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Re: Less strong equivalences

From: Kei Cheung <kei.cheung@yale.edu>
Date: Thu, 26 Mar 2009 08:59:59 -0400
Message-ID: <49CB7C4F.5030407@yale.edu>
To: Phillip Lord <phillip.lord@newcastle.ac.uk>
CC: Pat Hayes <phayes@ihmc.us>, eric neumann <ekneumann@gmail.com>, Bijan Parsia <bparsia@cs.manchester.ac.uk>, W3C HCLSIG hcls <public-semweb-lifesci@w3.org>
Phillip Lord wrote:

>Pat Hayes <phayes@ihmc.us> writes:
>>>From your descriptions, I can't tell which one would best handle the
>>>following situation:
>>>"Object 1 refers to exactly the same molecule (exemplar) as object 2 refers
>>That sure sounds like sameAs, applied to molecules. Why isn't sameAs good
>>enough here? What goes wrong?
>I can think of very few occasions when we want to talk about a molecule;
>we need to talk about classes of molecules. We can consider this as
>problematic even with a very simple example. 
>Let's assume we have two databases with information about Carbon. Do we
>use "sameAs" to describe the atoms that they are talking about? 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?
>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, 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. 
>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.
>Hence the evolutionary biologist says all the insulins are the same. The
>medic says that they are different. And neither of them care about
>different types of carbon (unless they are C14-dating). 
>I don't think that there is a generic solution here which is not too
>complicated to use. 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. 
That's the gap between practice and theory (philosophy). It's so 
difficult if not impossible to capture every possible context 
associating with an object/class at different levels (atomic, molecular, 
cellular, organismic, ...). Other dimensions include temporal (e.g., 
different developmental stages), spatial (e.g., transport proteins), 
environmental, variant, ... I agree that some of these problems are just 
too complicated and of combinatorial nature. My question is: is there 
any compromise between "crisp" sameAs and "fussy" sameAs?

Received on Thursday, 26 March 2009 13:01:33 UTC

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