W3C home > Mailing lists > Public > public-semweb-lifesci@w3.org > August 2007

RE: RDF for molecules, using InChI

From: Michel_Dumontier <Michel_Dumontier@carleton.ca>
Date: Thu, 02 Aug 2007 20:39:22 -0400
To: Eric Neumann <eneumann@teranode.com>, Michel_Dumontier <Michel_Dumontier@carleton.ca>, Egon Willighagen <egon.willighagen@gmail.com>, public-semweb-lifesci@w3.org
Message-id: <AB349814F1ECB143A5D4CD29C7A645690192D6EA@CCSEXB10.CUNET.CARLETON.CA>
Human readability is best achieved with rdfs:label :-)

 

Alternatively make a hash of the InCHI.

 

-=Michel=-

________________________________

From: Eric Neumann [mailto:eneumann@teranode.com] 
Sent: Thursday, August 02, 2007 5:46 PM
To: Michel_Dumontier; Egon Willighagen; public-semweb-lifesci@w3.org
Subject: RE: RDF for molecules, using InChI

 

 

Certainly url-encoding solves this format problem, but it would indeed
be nice to eventually settle on a format not requiring encoding so that
its wysiwyg for the human...

-Eric


-----Original Message-----
From: Michel_Dumontier [mailto:Michel_Dumontier@carleton.ca]
Sent: Thu 8/2/2007 4:42 PM
To: Eric Neumann; Michel_Dumontier; Egon Willighagen;
public-semweb-lifesci@w3.org
Subject: RE: RDF for molecules, using InChI

Correct me if I'm wrong, but I don't think InCHI is URI compliant [1]
(=, /) so we'll have to escape or use some encoding scheme.



-=Michel=-



[1] http://www.isi.edu/in-notes/rfc2396.txt





________________________________

From: Eric Neumann [mailto:eneumann@teranode.com]
Sent: Thursday, August 02, 2007 4:08 PM
To: Michel_Dumontier; Egon Willighagen; public-semweb-lifesci@w3.org
Subject: RE: RDF for molecules, using InChI





Michel,

For clarity sake, can you give an example of your InChi URI ? urn??

Eric


-----Original Message-----
From: Michel_Dumontier [mailto:Michel_Dumontier@carleton.ca]
Sent: Thu 8/2/2007 3:59 PM
To: Eric Neumann; Egon Willighagen; public-semweb-lifesci@w3.org
Subject: RE: RDF for molecules, using InChI

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 Friday, 3 August 2007 00:39:43 GMT

This archive was generated by hypermail 2.3.1 : Tuesday, 26 March 2013 18:00:49 GMT