
> Cow is_subset_of Mammal.
> Achham Cattle is a class.
> Achham Cattle is_instance_of Breed wherea Breed.name = "Achham Cattle"
> Achham Cattle is_subset_of Cow.
>
>
> Thoughts?
>   


yes.  your use of 'is a' and 'instance of' is somewhat confus(ing|ed).

FIRST, 'animal is a class' vs. 'animal is instance of kingdom' -- what's
the difference here? 
it appears to me that your 'class' here is equivalent to 'taxon';  and
'kingdom' is equivalent to 'taxon with the rank named 'kingdom''.
if this is the case, then the following hold (or might hold, if this
model is correct):
- the taxon named 'animalia' is an instance of the class named 'taxon'
- the taxon named 'animalia' is an instance of the class named 'taxon
with the rank 'kingdom'' (or simply: the class named 'kingdom')
the 'instance of' relation in both cases is the same.  it could be
called 'is a';  but see below (which applies to both versions alike).

SECOND, when you say 'animal is a class', you mean (i can't guess
otherwise) that the class named 'animal' is an instance of the
class-class named 'class'.  that's fine, but this sort of collides with
the typical interpretation of 'X is a Y' as 'every instance of X is an
instance of Y' (which would lead to 'every animal is a class').  you can
argue that here we have a class (animal) and a metaclass (class), so the
situation is clear, but that's overloading of 'is a' anyway, dispatched
on the meta-ness of classes.

THIRD, 'subset of' in the context of classes sounds bad; why not 'subclass'?

(FOURTH, the plural of 'taxon' is 'taxa'.)

vQ




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