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[ontolog-forum] Relating and Reconciling Ontologies

To: "[ontolog-forum]" <ontolog-forum@xxxxxxxxxxxxxxxx>
From: "John F. Sowa" <sowa@xxxxxxxxxxx>
Date: Thu, 21 Apr 2011 09:50:52 -0400
Message-id: <4DB0363C.6040805@xxxxxxxxxxx>
Barry, Azamat, et al.,    (01)

The note copied below was addressed to the Ontology Summit list.
But it addresses important issues that should be discussed in the
wider forum.  I presented some related slides there on Tuesday:    (02)

    http://www.jfsowa.com/talks/par.pdf    (03)

The concluding slide 6 advocated automated methods for relating
ontologies to one another and for extracting ontologies from
legacy software and from natural language texts.  This morning,
I added some pointers to suggested readings for further detail.    (04)

BS
> The mappings I know of between ontologies in practical use
> (for example between different anatomy ontologies) involve very
> costly manual effort, and even then they are still imperfect
> (and fragile as the mapped ontologies themselves change).    (05)

I agree.    (06)

Even worse, inter-annotator agreement among professionals who use
the ontologies (and the related terminologies) is very poor.  At
the Ontology Summit, I was discussing the issues with a physician
who cited a discouraging result:  agreement between any two
ophthalmologists who assign SNOMED codes to a set of cases is
about 60%.    (07)

The annotators don't even agree with themselves.  In the study,
the experimenters retested exactly the same ophthalmologists
a year later on a subset of exactly the same cases.  For each
of the "experts", their new answers had about a 60% agreement
with their answers the year before.    (08)

This is the fatal flaw in any system that depends on human experts
to link real-world data to formal definitions.  Unique identifiers
of formal definitions are hopelessly unreliable in any system that
depends on human annotators to select an option from a menu.    (09)

BS
> Can John point to examples of practically useful mappings created
> and updated automatically through appeal to some sort of Lindenbaum
> lattice-based technology?    (010)

Yes, indeed.  Every *correct* alignment of any two ontologies that
has ever been done by human or machine is a successful application
of the mappings shown in a Lindenbaum lattice.    (011)

The lattice is actually a very simple structure that can be
specified on one page.  It is the formal foundation for every
method of theory revision or ontology alignment.    (012)

The lattice is like arithmetic.  People were counting on their
fingers long before Peano stated his axioms.  The theory doesn't
say that counting on fingers is bad, but it can distinguish sound
methods from flaky ones.  Furthermore, it can provide guidelines
for designing automated and semi-automated tools that can be
much faster and more reliable than finger exercises.    (013)

AA
> Interoperability is a critical idea needing depth and breadth
> and common foundation framework.    (014)

At that level of detail, we agree.  But the framework must support
existing systems, future systems, and people at all levels of
education.  (And even experts in one field are novices in others.)    (015)

  1. There are trillions of dollars of legacy software that run the
     world economy.  It won't be replaced for a long, long time.    (016)

  2. Anything that replaces a legacy system has to interoperate with
     it during a long period of transition.  In fact, most systems
     that replace a legacy system build on and extend the implicit
     ontology in the old system.    (017)

  3. Anything that depends on people using unique identifiers must
     address the problem that even experts in a subject can't agree
     on what codes or categories to assign.    (018)

John    (019)

-------- Original Message --------
Subject: Re: [ontology-summit] Official Communique Feedback Thread
Date: Wed, 20 Apr 2011 10:39:51 -0400
From: Barry Smith
To: Ontology Summit 2011 discussion <ontology-summit@xxxxxxxxxxxxxxxx>    (020)

On Wed, Apr 20, 2011 at 9:50 AM, John F. Sowa <sowa@xxxxxxxxxxx> wrote:
> AGC
>> ... having one single ontology does not solve the problem. actually
>> IMHO it does not solve anything. it could probably be a good idea to
>> address the issue of interoperability across ontologies rather than
>> pretending to have "one ontology per domain".
>
> Yes, indeed.
>
> There are already a huge number of implemented and proposed ontologies,
> and the largest number of potential ontologies comes from the trillions
> of dollars of legacy software.  The total number is finite, but it is
> sufficiently large that infinity is the only practical upper bound.
>
> BS
>> Who will keep the N-squared mappings up to date, for an N that is
>> increasing, if AGC gets his way, without limit? Who will pay for this
>> ever increasing mapping effort? Who will oversee the mapping effort?
>
> The only reasonable solution is to provide automated methods for
> discovering the mappings.  Adolf Lindenbaum showed how to do that
> over 80 years ago -- it's called the Lindenbaum lattice.
>
> For a brief survey, see Section 6 and 7 of the following paper:
>
>     http://www.jfsowa.com/pubs/rolelog.pdf
>
> John    (021)

It would be nice, if it worked. But in practice, at least in the areas
with which I am familiar, it doesn't. The mappings I know of between
ontologies in practical use (for example between different anatomy
ontologies) involve very costly manual effort, and even then they are
still imperfect (and fragile as the mapped ontologies themselves
change). See e.g. the papers by Bodenreider (who does the best work in
this field) listed here:    (022)

http://mor.nlm.nih.gov:8000/pubs/offi.html    (023)

(and especially the items co-authored with Zhang).
Can John point to examples of practically useful mappings created and
updated automatically through appeal to some sort of Lindenbaum
lattice-based technology?    (024)

BS    (025)

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