W3C home > Mailing lists > Public > public-semweb-lifesci@w3.org > January 2007

Re: [biont] Nice wikipedia page on ontology

From: William Bug <William.Bug@DrexelMed.edu>
Date: Wed, 24 Jan 2007 23:55:37 -0500
Message-Id: <6137F350-94DF-4D77-B53C-7383F9D93295@DrexelMed.edu>
Cc: public-semweb-lifesci@w3.org
To: Xiaoshu Wang <wangxiao@musc.edu>
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".
>
> 1. http://example.com/x  rdfs:subClassOf   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/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>
>>
>>
>>
>>
>
>

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





Received on Thursday, 25 January 2007 04:55:48 UTC

This archive was generated by hypermail 2.4.0 : Friday, 17 January 2020 17:20:22 UTC