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Re: Less strong equivalences

From: Phillip Lord <phillip.lord@newcastle.ac.uk>
Date: Thu, 26 Mar 2009 15:58:15 +0000
To: Pat Hayes <phayes@ihmc.us>
Cc: eric neumann <ekneumann@gmail.com>, Bijan Parsia <bparsia@cs.manchester.ac.uk>, W3C HCLSIG hcls <public-semweb-lifesci@w3.org>
Message-ID: <877i2ctgx4.fsf@newcastle.ac.uk>
Pat Hayes <phayes@ihmc.us> writes:
>> We can consider this as
>> problematic even with a very simple example.
>>
>> Let's assume we have two databases with information about Carbon.
>
> meaning, I presume, the element with atomic number 14.

I was thinking of the carbon with atomic number 6. 



>> Maybe,
>> but what happens if one is talking about the structure of Carbon and
>> it's location in the periodic table, while the other is talking about
>> Carbon with the isotopic mix that we have in living organisms on earth?
>
> So what? They can be saying different things about the same element. Any
> isotopic mix of carbon is still carbon. 

Different isotopic mixes have different properties. Atomic masses,
melting points and so on. 


>> In biology, we have the same problem. Is porcine insulin the same as
>> human insulin? Is "real" human insulin the same as recombinant
>> human insulin? Well, the answer to all of these is no
>
> Fine, you just answered the basic ontological question.
>
>> , even though most
>> biologists will tell you that real and recombinant insulin are the same
>> because they have the same primary sequence; a medic will tell you
>> otherwise, because they have different effects. Why? Don't know.
>
> A deep question, but not a killer for ontology use.


It's not a deep question, just one to which we don't have an answer. 



>> If you make the distinctions that you might need some of the time, all
>> of the time, then you are going to end up with a very complicated model.
>
> Yes, you no doubt are. Tough. Its a complicated world.

Yes. And on of those complications is that we have to engineer for
usability as well as accuracy. 



> Formal ontologies are
> often, perhaps always, more complicated than the  informal 'knowledge' they
> set out to formalize. They are obliged to  make finer, more persnickety,
> distinctions between things.
>
>> Hence the evolutionary biologist says all the insulins are the same.
>
> I don't care what the anyone says, that is wrong. They are indistinguishable
> for certain purposes, but if anyone can distinguish  them at all, they are not
> the _same_.

I think that position is defensible, but unusable. 


> All these examples can be handled by making fussy distinctions between kinds
> of thing at different granularities: carbon molecules, carbon  isotopes,
> carbon the element; and then having mappings between them.   I don't know much
> about insulin, but it sounds from the above that the  same trick would work.
> It is tedious and hair-splitting to set this  up, but once in place its fairly
> easy to use: you just choose the  terminology corresponding to the 'level' you
> wish to be talk ing  about. sameAs works OK at each level, but you can't be
> careless in  using it across levels.
>
> If this makes you want to groan, I'm sorry. But ontology engineering is rather
> like programming. 

Actually, I quite like programming. I also know how to split things out
in the way you describe. 


> It requires an unusual attention to detail and a willingness to write
> a lot of boring stuff, because its for computers to use, and they are
> as dumb as dirt and have to have every little thing explained to them
> carefully. And yup, its complicated. Until AI succeeds, it will always
> be complicated.

I'd quite enjoy it if you could patronise me a little more please. 


>> The only solution (which is too complicated) I can
>> think of is to do what we do when we have this problem in programming;
>> you use a pluggable notion of equality, by using some sort of comparitor
>> function or object. I don't think that this is an issue for OWL myself;
>> I think it's something we may need to build on top of OWL.
>
> It belongs in your ontology for carbon and insulin, not in OWL.

Is that not what my last sentance says? 

Phil
Received on Thursday, 26 March 2009 15:59:03 UTC

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