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From: "Smith, Barry" <phismith@xxxxxxxxxxx>
Date: Sat, 05 May 2007 11:00:31 -0400
Message-id: <20070505150504.GJAT26916.mta16.adelphia.net@xxxxxxxxxxxxxxxxxxxxxxxxxxx>

>PatHayes writes:
>The real problem that
>we face is this. One can take two people who agree completely about
>the facts, and agree to use the very same logic to represent those
>facts in, and yet they will produce different ontologies. (The
>well-known example of how best to represent time and change is the
>one I know in the most detail.) Moreover, those ontologies can be
>formally inconsistent with one another. One cannot simply merge
>together sentences from two such ontologies and expect to get a
>sensible result. There are no *experiments* to resolve such
>ontological differences, since the two authors agree about the
>empirical facts; but one (for example) insists that there are two
>distinct ways of existing in time, while the other treats these
>simply as two (amongst many) ways to carve up a spatiotemporal
>universe. The two authors here might be Barry Smith and me,
>respectively. The differences are not empirical, but (sorry)
>philosophical: in fact, they are *ontological*, in the original,
>pre-AI, pre-Web, sense of that word. They reflect divergent,
>incompatible, ways of thinking about some aspect of the world.
>Differences like this cannot be resolved experimentally; and all the
>evidence so far available suggests that to even attempt to 'resolve'
>them, in the sense of deciding on a winner, is only going to alienate
>a sizeable fraction of the user base.
>Now, what should we do about this? All the proposals I have ever
>heard boil down to one of three alternatives: (1) ignore it and hope
>it will go away (2) for each such conceptual debate, decide on one of
>the alternatives and make it the single standard (somehow: perhaps by
>compulsion, as some military funders seem to assume; perhaps by
>commercial pressure, as PatC seems to suggest) or (3) find ways to
>translate between them as they arise. I strongly believe that the
>only long-term feasible method is (3), and we have made considerable
>progress along these lines, enough to suggest that the translations
>are always possible and often fairly easy, once one approaches the
>problem in a pragmatic frame of mind. If all ontologies were written
>in IKL, we could definitely do the translations for almost all of the
>problems I aware of. In particular, option (2) simply isn't going to
>work. People will simply not agree on what is the single right way to
>write ontologies. Nor should they have to: there is absolutely no
>reason why they should. Any attempt to enforce (or otherwise
>persuade) the entire planet will only produce the kind of
>interminable semi-philosophical debates that we are already having.    (01)

Pat is doing very well until he inserts the phrase 'enforce ... the 
entire planet' into the discussion. The OBO Foundry 
(http://obofoundry.org) is realizing alternative (2), for biomedical 
ontologies, by involving only certain parts of the planet on an 
entirely voluntary basis. One benefit we can claim is that we are 
giving non-experts in ontology much needed guidance as to how to 
represent, for example, size for tumors in such a way as to do 
justice to the fact that this varies with time. If all biologists 
working together on a given set of problems can be encouraged to 
represent this in the same way, then benefits of different sorts 
flow. We are visibly making progress as a result.    (02)

The OBO Foundry has no objection to mappings a la alternative (3) 
(see http://obofoundry.org/cgi-bin/table.cgi?show=mappings), though 
it has proved much more difficult in medicine than Pat here suggests. 
(3) may indeed be the right solution in the long run. But I believe 
that it can be successful only if different groups first follow 
alternative (2) in coherent fashion to create a solid basis for later 
mappings. For alternative (3) surely gives ontology developers too 
little guidance as to what to do in the short run. It is a bit like 
wanting to populate a library by encouraging people to write books 
using bits of Hebrew, bits of French, bits of Gaelic, and to 
encourage people not to worry about the resultant difficulties in 
understanding, because we will have Pat to translate it all into IKL 
and sort out translations as the need arises.
BS     (03)

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