- From: Miller, Michael D (Rosetta) <Michael_Miller@Rosettabio.com>
- Date: Tue, 24 Mar 2009 09:23:11 -0700
- To: "eric neumann" <ekneumann@gmail.com>
- Cc: "W3C HCLSIG hcls" <public-semweb-lifesci@w3.org>
- Message-ID: <C9EDB84D403E654CB78E37A506E406AF022CB8A9@ussemx1101.merck.com>
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 environment where it is done on a white board. another example would be someone who is going to perform a biological experiment (perhaps gene expression) where they will jot down in their notebook some terms from OBI to describe the type of experiment. the experiment doesn't work out so it is never published. by the by, i have also found the discussion useful, i do miss bill bug's input. cheers, michael Michael Miller Lead Software Developer Rosetta Biosoftware Business Unit www.rosettabio.com ________________________________ From: public-semweb-lifesci-request@w3.org [mailto:public-semweb-lifesci-request@w3.org] On Behalf Of eric neumann Sent: Tuesday, March 24, 2009 8:17 AM To: Bijan Parsia Cc: W3C HCLSIG hcls Subject: Re: blog: semantic dissonance in uniprot 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 when no record of the object exists in the digital space"? That is, if one defines a bunch of formal assertions on classes (based on real-world evidence/experience), do these work solely on digital KR and data forms, or do they go beyond that? I guess it may matter whether the "digital world" is being identified with the "conceptual world" of the mind... and that may be opening more cans of worms... What I'm getting at is that if the above question is true (ontologies only for digital forms), than the only things we can define ontologies for are the records of things; hence why talk about explicit record types if everything relevant is already a digital-record? In addition, I also don't see references to any object being fundamentally different to a digital record (san descriptive triples perhaps)... can someone provide me with a counter example? cheers, Eric On Tue, Mar 24, 2009 at 10:21 AM, Bijan Parsia <bparsia@cs.man.ac.uk> wrote: 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, and would probably resonate within the informatics groups at pharma companies. I think a key guidance principle here is to ensure that whatever is proposed "makes sense and works with molecular biologists" (scientists). Perhaps existing information resources need a major "enhancement" in order to work in a semantic web, but then let's make it quite clear (to all possible users) what the readily perceivable value of all these ontological adjustments will be. BTW, I'm perfectly happy, albeit not until summer, to do various sorts of empirical research to help ground this discussion. I've done surveys fo the web and user studies before. I would be interested in knowing what sorts of questions would help people make decisions. In this sense I *am* all about the data :) Cheers, Bijan.
Received on Tuesday, 24 March 2009 16:23:57 UTC