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cell component ontology

Smith, Barry phismith at
Tue Nov 8 06:04:51 PST 2005

Dear Larry (and, by transitivity, dear Peter, and everyone else),

Addressing Peter you write:

>You are clearly right that an ontology designer has a range of choices
>about which concepts will be modeled as instances and which as
>classes, and that the correct choice depends on the the uses for which
>an ontology is designed.  As you say in the excerpt below, you were
>intended in make a particular point in your set of choices.
>However, when contributing an ontology to the public, it seems to me
>that it is important to obey the principle of least commitment.  That
>is, an ontology provided to the public with the intention that it be
>used in many different ways should be constructed to make the fewest
>commitments (in formal semantic terms) compatible with the authors

I agree completely with the second paragraph, and with its 
implication that an ontology should represent classes (better called 
'types' or 'kinds') in reality. However, I still have problems with 
the first paragraph, because I still do not know how the word 
'instance' is to be understood.

An instance is, surely, (for example) this cell nucleus visible in 
the Petri dish on your bench, here, now. But then to replace a 
representation of (the class) cell nucleus in an ontology with a 
representation of exactly this one single cell nucleus would not be 
useful for any purpose.

If this reading of 'instance' is correct, then every class has 
instances -- not just classes treated as leaf nodes (i.e. classes 
with no children in the ontology), but even the various parent and 
grandparent classes.

If this reading of 'instance' is not correct, then which reading are 
we supposed to employ?
Yours, confusedly,

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