ontolog-forum
[Top] [All Lists]

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

To: "[ontolog-forum] " <ontolog-forum@xxxxxxxxxxxxxxxx>
From: "AzamatAbdoullaev" <abdoul@xxxxxxxxxxxxxx>
Date: Sun, 18 Dec 2011 20:07:33 +0200
Message-id: <3802C9000E8949FB911A046A28859A65@personalpc>
On Saturday, December 17, 2011 5:05 PM, John Bottoms wrote: "we are not 
ready to develop an ontology that covers all aspects of all realities."
It's hardly the job of ontology.    (01)

Ontology is about fundamental reality and its prime elements, structures and 
relationships. Application ontologies and particular sciences study separate 
realities, such as physical reality, biological reality, mental reality, 
social reality, information reality, digital reality, semantic reality, 
mixed reality, etc.    (02)

Azamat    (03)

----- Original Message ----- 
From: "John Bottoms" <john@xxxxxxxxxxxxxxxxxxxx>
To: <ontolog-forum@xxxxxxxxxxxxxxxx>
Sent: Saturday, December 17, 2011 5:05 PM
Subject: Re: [ontolog-forum] Paper on how to build your first ontology    (04)


Doug,    (05)

I started thinking about this problem (how to deal with legacy ontology
structures) and came back to  prior thoughts. The first is to preserve
the legacy system as much as possible. I also remembered that I have a
leaning toward an ontology pre-processor.  This is because there are so
many potential requirements that we are not ready to develop an ontology
that covers all aspects of all realities. For example, pre-processor
would allow the temporal elements to be omitted if they are not needed.
Adding them later is a separate exercise.    (06)

I'm not ready to do a pre-processor so my thoughts moved on to other
ways to accomplish similar functions. But every thing in an ontology
should have gone through some sort of validation. Allowing unqualified
data in would result in problems later.    (07)

What I finally settled on is a single control word for validating tags.
Each bit represents a type of validation. Nominally, 32 bits is quite a
few for now and should be fairly efficient. The implementation then
checks each bit in a "for" loop and a SWITCH/CASE statement invokes a
method for the validation. It handles legacy uses with minimal recoding
and allows more conventional uses of tags. I didn't want to define a
multi-use slot because there are some conventions there.    (08)

I find it interesting that we have so little discussion about ontology
structures for a base architecture that came from Minisky's very brief
paper (MIT Lab Memo 306) without more extensive discussion or consensus.
If you google "tags" you will see that the bulk of the responses are
about folksonomy type tags. I think Minsky had something else in mind,
but I want to take a look at Aristotle again. :^)    (09)

On a slightly different topic. I have been considering a "like" bit in
the ontology structure. This is because some view universals as
preferred classes. For example Lakoff points out the importance of the 4
categories, "women, fire and dangerous [& misc] things. These might be
universals to a native speaker (SME). A "like" bit gets incremented when
it is the final target of a search. After a number of searches the
ontology structure could be rebalanced to make top-down search access
faster. This is routinely done with B-tree structures but I'm sure there
are others.    (010)

-John Bottoms
  FirstStar Systems
  Concord, MA    (011)

On 12/16/2011 10:24 AM, doug foxvog wrote:
> On Wed, December 14, 2011 21:27, John Bottoms said:
>
>> 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.
> 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"?
>
> 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.
>
> 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.
>
> 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.
>
> 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.
>
> 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.
>
> -- doug f
>
>
>> 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?
>
>> -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
>>>>
>>>
>>>
>>>
>>> _________________________________________________________________
>>> Message Archives: http://ontolog.cim3.net/forum/ontolog-forum/
>>> Config Subscr: http://ontolog.cim3.net/mailman/listinfo/ontolog-forum/
>>> Unsubscribe: mailto:ontolog-forum-leave@xxxxxxxxxxxxxxxx
>>> Shared Files: http://ontolog.cim3.net/file/
>>> Community Wiki: http://ontolog.cim3.net/wiki/
>>> To join: http://ontolog.cim3.net/cgi-bin/wiki.pl?WikiHomePage#nid1J
>>>
>>
>> _________________________________________________________________
>> Message Archives: http://ontolog.cim3.net/forum/ontolog-forum/
>> Config Subscr: http://ontolog.cim3.net/mailman/listinfo/ontolog-forum/
>> Unsubscribe: mailto:ontolog-forum-leave@xxxxxxxxxxxxxxxx
>> Shared Files: http://ontolog.cim3.net/file/
>> Community Wiki: http://ontolog.cim3.net/wiki/
>> To join: http://ontolog.cim3.net/cgi-bin/wiki.pl?WikiHomePage#nid1J
>>
>
> =============================================================
> doug foxvog    doug@xxxxxxxxxx   http://ProgressiveAustin.org
>
> "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.
> =============================================================
>
>
> _________________________________________________________________
> Message Archives: http://ontolog.cim3.net/forum/ontolog-forum/
> Config Subscr: http://ontolog.cim3.net/mailman/listinfo/ontolog-forum/
> Unsubscribe: mailto:ontolog-forum-leave@xxxxxxxxxxxxxxxx
> Shared Files: http://ontolog.cim3.net/file/
> Community Wiki: http://ontolog.cim3.net/wiki/
> To join: http://ontolog.cim3.net/cgi-bin/wiki.pl?WikiHomePage#nid1J
>
>    (012)


_________________________________________________________________
Message Archives: http://ontolog.cim3.net/forum/ontolog-forum/
Config Subscr: http://ontolog.cim3.net/mailman/listinfo/ontolog-forum/
Unsubscribe: mailto:ontolog-forum-leave@xxxxxxxxxxxxxxxx
Shared Files: http://ontolog.cim3.net/file/
Community Wiki: http://ontolog.cim3.net/wiki/
To join: http://ontolog.cim3.net/cgi-bin/wiki.pl?WikiHomePage#nid1J    (013)


_________________________________________________________________
Message Archives: http://ontolog.cim3.net/forum/ontolog-forum/  
Config Subscr: http://ontolog.cim3.net/mailman/listinfo/ontolog-forum/  
Unsubscribe: mailto:ontolog-forum-leave@xxxxxxxxxxxxxxxx
Shared Files: http://ontolog.cim3.net/file/
Community Wiki: http://ontolog.cim3.net/wiki/ 
To join: http://ontolog.cim3.net/cgi-bin/wiki.pl?WikiHomePage#nid1J    (014)

<Prev in Thread] Current Thread [Next in Thread>