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Re: [ontolog-forum] Logic, Datalog and SQL

To: "[ontolog-forum]" <ontolog-forum@xxxxxxxxxxxxxxxx>
From: "John F. Sowa" <sowa@xxxxxxxxxxx>
Date: Sun, 11 Feb 2007 14:08:07 -0500
Message-id: <45CF6997.1060507@xxxxxxxxxxx>
Kathy,    (01)

Of course, I agree with all those points:    (02)

 > I would hope you agree that there are conditions (e.g.,
 > diseases, faults, crimes ...) that we could like to diagnose.
 > I hope you agree that conditions have symptoms...    (03)

As I have said many times, I have no objection whatever
to saying that microtheories are part of the ontology.    (04)

 > If ontologies contain only everything that everybody can
 > agree on without reservation, and everything else goes
 > into microtheories, then I'm afraid our ontologies are
 > going to be empty, and what we used to call ontologies
 > will have to be relabeled as microtheories.    (05)

Sure, microtheories can be part of the ontology.  The point
I have been making for years is that detailed axioms do not
belong in any level that is expected to be broadly used
across multiple domains and subdomains.    (06)

 > SUMO hasn't been officially adopted yet, has it?    (07)

I don't know what you mean by "adopted".  A lot of people
use it.  I think that SUMO, Cyc, and many other ontologies
are quite good for their purposes.    (08)

But the fact that there are multiple widely used ontologies
implies that any common upper level should contain only
the intersection, not the union of them.    (09)

 > Can you please explain to me what knowledge is NOT
 > derived from observation?    (010)

Anything that is legislated or agreed upon by convention.
For example, observation tells us that there are lots of
things orbiting the sun.  But legislation by a body of
experts determines whether a particular thing is called
a planet, a dwarf planet, an asteroid, a comet, or dust.    (011)

 > So you don't want a medical ontology to represent that
 > medical tests have sensitivity and specificity?    (012)

I wouldn't prohibit any kind of information from a domain
ontology.  If sensitivity and specificity are conventional
terms (i.e., at the level of planet vs. dwarf planet), then
they definitely belong in a very general ontology for medicine.
But the detailed values that have been obtained by observation
belong in more detailed subdomains.    (013)

 > In many such cases, it would be more accurate from a medical
 > standpoint to define the condition by means of a probability
 > model in which presence of the condition is a hidden
 > unobservable variable whose probability is inferred from
 > observable indicators.  That would require probabilistic
 > axioms in the ontology or microtheory or extended ontology
 > or whatever we are going to call it.    (014)

I would agree that the idea of probabilistic models deserves
to be specified at a very high level and that specific models
of that kind should be availabe in domain ontologies at various
levels.  But a particular theory of a particular illness would
be a very specialized model that would be better suited to a
lower-level domain ontology.    (015)

For example, smallpox has been diagnosed with considerable
accuracy for centuries, but the medical understanding of
the disease has changed enormously.  In order to relate
medical data from different periods of time, it's necessary
to have underspecified definitions at the higher levels, but
more detailed specifications, which may change over time,
at the lower levels.    (016)

Such a muti-level approach permits highly precise and
detailed reasoning at lower subdomains, but it also allows
less precise, but still very useful reasoning across
domains.    (017)

 > So what should the line be between ontology and microtheory?
 > I think this should not be legislated a priori on purely
 > philosophical grounds.    (018)

Even worse, it is most likely going to be legislated on
political grounds.    (019)

 > If the answer to those questions is no, then I think your
 > use of the term ontology differs greatly from the use it is
 > coming to have in the practice of ontological engineering.    (020)

The definition I proposed on January 30 includes everything
you've requested so far:    (021)

     A formal ontology consists of a theory T stated in some
     version of logic and a nonempty vocabulary V.  The
     vocabulary V is a subset of the names of types and relations
     used in T.    (022)

Following is the complete note.    (023)

__________________________________________________________________    (024)

Re: [ontology-summit] dimensions/aspects of ontology types?
From: John F. Sowa <sowa@xxxxxxxxxxx>
To: gruninger@xxxxxxxxxxxxxxx, Ontology Summit 2007 Forum 
Date: Jan 30 2007 - 10:58am    (025)

Folks,    (026)

As a general definition that covers all ontologies, formal
and informal, I endorse the suggestion by Michael Gruninger:    (027)

 > The ecumenical definition of "ontology" that Mike Uschold
 > and I have used is:
 > "An ontology includes a vocabulary of terms together with
 > a specification of the intended meaning of the terms."    (028)

But I also sympathize with Chris Menzel about having a
purely formal definition, especially for formal ontologies.
Unfortunately, the definition of ontology as the equivalent
of a logical theory does not distinguish the vocabulary
that is being defined by the theory from other terms that
may be used in the theory and defined elsewhere.    (029)

But that distinction can be made in a purely formal way
just by adding a metalevel note that distinguishes which
terms in the theory constitute the vocabulary that is
being specified.    (030)

Following is my suggested specialization of the Gruninger-
Uschold definition to cover formal ontologies:    (031)

    A formal ontology consists of a theory T stated in some
    version of logic and a nonempty vocabulary V. The vocabulary
    V is a subset of the names of types and relations used in T.    (032)

For example, the following statements constitute a theory, but
not an ontology, because they do not state which terms are being
defined:    (033)

    There is a man named Bob who is taller than a man named Joe.    (034)

    Every individual named Tiny Tim is shorter than any
    individual named Big Bad Bob.    (035)

    No letters in circular envelopes are delivered on Tuesdays.    (036)

This theory also has many other features that would make it
bad as the theory part of any ontology, such as the inclusion
of low-level statements about individuals. The question of what
makes a good or bad ontology is very important, but that is a
separate issue from the definition of "ontology".    (037)

Following is a better specification of an ontology.    (038)

Vocabulary: {loopyLetter}    (039)

Theory:    (040)

    Every loopyLetter is a letter in a circular envelope.    (041)

    No loopyLetter is delivered on a Tuesday.    (042)

This would be a special-case ontology that uses terms that may
be defined in other ontologies: letter, in, circular, envelope,
deliver, Tuesday.    (043)

John Sowa    (044)

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