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Re: blog: semantic dissonance in uniprot

From: Mark Wilkinson <markw@illuminae.com>
Date: Wed, 25 Mar 2009 10:13:13 -0700
To: "Oliver Ruebenacker" <curoli@gmail.com>
Cc: "Phillip Lord" <phillip.lord@newcastle.ac.uk>, "W3C HCLSIG hcls" <public-semweb-lifesci@w3.org>
Message-ID: <op.urcx4bdrnbznux@dd0710001l.icapture.ubc.ca>
On Wed, 25 Mar 2009 10:03:43 -0700, Oliver Ruebenacker <curoli@gmail.com>  

>> 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...
>   Must be an individual, then, doesn't it?

Well, the statement would *imply* that it is... so given that the  
individual "embryo" that was referred to as a uniprot tissue is the same  
individual "embryo" that the plant ontology was talking about, we can  
therefore conclude that (as Ben pointed-out) that this particular fly  
embryo is somehow embedded in some particular plant seed endosperm.


the problem with owl:sameAs is that it is much more rigourous than most of  
our ontologies are!  I don't think we need to throw it away, but we need  
to be ACUTELY aware of what it MEANS, and only use it in those VERY rare  
cases where we are saying that "Bill Clinton" is owl:sameAs "William  
Jefferson Clinton" (the example from the OWL spec)


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 17:19:49 UTC

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