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Re: Chemistry and the Semantic Web

From: Adrian Walker <adrianw@snet.net>
Date: Wed, 30 Jun 2004 07:22:47 -0400
Message-Id: <>
To: Eric Jain <Eric.Jain@isb-sib.ch>
Cc: public-semweb-lifesci@w3.org

Hi Eric --

At 09:12 AM 6/30/04 +0200, you wrote:
....RDF-aware applications (e.g. inference engines) are usually not able to 
make direct use of anything that is not RDF...

You may like to look at the online-runnable example RDFQueryLangComparisonq 
at our site.  It makes direct use of a triple form of RDF, and the system 
can also reason over relational databases.

HTH,   -- Adrian

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Dr. Adrian Walker
Reengineering LLC
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Phone: USA 860 583 9677
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>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 wrong.
>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 07:17:49 UTC

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