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

To: "[ontolog-forum] " <ontolog-forum@xxxxxxxxxxxxxxxx>
From: Michael Brunnbauer <brunni@xxxxxxxxxxxx>
Date: Sun, 12 May 2013 15:18:44 +0200
Message-id: <20130512131844.GA1887@xxxxxxxxxxxx>

Hello Rich,    (01)

>Here is a recent patent I found a few minutes ago
>which to some degree could be applicable, though
>it is addressed to generating ontologies for
>business applications:    (02)

If I understand this correctly, it describes a method of generating an
OWL ontology from an annotated XSD file. All terms in the generated ontology 
are already present in the XSD file or the annotations. XML files using that 
XSD can then be converted to triples using that ontology.     (03)

An approach like this enables you to query the data with SPARQL - which may
be a progress over what you could do before. But using reasoning or rules
for some advantage probably requires a much bigger investment of time.    (04)

> By that description, I am envisioning a system
> that searches (think And/Or graph search) for the
> best explanation in a logical combination of
> evidence fragments.    (05)

Something like this ?     (06)

 http://www.aaai.org/Papers/Workshops/2006/WS-06-08/WS06-08-010.pdf    (07)

> So a discovery system that browses through all
> that data could put together logical combinations
> of evidence from each case, and produce millions
> of explanations as logical combinations of
> evidence terminals.  Its that "logical
> combinations of evidence terminals" that I am
> calling (perhaps inelegantly) an ontology.      (08)

What do you do with the millions of "explanations" ? If you do not reason with
them, I would not see them as part of an ontology. Isn't the system supposed to
yield the best "explanation" instead of millions ?    (09)

> The reason I call it an ontology, even though it
> was not put together by humans, is because it
> represents the tightest explanation of the
> evidence in Occam's sense.    (010)

I would say what you mean is the smallest set of ground facts with a 
correlation to a given desease. If you mean this, you can hardly call it
an ontology.    (011)

> I am suggesting that perhaps we should jettison the
> human generation of the ontology and substitute a
> method for automatic generation of the ontology
> without concern for whether a human understands
> the reasoning at any intuitive level.    (012)

I do not see any real reasoning in the system you describe.    (013)

Regards,    (014)

Michael Brunnbauer    (015)

++  Michael Brunnbauer
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