Re: blog: semantic dissonance in uniprot

2009-03-24 Thread Bijan Parsia
On 24 Mar 2009, at 20:56, Kingsley Idehen wrote: Bijan Parsia wrote: On 24 Mar 2009, at 19:35, Kingsley Idehen wrote: [snip] Bijan, I am not mixing anything up. You're mixing me up! A this juncture I have nothing to add to the discussion. Ok. Could you summarize your point in plain lang

Re: blog: semantic dissonance in uniprot

2009-03-24 Thread Kingsley Idehen
Bijan Parsia wrote: On 24 Mar 2009, at 19:35, Kingsley Idehen wrote: [snip] Bijan, I am not mixing anything up. You're mixing me up! A this juncture I have nothing to add to the discussion. Ok. Could you summarize your point in plain language so that at future junctures when you have som

Re: blog: semantic dissonance in uniprot

2009-03-24 Thread Bijan Parsia
On 24 Mar 2009, at 19:35, Kingsley Idehen wrote: [snip] Bijan, I am not mixing anything up. You're mixing me up! A this juncture I have nothing to add to the discussion. Ok. Could you summarize your point in plain language so that at future junctures when you have something to add to the

Re: blog: semantic dissonance in uniprot

2009-03-24 Thread Kingsley Idehen
Michel_Dumontier wrote: I just want to focus on the essence of my comments to Michel and Peter who have issues with the use of 303 redirection to achieve separation of datum identity from descriptive representation, when using a particular URI scheme. I am simply interested in explaini

Re: blog: semantic dissonance in uniprot

2009-03-24 Thread Kingsley Idehen
Bijan Parsia wrote: On 24 Mar 2009, at 14:23, Kingsley Idehen wrote: [snip] Bijan, I am not assuming naivety on your part. Didn't suggest you were. Just was pointing out that my not understanding your questions or arguments was not a function of being naive about identity. I just want to

Re: blog: semantic dissonance in uniprot

2009-03-24 Thread Bijan Parsia
On 24 Mar 2009, at 14:23, Kingsley Idehen wrote: [snip] Bijan, I am not assuming naivety on your part. Didn't suggest you were. Just was pointing out that my not understanding your questions or arguments was not a function of being naive about identity. I just want to focus on the essenc

RE: blog: semantic dissonance in uniprot

2009-03-24 Thread Michel_Dumontier
> I just want to focus on the essence of my comments to Michel and Peter > who have issues with the use of 303 redirection to achieve separation > of > datum identity from descriptive representation, when using a particular > URI scheme. > > I am simply interested in explaining to them what this

Re: blog: semantic dissonance in uniprot

2009-03-24 Thread Bijan Parsia
On 24 Mar 2009, at 15:17, eric neumann wrote: Bijan, I have a (possibly) naive question, but one that comes up in the context of a digital record/rep of the protein : Are OWL ontologies supposed to be applied to only digital representations of real world things, No. Indeed, that's towar

CFP: Bio-Ontologies: Knowledge in Biology 2009

2009-03-24 Thread Phillip Lord
** Call for Papers Submissions are now invited Bio-Ontologies 2009: Knowledge in Biology, a SIG at Intelligent Systems for Molecular Biology 2009. *** Key Dates - Submissions Due: April 10th (Friday) - Notifications: May 1st (Friday) - Final Version Due: May 8th (Friday) - Workshop: June

Re: blog: semantic dissonance in uniprot

2009-03-24 Thread Phillip Lord
Oliver Ruebenacker writes: > Is it possible that referring to records instead of things is not > the result of confusion, but rather of cost-benefit considerations - > that records are cheap and identification is costly and open-ended? > What is it that can not be achieved by having better rec

RE: blog: semantic dissonance in uniprot

2009-03-24 Thread Miller, Michael D (Rosetta)
hi all, samw...@gmx.at wrote: >> Can any one name a real world example of where confusion between an >> entity and its record was issue? >> > > I would say that 80% of the RDF/OWL ontologies lingering somewhere on the web > are examples. They are just so ill-designed that nobody wants to u

RE: blog: semantic dissonance in uniprot

2009-03-24 Thread Miller, Michael D (Rosetta)
hi eric, this is probably a bit naive but i can think of two examples. one is that i often do paper examples (i'm a bit of a luddite) when i'm working out ideas so i might sketch out some object that i will then annotate from OWL ontologies to 'see how it works.' this might even be in a group

Re: blog: semantic dissonance in uniprot

2009-03-24 Thread Oliver Ruebenacker
Hello Bijan, Philip, All, I understand that what you are referring to are real problems, but I wonder why the most accurate way to characterize them is as "confusion between a thing and its record". It sounds as if there was a person who would one day exclaim "Oh my God! I always thought

Re: blog: semantic dissonance in uniprot

2009-03-24 Thread eric neumann
Bijan, I have a (possibly) naive question, but one that comes up in the context of a digital record/rep of the protein : Are OWL ontologies supposed to be applied to only digital representations of real world things, or do some believe they actually can be applied to the real-world things "even wh

RE: blog: semantic dissonance in uniprot

2009-03-24 Thread David Booth
Eric, On Sat, 2009-03-21 at 13:49 -0400, Michel_Dumontier wrote: > Eric and friends, > > I’m very sympathetic to the simplifying assumption of not > distinguishing between a record and the molecular entity it > represents, but . . . . I do not think this would be a wise "simplification". This i

Re: blog: semantic dissonance in uniprot

2009-03-24 Thread Kingsley Idehen
Bijan Parsia wrote: On 24 Mar 2009, at 13:01, Kingsley Idehen wrote: [snip] Bijan, Is "Identity" important or not? That's the question here. But it's not a well-defined question. But let me make a well-defined version (not meant to capture your question, but just to be clear example). In XS

Re: blog: semantic dissonance in uniprot

2009-03-24 Thread Bijan Parsia
On 24 Mar 2009, at 13:49, eric neumann wrote: I think this discussion has been quite useful and important, since there are some remaining issues to be clarified by this community. I think all points raised are good, but not equally valid. Bijan and Phil's thoughts are very useful for me, an

Re: blog: semantic dissonance in uniprot

2009-03-24 Thread Bijan Parsia
On 24 Mar 2009, at 13:01, Kingsley Idehen wrote: [snip] Bijan, Is "Identity" important or not? That's the question here. But it's not a well-defined question. But let me make a well-defined version (not meant to capture your question, but just to be clear example). In XSD, 1.0^^xsd:double i

Re: blog: semantic dissonance in uniprot

2009-03-24 Thread Bijan Parsia
On 24 Mar 2009, at 12:43, samw...@gmx.at wrote: On 24 Mar 2009, at 12:20, samw...@gmx.at wrote: Can any one name a real world example of where confusion between an entity and its record was issue? I would say that 80% of the RDF/OWL ontologies lingering somewhere on the web are example

Re: blog: semantic dissonance in uniprot

2009-03-24 Thread eric neumann
I think this discussion has been quite useful and important, since there are some remaining issues to be clarified by this community. I think all points raised are good, but not equally valid. Bijan and Phil's thoughts are very useful for me, and would probably resonate within the informatics group

Re: blog: semantic dissonance in uniprot

2009-03-24 Thread Kingsley Idehen
Bijan Parsia wrote: On 24 Mar 2009, at 05:06, Kingsley Idehen wrote: [snip] Michel, 303 redirection serves a single purpose: enforcement of the Identity principle for discrete data objects. If a datum lacks identity it cannot in away be resourceful. Identity principle? Resourceful? What is

Re: blog: semantic dissonance in uniprot

2009-03-24 Thread samwald
> On 24 Mar 2009, at 12:20, samw...@gmx.at wrote: > > > > >> Can any one name a real world example of where confusion between an > >> entity and its record was issue? > > > > I would say that 80% of the RDF/OWL ontologies lingering somewhere > > on the web are examples. > > Such a violation

Re: blog: semantic dissonance in uniprot

2009-03-24 Thread Kingsley Idehen
samw...@gmx.at wrote: Can any one name a real world example of where confusion between an entity and its record was issue? I would say that 80% of the RDF/OWL ontologies lingering somewhere on the web are examples. They are just so ill-designed that nobody wants to use them, and nobody C

Re: blog: semantic dissonance in uniprot

2009-03-24 Thread Bijan Parsia
On 24 Mar 2009, at 12:20, samw...@gmx.at wrote: Can any one name a real world example of where confusion between an entity and its record was issue? I would say that 80% of the RDF/OWL ontologies lingering somewhere on the web are examples. Such a violation of Sturgeon's Law[1] would b

Contd: blog: semantic dissonance in uniprot

2009-03-24 Thread Kingsley Idehen
Peter, Note the link below as it was inadvertently placed beneath my sign-off re. prior mail. Links: 1. http://www.cs.cmu.edu/afs/cs.cmu.edu/user/clamen/OODBMS/Manifesto/htManifesto/node4.html -- Object Identity -- Regards, Kingsley Idehen Weblog: http://www.openlinksw.com/

Re: blog: semantic dissonance in uniprot

2009-03-24 Thread Kingsley Idehen
Peter Ansell wrote: 2009/3/24 Kingsley Idehen : If you are going to honor the Identity principle on the Web, in an unobtrusive manner (i.e., leverage ubiquity of HTTP) there is no way around the above. I never thought of it as honour. The large number of ideals surrounding the redirect

Re: blog: semantic dissonance in uniprot

2009-03-24 Thread samwald
> Can any one name a real world example of where confusion between an > entity and its record was issue? I would say that 80% of the RDF/OWL ontologies lingering somewhere on the web are examples. They are just so ill-designed that nobody wants to use them, and nobody CAN use them. The creato

Re: blog: semantic dissonance in uniprot

2009-03-24 Thread Phillip Lord
Oliver Ruebenacker writes: > 2009/3/23 Michel_Dumontier : >> I do not think this would be a wise "simplification".  This is only a >> simplification from one perspective: because it avoids having to mint >> and maintain pairs of URIs instead of a single URI.  But the downstream >> cost is that i

Re: blog: semantic dissonance in uniprot

2009-03-24 Thread Bijan Parsia
On 24 Mar 2009, at 10:32, Oliver Ruebenacker wrote: Hello All, 2009/3/23 Michel_Dumontier : I do not think this would be a wise "simplification". This is only a simplification from one perspective: because it avoids having to mint and maintain pairs of URIs instead of a single URI. But

Re: blog: semantic dissonance in uniprot

2009-03-24 Thread Oliver Ruebenacker
Hello All, 2009/3/23 Michel_Dumontier : > I do not think this would be a wise "simplification".  This is only a > simplification from one perspective: because it avoids having to mint > and maintain pairs of URIs instead of a single URI.  But the downstream > cost is that it creates an ambigu

Re: blog: semantic dissonance in uniprot

2009-03-24 Thread Bijan Parsia
On 24 Mar 2009, at 05:06, Kingsley Idehen wrote: [snip] Michel, 303 redirection serves a single purpose: enforcement of the Identity principle for discrete data objects. If a datum lacks identity it cannot in away be resourceful. Identity principle? Resourceful? What is it to be resourcefu