Re: [biont] Nice wikipedia page on ontology

Bill, I wholeheartedly agree. Utility rather than dogma is a much 
better criterion for evaluation.

At 04:55 25/01/2007, William Bug wrote:
>Many thanks, Xiaoshu.
>
>It's very helpful to get a sense of the full spectrum of opinion on 
>this issue.
>
>I would agree for most all the folks on this list - myself included 
>- the most important aspect of an ontology is to provide a shared 
>semantics within a computational framework.
>
>I don't believe, however:
>1) That means the same thing to all "ontological engineers" - i.e., 
>I think applications vary widely in how they construct and use on 
>ontology in a computational framework - e.g., Robert's earlier 
>statement, ",One can make an ontology in a formal language like owl, 
>but still be informal in the ontological distinctions made"
>2) I don't believe that is ALL an ontology is.
>
>In reference to David Booth's earlier comment re: the redundancy of 
>"formal" ontology - it was wonderful to hear someone else say that, 
>for I've often felt my intended use for an ontology (and the 
>requirements that engenders) DOES in fact make "formal" a redundant 
>adjective.  The problem comes with point '2' above in this sense - 
>what ontology implies to me may need to be explicitly stated for 
>those to whom ontology does not carry that intrinsic property.   As 
>Robert stated most succinctly, not all ontologies are expressed 
>using a mathematical formalism even when they are ontologically 
>formal - and visa versa
>
>The Google results returned by "define: ontology" are equally 
>illuminating - and frightening.  The authors of these pages are 
>truly braver and more knowledgeable souls than I - which implies - 
>though the pronouncements I make regarding the development and 
>intended use of ontologies MAY be necessary they are in no way 
>sufficient to define the class "ontology"
>
>In the end, whether an artifact designed to promote a shared 
>semantics IS an ontology is less important than whether it can truly 
>support achieving the goals to which you apply it, whether you are a 
>philosopher, biomedical informaticist, or a car mechanic.
>
>Cheers,
>Bill
>
>
>On Jan 24, 2007, at 11:09 PM, Xiaoshu Wang wrote:
>
>>
>>Well, I think the discussion is good, but trying to define 
>>"exactly"  what an ontology is will always be a futile 
>>attempt.  Just like any concept,  we all actually know what we are 
>>talking about but cannot give it a precise definition. 
>>Nevertheless, does it really matter if we can define what an ontology is?
>>
>>For me, an ontology is just an engineer artifact created to be 
>>shared.  If an ontology cannot be shared engineeringly, it is 
>>useless.  For instance, can we consider an "ontology" defined in 
>>OBO to be an "ontology" in the semantic web?  I think not because 
>>if so, how an RDF engine understand it.  So pragmatically in an RDF 
>>world, anything in RDF is an ontology because it does not matter if 
>>it is an "ontology" or a "dataset", an RDF engine would have 
>>treated them in the same way.  Consider the following two statement 
>>about "<http://example.x>http://example.x".
>>
>>1. 
>>http://example.com/x  rdfs:subClassOf 
>><http://example.com/y>http://example.com/y      2. 
>>http://example.com/x  a http://example.com/c
>>
>>Will there be any different treatment for an RDF engine? They have 
>>to dereference the same URI and reason them accordingly, 
>>right?  Does it matter if we label one as an "ontology" and the 
>>other "not"?  This is the reason that I still cannot understand the 
>>motive behind the design of an owl:Ontology, it serves no purpose 
>>whatsoever. Cheers
>>
>>Xiaoshu
>>William Bug wrote:
>>>That's much better for Wikipedia than getting too deep into ABox and TBox.
>>>
>>>Thanks, 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/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/>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>
>>>>>>     [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>
>>>>>>> 
>>>>>>><<mailto:alanruttenberg@gmail.com>mailto:alanruttenberg@gmail.com>> writes:
>>>>>>>
>>>>>>>       Alan> Start at 
>>>>>>> <http://en.wikipedia.org/wiki/Formal_Ontology>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>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>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 - 
><mailto:William.Bug@DrexelMed.edu>William.Bug@DrexelMed.edu
>
>
>