- From: Pat Hayes <phayes@ihmc.us>
- Date: Thu, 26 Mar 2009 10:22:31 -0500
- To: Kei Cheung <kei.cheung@yale.edu>
- 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>
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. 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 15:25:51 UTC