W3C home > Mailing lists > Public > public-semweb-lifesci@w3.org > March 2009

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:

http://www.nature.com/nature/journal/v95/n2372/abs/095178b0.html

"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."

Cheers,

-Kei

>
> Pat
>
>
>>
>> -Kei
>>
>>
>
> ------------------------------------------------------------
> IHMC                                     (850)434 8903 or (650)494 3973
> 40 South Alcaniz St.           (850)202 4416   office
> Pensacola                            (850)202 4440   fax
> FL 32502                              (850)291 0667   mobile
> phayesAT-SIGNihmc.us       http://www.ihmc.us/users/phayes
>
>
>
>
>
>
Received on Thursday, 26 March 2009 15:40:13 UTC

This archive was generated by hypermail 2.4.0 : Friday, 17 January 2020 17:20:41 UTC