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Re: Chemistry and the Semantic Web

From: Peter Murray-Rust <pm286@cam.ac.uk>
Date: Thu, 01 Jul 2004 09:31:43 +0100
Message-Id: <>
To: Eric Jain <Eric.Jain@isb-sib.ch>
Cc: public-semweb-lifesci@w3.org, h.rzepa@ic.ac.uk

At 10:22 01/07/2004 +0200, Eric Jain wrote:

>>CMLRSS already does this for CML (sic).
>CMLRSS allows any CML data to be represented directly in RDF. Correct?

I don't think so.

If you mean "are all CML primitives represented in RDF?" - i.e. at the atom 
and bond level, then no. This is an interesting idea and was suggested to 
me by Tim Berners-Lee a year or two ago. In principle one could rewrite 
chemical informatics software completely in RDF triples. However I suspect 
that at present the overhead both in terms of recoding and performance 
would be enormous.

If I want to diagonalise a matrix (e.g. in quantum mechanics) I look to 
procedural code, not RDF. I can see that computation of molecular mass 
could be RDF-ised. In principle the RDF-isation of chemical substructure 
search could also be done. I suspect that RDF has to use some primitives 
eventually and we have set the chemical level reasonably high.

Does this answer the Q? :-)


Peter Murray-Rust
Unilever Centre for Molecular Informatics
Chemistry Department, Cambridge University
Lensfield Road, CAMBRIDGE, CB2 1EW, UK
Tel: +44-1223-763069
Received on Wednesday, 7 July 2004 14:50:54 UTC

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