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

From: Bijan Parsia <bparsia@cs.manchester.ac.uk>
Date: Wed, 25 Mar 2009 21:47:21 +0000
Cc: W3C HCLSIG hcls <public-semweb-lifesci@w3.org>
Message-Id: <71288425-8EBB-42E6-89D5-5AE1BFEE796E@cs.manchester.ac.uk>
To: eric neumann <ekneumann@gmail.com>
Eric,

Thanks for the use case!

On 25 Mar 2009, at 21:31, 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"


At the moment, I don't see why it's *different* than sameAs.

So, in A sameAs B, we say that the object *denoted* by A is the very  
same object as that *denoted* by B.

That is, there's one object, and the terms A and B are names for the  
very same object (though we don't have access to the notion of "name"  
from our axioms).

This is, in part, because my natural reading of the above is that  
"refers" is the same as "denotes".

Another possible reading is:
	"Object 1 is related somehow to exactly the same molecule as object 2  
is"

This would mean that Objects 1 and 2 are distinct object.s

> 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 
> >

Can you explicate this a bit more for me? I.e., could you present what  
you expect this to do or not do?

> 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.

Is it that most, but not all of the time, you can treat is as sameAs  
but sometimes you don't want to?

> 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. : )

We need to make me understand the relation :)

> Remember also, even though these URIs may be of instances in terms  
> of records,

instances of what?

> 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.

We cannot?

> 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...

I suspect there's more weight on "exemplar" than I know how to give at  
the moment :)

Cheers,
Bijan.
Received on Wednesday, 25 March 2009 21:47:59 UTC

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