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RE: blog: semantic dissonance in uniprot

From: Michel_Dumontier <Michel_Dumontier@carleton.ca>
Date: Wed, 25 Mar 2009 21:46:39 -0400
Message-ID: <AB349814F1ECB143A5D4CD29C7A6456903AAD9DC@CCSEXB10.CUNET.CARLETON.CA>
To: "David Booth" <david@dbooth.org>, "W3C HCLSIG hcls" <public-semweb-lifesci@w3.org>
David,
 I agree that different URIs should be used when trying to denote
different things. Like for instance, we might have different URIs for
different representations (eg html, xhtml, rdf, etc). I know the
NeuroCommons people like to formulate URIs with the representation and
others, like UniProt add a suffix to the ID. I've also shown you a case
where multiple descriptions can exist
(http://ontology.dumontierlab.com/Protein) - so what to do then? Is the
approach I've taken reasonable? It certainly can't conform to the 303
redirection and content negotiation.

Anyways, if the difference between an entity and a representation is
_actually_ what we've been talking about all along - then I think I was
ridiculously confused by the lack of specificity in the preceding email
communications.

 If however, what we've been talking about is that identifiers like  
 	http://purl.uniprot.org/uniprot/Q16665

are actually database records, and not molecular entities, then we can
settle this quickly:

Uniprot RDF file: http://www.uniprot.org/uniprot/Q16665.rdf 
(is this what people were referring to as a Record???)

Contains: 

<rdf:Description rdf:about="http://purl.uniprot.org/uniprot/Q16665">
 <rdf:type rdf:resource="http://purl.uniprot.org/core/Protein" />


It's clear that the entity denoted by :Q16665 is rdf:type :Protein and
is the subject of statements that are biological in nature such as being
located in sub-cellular compartments or being involved in biochemical
reactions. It is clearly not a Record. This is generally the case for
nearly all entries in biomolecular databases.

Cheers,

-=Michel=-

Anxiously waiting see if this clears up things or generates controversy
.. it's hard to predict!



> If nobody ever wants to use the same property to talk about the
> database
> record as was used to talk about the molecule, and nobody ever makes
an
> assertion that implies that the class of database records is disjoint
> from the class of molecules, then I don't see any harm in using the
> same
> URI to ambiguously denote both.   But if one is trying to design data
> to
> be reusable by others in unforeseen ways, there clearly *is* a risk
> that
> someone will want to make such assertions in conjunction with the
data,
> and if that happens there is a clear harm.  This risk is easy to avoid
> by using separate URIs.
> 
> There *are* trade-offs.  Minting two URIs instead of one *does* add
> some
> complexity, though as I pointed out that additional complexity can be
> mitigated to the point that it is a *very* low cost.  Still, different
> people will weigh these trade-offs differently, and what's best for
one
> situation may not be best for another, as I indicated in my original
> post.
> 
> Furthermore, even if one does use the same URI to ambiguously denote
> both a database record and a molecule, that is not the end of the
world
> either.  It is possible (though more difficult) to later separate out
> and relate the different senses of an ambiguous URI, as I have
> described:
> http://dbooth.org/2007/splitting/
> Ambiguity is inescapable, and ambiguity between a thing and a page
that
> describes that thing is not fundamentally different from other kinds
of
> ambiguity (except perhaps that we are aware of it in advance and it
can
> be easily avoided), as explained here:
> http://dbooth.org/2007/splitting/#httpRange-14
> 
> Finally, although it is flattering that you have named this suggestion
> after me, I cannot take credit.  As I pointed out in my original post,
> the suggestion to differentiate between a molecule and the database
> record that describes that molecule originates with the Architecture
of
> the World Wide Web:
> http://www.w3.org/TR/webarch/#URI-collision
> and best practices for implementing this distinction are described in
> Cool URIs for the Semantic Web:
> http://www.w3.org/TR/cooluris
> 
> David Booth
> 
> 
Received on Thursday, 26 March 2009 01:47:49 UTC

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