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Re: blog: semantic dissonance in uniprot

From: Mark Wilkinson <markw@illuminae.com>
Date: Wed, 25 Mar 2009 09:25:30 -0700
To: "Phillip Lord" <phillip.lord@newcastle.ac.uk>, "W3C HCLSIG hcls" <public-semweb-lifesci@w3.org>
Message-ID: <op.urcvwsmnnbznux@dd0710001l.icapture.ubc.ca>
On Wed, 25 Mar 2009 03:41:37 -0700, Phillip Lord  
<phillip.lord@newcastle.ac.uk> wrote:

> If I remember correctly the original post that started this of Ben has
> it about right. We need some tags which say "these two database records
> are about the same protein, well, sort of, at least in this case, for
> the purposes of what I am doing".

I agree - the issue also came up at the BioHackathon last week...  
basically, as Tom Oinn phrased it, "if you're thinking of using  
owl:sameAs... don't!"

Another predicate is needed that is less "rigourous" - owl:kindOfLike  :-)

I think there is another, potentially more nefarious concern in the  
statement that Ben was objecting to in his post.  The statement was:

http://www.uniprot.org/tissues/229 (subject)
http://www.w3.org/2002/07/owl#sameAs (predicate)
http://purl.uniprot.org/po/0009009 (object)

my concern is whether http://purl.uniprot.org/po/0009009 is intended to be  
a class, or intended to be an instance... since owl:sameAs is only  
supposed to be used to claim the "identicalness" of two individuals, not  
an individual to a class...

Oh what a tangled "Web" we weave!  ;-)


Mark D Wilkinson, PI Bioinformatics
Assistant Professor, Medical Genetics
The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research
Providence Heart + Lung Institute
University of British Columbia - St. Paul's Hospital
Vancouver, BC, Canada
Received on Wednesday, 25 March 2009 16:32:04 UTC

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