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Re: [biont] Nice wikipedia page on ontology

From: Joanne Luciano <jluciano@predmed.com>
Date: Thu, 25 Jan 2007 08:30:26 -0500
Message-Id: <C96FE0E7-D598-459E-9B22-7B0FFF4112D7@predmed.com>
Cc: William Bug <William.Bug@DrexelMed.edu>, Xiaoshu Wang <wangxiao@musc.edu>, public-semweb-lifesci@w3.org
To: Robert Stevens <robert.stevens@manchester.ac.uk>

On Jan 25, 2007, at 4:16 AM, Robert Stevens wrote:

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

Worked for Darwin :-)
Works for me.

>
> 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"

For posterity (and the record) here's what google.com define:ontology  
returns (on January 25, 2007):

Related phrases:   gene ontology   web ontology language   ontology  
language   standard ontology   ontology media   upper ontology    
plato's ontology   ontology mapping   protein ontology   cognitive  
ontology

Definitions of ontology on the Web:

     * specification of a conceptualisation of a knowledge domain. An  
ontology is a controlled vocabulary that describes objects and the  
relations between them in a formal way, and has a grammar for using  
the vocabulary terms to express something meaningful within a  
specified domain of interest. The vocabulary is used to make queries  
and assertions. Ontological commitments are agreements to use the  
vocabulary in a consistent way for knowledge sharing. ...
       members.optusnet.com.au/~webindexing/Webbook2Ed/glossary.htm

     * Ontologies resemble faceted taxonomies but use richer semantic  
relationships among terms and attributes, as well as strict rules  
about how to specify terms and relationships. Because ontologies do  
more than just control a vocabulary, they are thought of as knowledge  
representation. The oft-quoted definition of ontology is "the  
specification of one's conceptualization of a knowledge domain."
       www.noisebetweenstations.com/personal/essays/metadata_glossary/ 
metadata_glossary.html

     * the study of the broadest range of categories of existence,  
which also asks questions about the existence of particular kinds of  
objects, such as numbers or moral facts.
       www.filosofia.net/materiales/rec/glosaen.htm

     * The study of the nature of being, reality, and substance.
       www.carm.org/atheism/terms.htm

     * A branch of metaphysics concerned specifically with what  
(kinds of) things there are.
       www.shef.ac.uk/~phil/other/philterms.html

     * a study of the ultimate nature of things.
       www.willdurant.com/glossary.htm

     * The science of being or reality in the abstract, particularly  
as related to ideas or theories.
       www.mises.org/easier/O.asp

     * the study of being and what constitutes objective and  
subjective existence, and what it means to exist
       web.cn.edu/kwheeler/lit_terms_P.html

     * branch of philosophy concerned with the study of being, of  
reality in its most fundamental and comprehensive forms.
       www.atf.org.au/papers/glossary.asp

     * A description (like a formal specification of a program) of  
the concepts and relationships that can exist for an agent or a  
community of agents. In biomedicine, such ontologies typically  
specify the meanings and hierarchical relationships among terms and  
concepts in a domain.
       www.cordis.lu/ist/ka1/administrations/publications/glossary.htm

     * A branch of philosophy focusing upon the origins, essence and  
meaning of being.
       www.adamranson.freeserve.co.uk/critical%20concepts.htm

     * a network of relationships that are self-describing and used  
to track how items or words relate to one another. For example, a  
“lives at” link or “works for” link in an ontology would be  
used to track these types of relationships and their corresponding  
values for listed individuals. Ontology is the framework of the  
semantic web, and permits intelligent navigation.
       www.electronicscriptorium.com/glossary.html

     * One of the major branches of philosophy, most often contrasted  
with epistemology. Essentially, ontology is the study of what  
actually is. For most people, for most purposes, ontology ultimately  
comes down to physics.
       home.comcast.net/~johnrgregg/glossary.htm

     * the collection of distinct entities that is considered to  
exist within a particular view of a portion of the universe.
       www.geocities.com/CapitolHill/1284/glossdef.html

     * is derived from the two Greek words (ontos) meaning "to be"  
and (logos) meaning "word." Ontology is the science or study of being.
       www.theapologiaproject.org/glossary.htm

     * The creation of a systematically ordered data structure that  
enhances exchange of information between computers and scientists.  
Ontologies enable the definition and sharing of domain-specific  
vocabularies.
       www.genpromag.com/Glossary~LETTER~O.html

     * The science or study of being; that department of metaphysics  
which relates to the being or essence of things, or to being in the  
abstract. 1721 BAILEY, Ontology, an Account of being in the Abstract.  
a1832 BENTHAM Fragm. Ontol. Wks. 1843 VIII. 195 The field of  
ontology, or as it may otherwise be termed, the field of supremely  
abstract entities, is a yet untrodden labyrinth.
       www.ics.uci.edu/~alspaugh/glossary-ext.html

     * This comes from ont-, the present participle of einai, "to be  
- more as is." To philosophers, ontology is a rarefied "branch of  
metaphysics dealing with the nature of being." The term was co-opted  
by the artificial intelligence community to encompass the systems of  
knowledge and rules needed for specific AI applications. On the Web,  
the term applies to the many ongoing efforts to develop topic- 
specific sets of XML-friendly language, rules and definitions. ...
       www.computerworld.com/managementtopics/ebusiness/story/ 
0,10801,70557,00.html

     * A hierarchical taxonomy of terms describing a certain area of  
knowledge.
       nordbotten.ifi.uib.no/ADM/ADM_text/ADMglossary.htm

     * The branch of METAPHYSICS which studies the nature of  
existence. Central questions include: What kinds of objects exist?  
What is it for something to exist?
       www.abdn.ac.uk/philosophy/guide/glossary.shtml

     * The study of being.
       www.dtl.org/trinity/misc/glossary.htm

     * Ontology is the newest label attached to some KOSs. Ontologies  
are being developed as specific concept models by the Knowledge  
Management community. They can represent complex relationships  
between objects, and include the rules and axioms missing from  
semantic networks. Ontologies that describe knowledge in a specific  
area are often connected with systems for data mining and knowledge  
management. [2]
       www.und.nodak.edu/dept/library/Departments/abc/SACSEM- 
SemInGlossary.htm

     * in Philosophy, the study or 'science' of Being, and Knowing  
about 'Being'. This includes discussions and treatises on  
consciousness of existence, whether 'existence preceeds essence' or  
vice versa, and other concepts of 'self-in-the-world' or 'being-in- 
the-world'
       www.shoaheducation.com/definitions.html

     * The study of nature of existence.
       nandankanan.tripod.com/scienceterms.htm

     * (Gk., on, "being," logos, "logic") Philosophic inquiry into  
the ultimate nature of things, what it means to be.
       www.li.suu.edu/library/humtxt/glossary/glossary.htm

     * the metaphysical study of the nature of being and existence
       wordnet.princeton.edu/perl/webwn

     * In philosophy, ontology (from the Greek ον = being and  
λόγος = word/speech) is the most fundamental branch of  
metaphysics. It studies being or existence as well as the basic  
categories thereof -- trying to find out what entities and what types  
of entities exist. Ontology has strong implications for the  
conceptions of reality.
       en.wikipedia.org/wiki/Ontology

     * In computer science, an ontology is the product of an attempt  
to formulate an exhaustive and rigorous conceptual schema about a  
domain. An ontology is typically a hierarchical data structure  
containing all the relevant entities and their relationships and  
rules within that domain (eg. a domain ontology). The computer  
science usage of the term ontology is derived from the much older  
usage of the term ontology in philosophy.
       en.wikipedia.org/wiki/Ontology_(computer_science)

Cheers,
Joanne


>>
>> 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
>>
>>
>>

Joanne Luciano, PhD
Predictive Medicine, Inc.
45 Orchard Street
Belmont MA 02478-3008
Email: jluciano@predmed.com




Received on Thursday, 25 January 2007 13:30:41 UTC

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