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RE: blog: semantic dissonance in uniprot

From: Michel_Dumontier <Michel_Dumontier@carleton.ca>
Date: Mon, 23 Mar 2009 23:54:33 -0400
Message-ID: <AB349814F1ECB143A5D4CD29C7A6456903A3AE2B@CCSEXB10.CUNET.CARLETON.CA>
To: "David Booth" <david@dbooth.org>
Cc: "W3C HCLSIG hcls" <public-semweb-lifesci@w3.org>
  There's nothing like resurrecting this discussion one more time ;-)

For all representations one should make simplifying assumptions in order to increase the usability of the system.

In the life sciences, scientists don't care about database records - they care about the molecules and the biological processes for which facts have been collected about. It is an artifact of database KR that we have such records in the first place. You probably won't see "Record" in a bio-ontology.

IMHO, 303 redirects simply complicate matters and is not useful.

We track provenance with namespace and/or graphs. What could be simpler?


-----Original Message-----
From: David Booth [mailto:david@dbooth.org] 
Sent: Monday, March 23, 2009 10:27 PM
To: Michel_Dumontier
Cc: W3C HCLSIG hcls
Subject: RE: blog: semantic dissonance in uniprot


On Sat, 2009-03-21 at 13:49 -0400, Michel_Dumontier wrote:
> Eric and friends,
>  Ióm very sympathetic to the simplifying assumption of not
> distinguishing between a record and the molecular entity it
> represents, but . . . .

I do not think this would be a wise "simplification".  This is only a
simplification from one perspective: because it avoids having to mint
and maintain pairs of URIs instead of a single URI.  But the downstream
cost is that it creates an ambiguity (or "URI collision")
that may cause trouble and be difficult to untangle later as the data is
used in more and more ways.  For example, if any of the same predicates
need to be used on both the record and the molecular entity, they will
become hopelessly confused.  Also, if disjointness assertions are
included then this overloading may cause logical contraditions.

Cool URIs for the Semantic Web
describes best practices for minting URIs using 303 redirects to enable
the record to be obtained (indirectly) by following the URI for a
molecular entity.  If minting a separate URI for the molecular entity
seems onerous, it is trivial to use a 303-redirect service such as
to do the job for you.  And if you want to set up your own 303-redirect
service, that site will even show you the exact files that are used to
implement it:

Provenance (who said what) is extremely important in scientific anaylsis
-- explicitly tracking the evidence leading to scientific assertions.
It is easy for me to envision applications that will both use assertions
about a molecular entity *and* assertions about the records that
describe those molecular entities.

If you are just minting disposable URIs that aren't intended to be very
reusable anyway, then this ambiguity is not a problem, and it may be the
quickest solution to your problem.  But if you want your URIs to be long
lived and used by others for other applications, I think it would be a

David Booth
Received on Tuesday, 24 March 2009 03:55:36 UTC

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