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Re: Chemistry and the Semantic Web

From: Eric Jain <Eric.Jain@isb-sib.ch>
Date: Wed, 30 Jun 2004 09:12:46 +0200
Message-ID: <40E267EE.5050507@isb-sib.ch>
To: Eric.Neumann@aventis.com
Cc: public-semweb-lifesci@w3.org

Eric.Neumann@aventis.com wrote:
> Question: How would one apply RDF for such cases? Would one use CML 
> (chemical markup language) to describe the chemical structure and have 
> an RDF statement refer to part of that doc via XPath/XPointers? How 
> about other structural formats like SMILE and CHUCKLES? Would the 
> documents be referenced using an LSID mechanism? Could this become the 
> basis for allowing research findings around chemistry and assays to 
> become consolidated as part of a R&D knowledge base?

This is an interesting question, and certainly also relevant to any 
classical bioinformatics data sources that contain more quantitative 
than qualitative data (e.g. 3D structures, 2D gel images and microarray 
data). I don't really have any solutions, just some ideas:

In those cases where it is possible to embed identifiers in the data, 
these could be referenced with identifiers such as 
urn:lsid:foo.org:bar:10. A resolution server can then be set up to 
extract the referenced data when required. Note that the original format 
need not contain full LSIDs.

If embedding identifiers is not an option, you could keep an 
LSID-to-XPath mapping on the resolution server. Using XPath statements 
directly as resource identifiers doesn't seem practical, though I may be 

In any case, you may end up duplicating parts of the non-RDF data into 
RDF, as RDF-aware applications (e.g. inference engines) are usually not 
able to make direct use of anything that is not RDF...
Received on Wednesday, 30 June 2004 03:12:47 UTC

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