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Re: [ontolog-forum] Genetic discovery using ontology mapping of observat

To: ontolog-forum@xxxxxxxxxxxxxxxx
From: John F Sowa <sowa@xxxxxxxxxxx>
Date: Sat, 11 May 2013 07:57:16 -0400
Message-id: <518E321C.6010608@xxxxxxxxxxx>
Rich and Michael,    (01)

I agree with Michael's answer to Rich's question, but I'd like to add
a few more comments.    (02)

> Could a genetic ontology be useful for mapping the disease biochemistry
> and environmental exposures to genetic profiles?  Perhaps such an ontology
> could be constructed automatically, step by step, through identifying
> subjects with known genetic spectrum and known environmental exposures
> versus diagnosed conditions.    (03)

> But why should ontology-based tools be better than the tools already used?
> You would have to have a close look at those tools and the problems they
> solve to answer that question.    (04)

Yes, that is the fundamental question.  Scientists in every field have
developed highly sophisticated tools for analyzing and reasoning about
their subjects.    (05)

In almost all cases, their tools are far more precise, detailed,
and sophisticated than the tools currently available for ontology.
The Cyc tools are rather sophisticated, but they offer little help
for the sciences.  And compared to Cyc, OWL is pathetic.    (06)

> A data model is not an ontology because it serves the needs of a specific
> application.  But what needs does an ontology serve?  This data model /
> ontology distinction puzzles me more and more.    (07)

I don't blame you for being puzzled. The simplest explanation is that
they came from different sources.  The term 'data model' originated
in the "database wars" of the 1970s.  There were three competing
technologies, each with its preferred "data model":  hierarchical
(IMS), network (Codasyl DBTG), and relational.    (08)

The goal of the conceptual schema was to allow software to access
data in any format, independent of the way it was stored.  In fact,
its goals were similar to the original goals by Tim Berners-Lee
for the Semantic Web.    (09)

But the same mentality that dragged the SW down to little more than
YADM (Yet Another Data Model), the hopes for the conceptual schema
were never realized.    (010)

John    (011)

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