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RE: URL +1, LSID -1

From: Michel_Dumontier <Michel_Dumontier@carleton.ca>
Date: Tue, 10 Jul 2007 13:13:48 -0400
To: public-semweb-lifesci <public-semweb-lifesci@w3.org>
Cc: Mark Wilkinson <markw@illuminae.com>, Benjamin Good <goodb@interchange.ubc.ca>, Natalia Villanueva Rosales <naty.vr@gmail.com>
Message-id: <AB349814F1ECB143A5D4CD29C7A64569017BF01E@CCSEXB10.CUNET.CARLETON.CA>

Unfortunately, this again demonstrates the problem in which the
identifier for a biological entity - say mitochondrial Aspartate
aminotransferase resolves to a nicely formatted HTML page. What if I
have a semantic web application in which I would like to retrieve more
information about this resource? Since the document is not an RDF
document with machine understandable statements about it, it seems that
my application wouldn't be able to learn anything more about
http://purl.uniprot.org/uniprot/P12345

Moreover, if I, a biological scientist, wish to make a statement (add
new knowledge) about this protein, I certainly wouldn't want to do so
using this identifier.

IMHO, if you are going to use URLs to identify RDF resources, then make
sure that RDF content is available at that location. Currently, the RDF
resource 
http://purl.uniprot.org/uniprot/P12345 does not exist there and is
actually defined at http://purl.uniprot.org/uniprot/P12345.rdf

Houston, we have a problem.

It's great to make human readable pages - I for one love nicely
formatted pages. But please add a statement (say using the predicate
HTMLPage or something to that effect) to an RDF document that the web
page is located at http://purl.uniprot.org/uniprot/P12345.html (yai!
which resolves correctly)

The use of a location free identifier such as an LSID provides me with
the capability to make statements about resources that I care about.
LSIDs and URLs can live together just fine. Using owl:sameAs predicate
to bind them together is one easy way of doing this.  Just make sure
you're talking about the same thing.

Cheers,

-=Michel=-
 
Michel Dumontier
Assistant Professor of Bioinformatics
 
Department of Biology, School of Computer Science, Institute of
Biochemistry 
Carleton University 

Member of the Ottawa Institute of Systems Biology 
Member of the Ottawa-Carleton Institute for Biomedical Engineering
 
Office: 4610 Carleton Technology and Training Center
Mailing: 209 Nesbitt, 1125 Colonel By Drive, Ottawa, ON K1S5B6
Tel:  +1 (613) 520-2600 x4194
Fax:  +1 (613) 520-3539
Web:  http://dumontierlab.com
Skype: micheldumontier

> -----Original Message-----
> From: public-semweb-lifesci-request@w3.org
[mailto:public-semweb-lifesci-
> request@w3.org] On Behalf Of Eric Jain
> Sent: Tuesday, July 10, 2007 12:48 PM
> To: public-semweb-lifesci
> Subject: URL +1, LSID -1
> 
> 
> In the latest release of UniProt (11.3), all URIs of the form:
> 
>    urn:lsid:uniprot.org:{db}:{id}
> 
> have been replaced with URLs:
> 
>    http://purl.uniprot.org/{db}/{id}
> 
> In general, these URLs can be resolved to a human readable web page (a
few
> are still broken, will be fixed). Some of these web pages may (or may
not)
> be linked to a machine-readable representation via link-rel=alternate.
> 
> As an optimization for "Semantic Web" crawlers, there is experimental
> support for "Accept" headers (i.e. set it to "application/rdf+xml").
> 
> Some examples:
> 
> http://purl.uniprot.org/uniprot/P12345
> http://purl.uniprot.org/taxonomy/9606
> http://purl.uniprot.org/pdb/1BRC
> 
Received on Wednesday, 11 July 2007 06:17:38 UTC

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