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:* [EMAIL PROTECTED] <
mailto:[EMAIL PROTECTED]>
[ mailto:[EMAIL PROTECTED] 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
<[EMAIL PROTECTED] < mailto:[EMAIL PROTECTED]>
< mailto:[EMAIL PROTECTED]>> 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 -
[EMAIL PROTECTED] < mailto:[EMAIL PROTECTED]>
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 - [EMAIL PROTECTED]
< mailto:[EMAIL PROTECTED]>
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 - [EMAIL PROTECTED]
Joanne Luciano, PhD
Predictive Medicine, Inc.
45 Orchard Street
Belmont MA 02478-3008
Email: [EMAIL PROTECTED]
