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Re: Less strong equivalences

From: Pat Hayes <phayes@ihmc.us>
Date: Thu, 26 Mar 2009 10:22:31 -0500
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: <DB417950-9FA2-41AC-95FD-B88BCCEE0C46@ihmc.us>
To: Kei Cheung <kei.cheung@yale.edu>

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  


> -Kei

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Received on Thursday, 26 March 2009 15:25:51 UTC

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