Re: [biont] Nice wikipedia page on ontology

2007-01-24 Thread William Bug
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

Re: [biont] Nice wikipedia page on ontology

2007-01-24 Thread Xiaoshu Wang
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

RE: [biont] Nice wikipedia page on ontology

2007-01-24 Thread Booth, David (HP Software - Boston)
A problem I have with the term "formal ontology" is that it seems redundant: an ontology (in the computer science sense) is already formal in the same sense as a "formal specification" or a "formal language": http://www.ee.oulu.fi/research/ouspg/sage/glossary/ [[ Formal Expressed in a restrict

Re: Hosted Triple Store Oracle RDF DM - and access to BioRDF examples in general

2007-01-24 Thread William Bug
Thanks, Susie. Thanks too for the clarification on the "native triple store". I thought based on the fact there is a triple import mechanism and - as you said - you are leveraging the native graph processing/indexing engine already in Oracle - meant the implementation of RDF in Oracle wa

Re: Hosted Triple Store Oracle RDF DM - and access to BioRDF examples in general

2007-01-24 Thread Susie Stephens
The URL for Oracle's manual is actually: http://download.oracle.com/otndocs/tech/semantic_web/pdf/rdfrm.pdf Cheers, Susie William Bug wrote: Scott has a link up to the Oracle RDF DM http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Hosted_Triple_Store http://download.oracle.com/otndocs/tech/sem

RE: [biont] Nice wikipedia page on ontology

2007-01-24 Thread Robert Stevens
this distinction is quite telling. Putting "define: ontology" into Google has very revealling results. At 15:28 24/01/2007, Gao, Yong wrote: Perhaps the terms "formal" and "ontology" should be defined or linked on the page? Both terms themselves are quite ambiguous. The formal ontology pag

Re: [biont] Nice wikipedia page on ontology

2007-01-24 Thread Alan Ruttenberg
On Jan 24, 2007, at 11:57 AM, Phillip Lord wrote: Phil> Hmmm. Sure I wrote more than that in my original email. Didn't see more. But great that everybody jumped in :) Phil> Yeah, Robert has my main beef which is the distinction between the representation language and the representation i

RE: [biont] Nice wikipedia page on ontology

2007-01-24 Thread David Decraene
A lot of confusion might also come from the word 'formal', it must be interpreted in it's philosophical sense, as the intended wikipedia article attempted to describe (in a rudimentary manner), e.g. concerning theories of enduring versus perduring entities, dependent and independents, of inhere

Re: [biont] Nice wikipedia page on ontology

2007-01-24 Thread Phillip Lord
Hmmm. Sure I wrote more than that in my original email. Yeah, Robert has my main beef which is the distinction between the representation language and the representation itself. The use of "algorithms" is clearly wrong and I don't think that an upper ontology provides consistency checks, nor th

Re: [biont] Nice wikipedia page on ontology

2007-01-24 Thread Irene Celino
I agree with Phil and Robert. Even if it does not contain a definition I fully agree with, a slighty better wikipedia page is [1], which makes a distinction between domain ontologies and upper ontologies [2]. But I'm just a semantic web girl and not an ontologist... Irene [1] http://en.wikipedia

Re: Minutes for today's BIONT Telcon

2007-01-24 Thread Chimezie Ogbuji
As promised are the links to the relevant literature I discussed which influenced the development of the POMR ontology: 1) HL7 RIM: An Incoherent Standard (http://ontology.buffalo.edu/HL7/doublestandards.pdf) 2) Knowledge Representation for Relevance Ranking of Patient-Record Content in Pri

Re: [biont] Nice wikipedia page on ontology

2007-01-24 Thread Kei Cheung
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

Re: [biont] Nice wikipedia page on ontology

2007-01-24 Thread William Bug
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 acces

Re: [biont] Nice wikipedia page on ontology

2007-01-24 Thread Kei Cheung
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 ontol

Re: [biont] Nice wikipedia page on ontology

2007-01-24 Thread William Bug
Thanks, Carole. Which reminds me - there were two additional references I'd add to the bottom of the page: The Motagues and the Capulets Carole Goble and Chris Wroe http://www3.interscience.wiley.com/cgi-bin/abstract/109925284/ ABSTRACT?CRETRY=1&SRETRY=0 The recent Upper Ontology Summit (M

RE: [biont] Nice wikipedia page on ontology

2007-01-24 Thread Gao, Yong
Perhaps the terms "formal" and "ontology" should be defined or linked on the page? Both terms themselves are quite ambiguous. The formal ontology pages links to ontology in philosophy (http://en.wikipedia.org/wiki/Ontology), why not the computer science one ( http://en.wikipedia.org/wiki/Ontolo

Re: [biont] Nice wikipedia page on ontology

2007-01-24 Thread William Bug
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 i

Re: [biont] Nice wikipedia page on ontology

2007-01-24 Thread Carole Goble
Bill Hear hear!! Well said. Carole I was thinking initially Phil's concerns may have been more in terms of the wording used on the page, but Robert makes it more clear the issues are much more fundamental than that. All of Robert's points sound very much to the root of why there would be c

Re: [biont] Nice wikipedia page on ontology

2007-01-24 Thread William Bug
I was thinking initially Phil's concerns may have been more in terms of the wording used on the page, but Robert makes it more clear the issues are much more fundamental than that. All of Robert's points sound very much to the root of why there would be concerns this is not a comprehensive

RE: [biont] Nice wikipedia page on ontology

2007-01-24 Thread David Decraene
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 choic

RE: [biont] Nice wikipedia page on ontology

2007-01-24 Thread Davide Zaccagnini
David Decreane from L&C started that page and wrote good part of the content. I'm passing him your kind comments. Thanks Davide -Original Message- From: [EMAIL PROTECTED] on behalf of William Bug Sent: Tue 1/23/2007 4:06 PM To: Alan Ruttenberg Cc: public-semweb-lifesci hcls Subject: R

Re: [biont] Nice wikipedia page on ontology

2007-01-24 Thread Robert Stevens
'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 m

Re: [biont] Nice wikipedia page on ontology

2007-01-24 Thread Alan Ruttenberg
How would you phrase it? -Alan On Jan 24, 2007, at 8:55 AM, Phillip Lord wrote: "Alan" == Alan Ruttenberg <[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

Re: [biont] Nice wikipedia page on ontology

2007-01-24 Thread Phillip Lord
> "Alan" == Alan Ruttenberg <[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 On