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Re: Less strong equivalences (was Re: blog: semantic dissonance in uniprot)

From: Pat Hayes <phayes@ihmc.us>
Date: Thu, 26 Mar 2009 01:53:52 -0500
Cc: Bijan Parsia <bparsia@cs.manchester.ac.uk>, W3C HCLSIG hcls <public-semweb-lifesci@w3.org>
Message-Id: <436551CF-8CB6-40E4-909D-8290FCD2EE1C@ihmc.us>
To: eric neumann <ekneumann@gmail.com>

On Mar 25, 2009, at 4:31 PM, eric neumann wrote:

> Bijan,
> From your descriptions, I can't tell which one would best handle the  
> following situation:
> "Object 1 refers to exactly the same molecule (exemplar) as object 2  
> refers to"

That sure sounds like sameAs, applied to molecules. Why isn't sameAs  
good enough here? What goes wrong?

> This is the kind of "similar" used in most internal genomic/compound  
> systems...
> <http://myOrg.com/sw/mxid/PHLP0005>  :isIdentifiedwith  <http://www.uniprot.org/uniprot/P16233 
> >
> It really isn't probabilistic anymore since the scientists have all  
> agreed and defined their entry based on some of the info from the  
> public entity; for most situations it is an 'exact mapping' to the  
> referred molecules. I agree owl:sameAs was not intended for this  
> kind of relation, but is is extremely common, and a specialized  
> relation for this would be very much desired. : )
> Remember also, even though these URIs may be of instances in terms  
> of records, the molecule referenced is not really "a specific single  
> molecule" found in nature (conceptually possible, but never thought  
> of this way in may experience). In fact, this is almost always the  
> case in molecular biology (genes, genomes, SNPs, proteins, etc),  
> while when dealing with macro-humans, we can refer to an exact  
> instance in the real world.

I assume that the intended referent is a 'typical molecule' or a  
'molecular pattern' rather than a particular, single molecule. Yes, of  
course: but that doesn't affect the use of sameAs. Whatever these  
'molecules' are that your ontology is talking about, sameAs means the  
same one of those.

> Perhaps we really need a set of basic relations (and meta classing?)  
> for this scale of scientific phenomena to keep it distinct from  
> organism examples in clinical studies and experiments...

The basic ontology issues of identity and so on should work at any  
scale from quarks to galaxy clusters.


> Eric
> On Wed, Mar 25, 2009 at 4:05 PM, Bijan Parsia <bparsia@cs.manchester.ac.uk 
> > wrote:
> Oh, another possibility, 4) probabilistic sameAs. That's probably  
> more researchy than similarity logics, but more in the next few year  
> timeline rather than in the "have no idea" timeline.
> Cheers,
> Bijan.

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Received on Thursday, 26 March 2009 06:55:38 UTC

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