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Re: Less strong equivalences

From: Kei Cheung <kei.cheung@yale.edu>
Date: Thu, 26 Mar 2009 11:39:26 -0400
To: Pat Hayes <phayes@ihmc.us>
Cc: Phillip Lord <phillip.lord@newcastle.ac.uk>, eric neumann <ekneumann@gmail.com>, Bijan Parsia <bparsia@cs.manchester.ac.uk>, W3C HCLSIG hcls <public-semweb-lifesci@w3.org>
Message-id: <49CBA1AE.3040906@yale.edu>
Pat Hayes wrote:
> On Mar 26, 2009, at 7:59 AM, Kei Cheung wrote:
>> 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, ...).
> Its difficult. It takes time and work, and often you need specialists 
> to help you do it right. Its not something that you can toss off one 
> afternoon over a beer. It costs real money. (And its called 
> "engineering", by the way, for this reason.) But it can be done, its 
> by no means impossible.
>> 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.
> I don't agree. Im working (with others) on a temporal ontology for 
> biological applications right now. It is complicated, but not "just 
> too" complicated.
>> My question is: is there any compromise between "crisp" sameAs and 
>> "fussy" sameAs?
> No way to answer, as nobody has yet told us ANYTHING about what the 
> vague sameAs is supposed to be like, only what its not supposed to be 
> like.
This article published almost 100 years ago in Nature might shed some 
light to this problem:


"Inexact Analogies in Biology
THE philosopher of the forum is notorious for the looseness of his 
analogical arguments from biology, and biologists themselves deserve 
castigation for their lax terminology. Even a Galton can write: " 
Parents are very indirectly and only partially related to their own 
children." Every word has its halo, and may be regarded according to 
one's point of view as either a potted poem or a tabloid theory."



> Pat
>> -Kei
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Received on Thursday, 26 March 2009 15:40:13 UTC

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