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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
>>>to"
>>>      
>>>
>>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. 
>
>Phil
>
>
>  
>
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?

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

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