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RE: RDF for molecules, using InChI

From: Michel_Dumontier <Michel_Dumontier@carleton.ca>
Date: Thu, 02 Aug 2007 15:59:10 -0400
To: Eric Neumann <eneumann@teranode.com>, Egon Willighagen <egon.willighagen@gmail.com>, public-semweb-lifesci@w3.org
Message-id: <AB349814F1ECB143A5D4CD29C7A645690192D6B9@CCSEXB10.CUNET.CARLETON.CA>
Hi,

 

I support the use of InChI as URI. Of course, the use of such a URI will
annoy those that want URL resolvable URIs... another reason to relate
the URI and the resolvable URL with an owl:sameAs predicate.

 

 

<rdf:RDF
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:iupac="http://www.iupac.org/">
 
<rdf:Description
 rdf:about="http://cb.openmolecules.net/rdf/?InChI=1/CH4/h1H4">
 
 <iupac:inchi>InChI=1/CH4/h1H4</iupac:inchi>

...

 

-=Michel=-

________________________________

From: public-semweb-lifesci-request@w3.org
[mailto:public-semweb-lifesci-request@w3.org] On Behalf Of Eric Neumann
Sent: Thursday, August 02, 2007 2:09 PM
To: Egon Willighagen; public-semweb-lifesci@w3.org
Subject: RE: RDF for molecules, using InChI

 

 

Egon,

I commend you on two fronts: 1) developing a chem data model that
utilizes InChi as part of the URI, and 2) demonstrating how something as
simle as an XSLT can be used to organize viewable html ( I also see your
OpenMolecules page supports the use of RDFa-- great job!).

We've discussed a little bit on trying to promote the development of
Chemical URIs, possibly using InChi. We've heard others have been
proposing to do this as well. Is the OpenMolecules program connected to
work at U of Southampton on chemical identifiers?

I think it would be great if most of the chem and life sci community
could agree on a single chemical URI model that is open and annotatable!
Are you hoping to see this happen as well?

cheers,
Eric

-----Original Message-----
From: public-semweb-lifesci-request@w3.org on behalf of Egon Willighagen
Sent: Thu 8/2/2007 7:39 AM
To: public-semweb-lifesci@w3.org
Subject: RDF for molecules, using InChI


Hi all,

I played a bit with RDF for molecular data a bit this week, and now
have a RDF provider service (try methane [1]), which is written in
PHP, uses XSLT to create a HTML frontend (*). It works for any
molecule/InChI, but depends on 'plugins' to set up any other than the
implied properties (i.e. reproduce the InChI). The methane example
mentioned shows some information extracted from Chemical blogspace
[2], but I plan to write other plugins too, e.g. for PubChem,
ChemSpider and other databases.

I have written up some thoughs at [3], and would much like to hear
your opinions and comments.

Looking forward to hearing from you,

kind regards,

Egon Willighagen
http://chem-bla-ics.blogspot.com/

*) FireFox 2.0.0.6 and IE pick up the declared stylesheet, but
Konqueror/Linux does not.

1.http://cb.openmolecules.net/rdf/?InChI=1/CH4/h1H4
2.http://cb.openmolecules.net/
3.http://chem-bla-ics.blogspot.com/2007/07/rdf-ing-molecular-space.html
Received on Thursday, 2 August 2007 19:59:23 GMT

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