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Re: [biont] Nice wikipedia page on ontology

From: Kei Cheung <kei.cheung@yale.edu>
Date: Wed, 24 Jan 2007 10:55:50 -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: <45B78186.9050402@yale.edu>

I'm hearing, as Carole put it.  :-) 

-Kei

>
> On the other hand, some may not agree with the focus on the lexicon - 
> "Ontology is defined as a formal specification of a vocabulary, 
> including axioms relating the terms" -  though I do like the 
> accessibility of that description.
>
> Of course, you could additionally reference the Wikipedia entries for 
> Abox & Tbox:
> http://en.wikipedia.org/wiki/ABox
> http://en.wikipedia.org/wiki/TBox
>
> Cheers,
> Bill
>
>
> On Jan 24, 2007, at 10:40 AM, Kei Cheung wrote:
>
>> 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>
>>>>     [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>
>>>>>     <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>
>>>
>>>
>>>
>>>
>>
>>
>
> 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 15:56:06 UTC

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