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Re: [ontolog-forum] Two ontologies that are inconsistent but both needed

To: "John F. Sowa" <sowa@xxxxxxxxxxx>, "[ontolog-forum]" <ontolog-forum@xxxxxxxxxxxxxxxx>
From: "Smith, Barry" <phismith@xxxxxxxxxxx>
Date: Sat, 09 Jun 2007 09:02:01 -0400
Message-id: <20070609130311.UOSY28813.mta9.adelphia.net@xxxxxxxxxxxxxxxxxxxxxxxxxxx>
At 08:44 AM 6/9/2007, John F. Sowa wrote:
>I agree on that point:
> > For we have, after all, more important work to do.
>But as I have said in previous notes, I have serious
>concerns about whether some very general and very detailed
>axiomatizations that people are proposing are worth doing.
>As an example of something very large that is certainly
>worth doing is the enormous amount of detailed modeling
>of the Boeing 787, which has cost billions of dollars.
>Yet that very large model is conceptually much simpler
>than Cyc or many of the other ontologies that have been
>  1. The airplane ontology, although large, consists of
>     a system of many independently developed models,
>     with well-defined interfaces.
>  2. The very difficult issues that Cyc must face, which
>     include social interactions of people, organizations,
>     societies, and the environment, are not required for
>     models of the 787.
>  3. The fact that the 787 and all its components are
>     artifacts implies that the engineers have total
>     control over each component.  Whenever they find
>     interactions that are difficult to axiomatize,
>     they have the option of redesigning the components.
>  4. The interfaces to any component are much simpler
>     than the components themselves, and they allow
>     engineers working on either side of the interface
>     to ignore any details on the other side that are
>     not specified in the interface.
>None of these simplifications apply to large ontologies
>such as Cyc and certain others that people have been
>In bioinformatics, for example, there are very large
>terminologies, which are widely used.  But unlike the
>Boeing 787, which has detailed mathematical and logical
>specifications for each component, the components of the
>human body have no formal specification, and most of
>the interactions across interfaces are unknown.
>That is why I have serious concerns about taking informal
>terminologies and dressing them up with formal axioms.
>I agree that axioms are necessary to do detailed reasoning,
>but one tiny mistake in one axiom can become a matter of
>life or death.
>    (01)

I think that these are indeed important 
differences between the aircraft case and the 
biology case, and I agree with you that we need 
to be cautious in what we do, or claim on behalf 
of, formal axioms. On the other hand, while we do 
not yet have detailed mathematical and logical
specifications for each component of e.g. the 
human body, including interactions across 
interfaces, there are many people working on 
providing just these things and they are already 
making considerable progress. Ontology is serving 
this work in a variety of ways.    (02)

Some of the ontologies in the OBO Foundry, for 
instance, work, as a very useful, flexible 
framework for cataloguing the entities about 
which biologists are collecting data and thereby 
integrating this data and making it surveyable. 
By serving this purpose they help research, e.g. 
in the systematic analysis of the genetic 
alterations involved in human cancers (e.g. in 
Sj÷blom T, et al. The consensus coding sequences 
of human breast and colorectal cancers. Science. 2006 Oct 13;314(5797):268-74.)
BS     (03)

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