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Re: blog: semantic dissonance in uniprot

From: Pat Hayes <phayes@ihmc.us>
Date: Wed, 25 Mar 2009 23:46:57 -0500
Cc: "Phillip Lord" <phillip.lord@newcastle.ac.uk>, "W3C HCLSIG hcls" <public-semweb-lifesci@w3.org>
Message-Id: <8FE87E48-7E3E-4799-8AD5-5352C2A3808A@ihmc.us>
To: Mark Wilkinson <markw@illuminae.com>

On Mar 25, 2009, at 11:25 AM, Mark Wilkinson wrote:

> 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!  ;-)

Well, if you can tell us how to do some weaving, we maybe can make  
progress. The properties of sameAs are fairly easy to list. It is  
transitive, reflexive, symmetric and substitutive: if A sameAs B and  
something is true of A, then its also true of B.  So, which of these  
_aren't_ correct for the application you have in mind? Can you say why  
not (an example will do)? "Less rigorous" doesn't cut it.

Pat Hayes

>
> M
>
>
> -- 
> 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
>
>
>

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Received on Thursday, 26 March 2009 04:48:48 UTC

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