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Re: [biont] Nice wikipedia page on ontology

From: Kei Cheung <kei.cheung@yale.edu>
Date: Wed, 24 Jan 2007 10:40:43 -0500
To: William Bug <William.Bug@DrexelMed.edu>
Cc: David Decraene <David@landcglobal.com>, Robert Stevens <robert.stevens@manchester.ac.uk>, Phillip Lord <phillip.lord@newcastle.ac.uk>, Alan Ruttenberg <alanruttenberg@gmail.com>, public-semweb-lifesci hcls <public-semweb-lifesci@w3.org>
Message-id: <45B77DFB.8010601@yale.edu>

Just to add to Bill's comments. According to the following paper:

http://www.springerlink.com/content/hnn72w7r18238467/

Ontology is defined as a formal specification of a vocabulary, including 
axioms relating the terms. A dataset is defined as a set of facts 
expressed using a particular ontology.

-Kei

William Bug wrote:

> I think you are right, David - axioms would be better, as algorithms 
> implies - though doesn't proscribe - an implementation strategy that 
> may not be relevant to all uses of formal ontologies.  Perhaps the use 
> of algorithms relates to Tom Gruber's oft quoted description of what 
> an ontology is - a description that does not fit for everyone using 
> formal ontologies.
>
> Maybe some mention of how formal ontologies are used to test formal 
> assertions and some mention of the difference between the TBox & the 
> ABox (using more accessible expressions) would be useful as well.
>
> Again - thanks for trying to put this out there.  I do think it can be 
> a very useful resource.
>
> Cheers,
> Bill
>
>
> On Jan 24, 2007, at 10:03 AM, David Decraene wrote:
>
>> I'd like to comment on these statements:
>> Perhaps it can be phrased better, but 'algorhythms' refers to the 
>> fact that a formal upper level ontology has built-in DISJOINT (and 
>> other) axioms which reflect back onto their children (ergo the 
>> consistency check phrase). Axioms is perhaps a better choice.
>>  
>> Also, the formal in formal ontology has nothing to do with the 
>> language of representation (perhaps that part can be phrased better 
>> as well to avoid confusion) but to the formalism (formality of the 
>> ontology as you refer to it) that is embedded in the framework.
>>  
>> I do not disagree that this page can be improved further (which is 
>> the purpose and strongpoint of wikipedia), but explaining in laymans 
>> terms what a formal ontology is about is a challenge.
>>  
>>  
>>
>>     -----Original Message-----
>>     *From:* public-semweb-lifesci-request@w3.org
>>     [mailto:public-semweb-lifesci-request@w3.org]*On Behalf Of
>>     *Robert Stevens
>>     *Sent:* woensdag 24 januari 2007 15:45
>>     *To:* Phillip Lord; Alan Ruttenberg
>>     *Cc:* public-semweb-lifesci hcls
>>     *Subject:* Re: [biont] Nice wikipedia page on ontology
>>
>>     /'d be inclined to agree with Phil. I don't where the bit about
>>     "algorithms" has come from. The other mistake, I think, is not to
>>     make the distinction between formality of language for
>>     representaiton and the formality of the ontology itself. The
>>     latter is, I think, a matter of the distinctions made. One can
>>     make an ontology in a formal language like owl, but still be
>>     informal in the ontological distinctions made.
>>
>>     /Formal ontological distinctions can be encapsulated in an upper
>>     level, but upper level otnoogies are not necessarily formal.... 
>>      
>>     the phrase also explicitely refers to upper level ontologies that
>>     are formal in nature... 
>>
>>     Anyway, it is bad at almost any level
>>
>>     Robert.
>>     ,At 13:55 24/01/2007, Phillip Lord wrote:
>>
>>>     >>>>> "Alan" == Alan Ruttenberg <alanruttenberg@gmail.com
>>>     <mailto:alanruttenberg@gmail.com>> writes:
>>>
>>>       Alan> Start at http://en.wikipedia.org/wiki/Formal_Ontology
>>>
>>>       Alan> -Alan
>>>
>>>
>>>     Well, it starts of with this....
>>>
>>>     "A Formal ontology is an ontology modeled by algorithms. Formal
>>>     ontologies are founded upon a specific Formal Upper Level Ontology,
>>>     which provides consistency checks for the entire ontology and, if
>>>     applied properly, allows the modeler to avoid possibly erroneous
>>>     ontological assumptions encountered in modeling large-scale
>>>     ontologies. "
>>>
>>>
>>>
>>>     Almost none of which I would agree with. 
>>
>
> Bill Bug
> Senior Research Analyst/Ontological Engineer
>
> Laboratory for Bioimaging  & Anatomical Informatics
> www.neuroterrain.org
> Department of Neurobiology & Anatomy
> Drexel University College of Medicine
> 2900 Queen Lane
> Philadelphia, PA    19129
> 215 991 8430 (ph)
> 610 457 0443 (mobile)
> 215 843 9367 (fax)
>
>
> Please Note: I now have a new email - William.Bug@DrexelMed.edu 
> <mailto:William.Bug@DrexelMed.edu>
>
>
>
>
Received on Wednesday, 24 January 2007 15:40:58 UTC

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