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Re: [ontolog-forum] Paper on how to build your first ontology

To: "[ontolog-forum]" <ontolog-forum@xxxxxxxxxxxxxxxx>
From: "doug foxvog" <doug@xxxxxxxxxx>
Date: Fri, 16 Dec 2011 10:24:38 -0500 (EST)
Message-id: <64287.129.6.59.206.1324049078.squirrel@xxxxxxxxxxxxxx>
On Wed, December 14, 2011 21:27, John Bottoms said:    (01)

> I have been doing the Ontology101 thing with an existing ontology and
> have run into an issue with the schema. Besides the slots the concept
> includes a special slot for "tags". It then has a validation function
> that insists that tags be numeric values.    (02)

I would suggest that if you do not want numeric tags, you don't use that
part of the system.  Why not just create additional slots/attributes
for what you need instead of (numeric) "tags"?    (03)

FWIW, the Noy-McGuiness Ontology 101 discussion of classes vs. instances
is not based on logic, but on pragmatics due to the the limitations of
the language that they use.  They say that "[i]ndividual instances are the
most specific concepts represented in a knowledge base".  Giving examples
of "instances" that should be "classes" if one wanted more detail when
describing that area.  They also discuss considering wine growing
"regions" as being classes which have other "regions" as subclasses or
instances, depending upon whether those subregions had their own subregion.    (04)

Such a design is very fragile, causing the ontology to break if one
wishes to add more detail in a given area.  The evident reason for it
is the limitations of the language being used, e.g. restrictions on
how classes can be referred to in the system.    (05)

To be logically stable, one should design an ontology such that classes
are types of things that MAY have instances, whether or not there are
actual instances currently defined in the ontology or included in any
knowledge base using the ontology.  An individual would be something that
MAY NOT have its own instances.    (06)

Carefully defining what terms mean should make the relationship between
them clear.  For example, whether BurgandyWine an type of RedWine or an
instance of RedWine depends on whether you define RedWine as something
whose instances are varieties of wine or amounts of liquid that (some)
people like to drink.    (07)

Many ontologies naturally refer to types of types, i.e., metaclasses.
If your represenation language does not allow you to define metaclasses,
then you are tempted to design non-logical twists in order to model the
domain.  The best solution is to switch to a language that is not so
limiting.    (08)

-- doug f    (09)


> I can't get to the author so
> I'm in a quandary. Should I just go ahead and make it into something I
> can use, or should I shoehorn the tags into integer values using a table
> or an enum?    (010)


> -John Bottoms
>   FirstStar Systems
>   Concord, MA USA
>
> On 12/14/2011 6:18 PM, Rich Cooper wrote:
>> Dear Ontologizers,
>>
>> On this forum, we have occasionally tried to
>> construct small example ontologies for
>> illustrative purposes, and occasionally for
>> practical purposes.  Here is a paper that may be
>> of interest to others on the forum:
>>
>> http://protege.stanford.edu/publications/ontology_
>> development/ontology101-noy-mcguinness.html
>> "Ontology Development 101: A Guide to Creating
>> Your First Ontology"
>> By Natalya F. Noy  and Deborah L. McGuinness
>> Stanford University, Stanford, CA, 94305
>> noy@xxxxxxxxxxxxxxxx   and    dlm@xxxxxxxxxxxxxxxx
>>
>>
>> But the paper is truly naïve in its claims.  One
>> particular quote stood out to me glaringly:
>>
>>              Separating the domain knowledge
>> from the operational knowledge is another common
>> use of ontologies. We can describe a task of
>> configuring a product from its components
>> according to a required specification and
>> implement a program that does this configuration
>> independent of the products and components
>> themselves (McGuinness and Wright 1998). We can
>> then develop an ontology of PC-components and
>> characteristics and apply the algorithm to
>> configure made-to-order PCs. We can also use the
>> same algorithm to configure elevators if we "feed"
>> an elevator component ontology to it (Rothenfluh
>> et al. 1996).
>>
>> I find this assertion amazingly naïve, though
>> commonly held among ontologists it seems.  More
>> acknowledgements of the historic data about such
>> reuse should be made any time this kind of claim
>> is made.
>>
>> The historic data shows that such reuse is not
>> generally effective in practice.  The better
>> approach is to design a more generic algorithm
>> (i.e., the object oriented version)  in the first
>> place, and then to forecast the cost, schedule and
>> difficulties of applying that algorithm to new
>> areas.
>>
>> It is unfounded to claim that the PC configuration
>> algorithm would necessarily have similar
>> requirements to the elevator configuration
>> algorithm.  History shows that it won't; stating
>> the problem in a single sentence doesn't make the
>> problem simple.
>>
>> Historically, that claim has not held up, and
>> there is nothing in ontological progress to
>> believe that it will in any near future.
>>
>> -Rich
>>
>> Sincerely,
>> Rich Cooper
>> EnglishLogicKernel.com
>> Rich AT EnglishLogicKernel DOT com
>> 9 4 9 \ 5 2 5 - 5 7 1 2
>> -----Original Message-----
>> From: ontolog-forum-bounces@xxxxxxxxxxxxxxxx
>> [mailto:ontolog-forum-bounces@xxxxxxxxxxxxxxxx] On
>> Behalf Of Michael Gruninger
>> Sent: Wednesday, December 14, 2011 7:32 AM
>> To: [ontolog-forum]
>> Subject: Re: [ontolog-forum] Ontology, Analogies
>> and Mapping Disparate Fields
>>
>>
>> Hi Ali,
>> here is the submitted version of the modularity
>> paper.
>> You can put it up on your own url somewhere until
>> it is
>> accepted by Applied Ontology.
>>
>> - michael
>>
>> Quoting Ali SH<asaegyn+out@xxxxxxxxx>:
>>
>>> Hi all,
>>>
>>> Just wanted to pass along a link to an ontology
>> related story (though it's
>>> barely framed as such) in a relatively
>> mainstream technology news outlet:
>> http://www.physorg.com/news/2011-12-link-patterns-
>> spider-silk-melodies.html
>>> While these are the originating papers (
>>>
>> http://arxiv.org/ftp/arxiv/papers/1111/1111.5297.p
>> df [1]) and (
>> http://math.mit.edu/~dspivak/informatics/ologs--ba
>> sic.pdf [2])
>>> It seems to me that the author is reinventing
>> the wheel (though with a nice
>>> twist re formulating / expressing o-logs and
>> "sketches").
>>> Especially since their review of the ontology
>> field (in the *
>>> ologs--basic.pdf* paper) seems to extend only to
>> RDF/OWL and completely
>>> ignores (or misses) work on Common Logic,
>> conceptual graphs and the most
>>> glaring omission - the work on category theory
>> in Bremen. Incidentally,
>>> such an omission appears to be an unfortunate
>> corollary of the crowding out
>>> of any non-RDF/OWL work.
>>>
>>> In any event, it's interesting work, though the
>> correlation between the two
>>> seemingly disparate fields (spider silks and
>> melody) reminds me more of the
>>> seminal "Unreasonable Effectiveness of
>> Mathematics in the Natural Sciences"
>>> speech -
>> http://www.dartmouth.edu/~matc/MathDrama/reading/W
>> igner.html [3]
>>> A lot of semantic mapping to date has indeed
>> focused on DL level mappings
>>> (cf Euzenat&  Shvaiko's Ontology Matching book
>> [4]), but there is a rich
>>> set of logical mappings which can capture a lot
>> of these structural
>>> similarities between disparate fields. I know
>> I've repeated this claim
>>> before, but the limited expressivity of DL's
>> mutes many of these mappings,
>>> because well, they generally aren't captured
>> (can't be expressed) in the
>>> formalism. There is something to be said for
>> picking the correct language
>>> to describe a domain, where difficult problems
>> become much simpler. I
>>> suspect this will be one of the first major
>> obstacles in orchestrating
>>> services based on LOD sets beyond the low
>> hanging fruit currently being
>>> explored.
>>>
>>> In a previous discussion with Bijan, we were
>> talking past each other re
>>> reasoning over expressive ontologies. I kept on
>> talking about reasoning
>>> "off-line", while he insisted such projects were
>> fatally intractable. I
>>> later realized the disconnect was that I was
>> talking about verifying an
>>> expressive ontology (which you only need to do
>> once, hence off-line), while
>>> he was thinking that you need to process the
>> entire ontology for every
>>> query. Verification need be done only once (and
>> indeed, off-line), while
>>> the deployment of queries over fragments of the
>> ontology can then deploy
>>> more optimized tools.
>>>
>>> I think there's an attractive case for
>> articulating in some way, in some
>>> place, an expressive version of an ontology,
>> even if for certain services /
>>> tasks you only deploy a decidable fragment of
>> said ontology. For one, it
>>> can greatly facilitate semantic mappings, while
>> secondly, it makes the
>>> entire project more upwards compatible,
>> especially as the major DL's are
>>> continually adding greater expressivity. The
>> expressive version of the
>>> reference ontology can function a sort of road
>> map for deployment, a sort
>>> of technology agnostic commitment, whereas DL or
>> otherwise deployed
>>> artifacts are technology dependent products /
>> services...
>>> Lastly, I'd point out that the group at the
>> University of Toronto does have
>>> a paper on this topic (modularizing and reducing
>> expressive ontologies into
>>> ontologies of other types that preserve the
>> logical structure of the
>>> models), which has the incidental benefit of
>> being able to identify logical
>>> similarity between theories according to an open
>> repository... I will see
>>> if I have permission to distribute a pre-print
>> to the list (Michael?).
>>> ===
>>> [1] Tristan Giesa, David I. Spivak and Markus J.
>> Buehler "Reoccurring
>>> Patterns in Hierarchical Protein Materials and
>> Music: The Power of
>>> Analogies" BioNanoScience Volume 1, Number 4,
>> 153-161, DOI:
>>> 10.1007/s12668-011-0022-5
>>> [2] D.I. Spivak, R.E. Kent "Ologs: a categorical
>> framework for knowledge
>>> representation". PLoS ONE (in press): e24274.
>> (2011)
>>> doi:10.1371/journal.pone.0024274
>>> [3] Wigner, E. P. (1960). "The unreasonable
>> effectiveness of mathematics in
>>> the natural sciences. Richard courant lecture in
>> mathematical sciences
>>> delivered at New York University, May 11, 1959".
>> Communications on Pure and
>>> Applied Mathematics 13: 1-14.
>> doi:10.1002/cpa.3160130102.
>>> [4] Jérôme Euzenat, Pavel Shvaiko. *Ontology
>> Matching*. Springer-Verlag,
>>> Berlin Heidelberg (DE), 2007
>>>
>>> Best,
>>> Ali
>>>
>>
>>
>>
>>
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=============================================================
doug foxvog    doug@xxxxxxxxxx   http://ProgressiveAustin.org    (012)

"I speak as an American to the leaders of my own nation. The great
initiative in this war is ours. The initiative to stop it must be ours."
    - Dr. Martin Luther King Jr.
=============================================================    (013)


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