- From: Joanne S. Luciano <jluciano@predmed.com>
- Date: Wed, 30 Jun 2004 08:59:34 -0400
- To: <Eric.Neumann@aventis.com>, <public-semweb-lifesci@w3.org>
- Message-ID: <AC7E074AAF69A345827FFA7AE09C24CD064BE9@predmed-mail.predmed.local>
I was just looking at Oracle's Spatial Network Data Model this morning and wondering if that might be a good place to start. This may be overly simplistic, but the NDM Schema has two components, Meta Data (Name, Type and the Table info) and Tables for Nodes, Link's and Paths. Would take more time to think this through, but perhaps it something you may want to take a look at. Joanne _____ From: public-semweb-lifesci-request@w3.org [mailto:public-semweb-lifesci-request@w3.org] On Behalf Of Eric.Neumann@aventis.com Sent: Tuesday, June 29, 2004 5:15 PM To: public-semweb-lifesci@w3.org Subject: Chemistry and the Semantic Web In looking at some areas outside of the scope of traditional bioinformatics (but still part of drug discovery), it would appear that the Chemistry Domain could greatly benefit from Semantic Web approaches. For instance, it might be useful to somehow allow scientists to annotate select groups of chemical structures using interconnecting relations that have specific significance to a drug discovery project. Example: a set of azaindoles may show CDK2 toxicity if they contain a polar group at position 3 on the indole group. A mechanism of action may even be proposed (using RDF) for this toxicity and associated with the non-selective binding to a pocket on CDK2. Alternatively, some side groups could be found to dramatically affect Pharmacokinetics (PK), so this would be great to RDF-link-in as well. 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 a big issue here at Aventis with many projects. Linking mechansisms and interactions to chem structures would be significant for enhancing innovation and productivity. I think this builds on applying LSIDs to chemical structures (via CAS, etc), but goes beyond on how to represent the interpretations of assays and models of action as part of drug development. Eric Eric Neumann, Ph.D. Global Head of Knowledge Management Aventis - DI&A Tel: 908-231-3510 Fax: 908-231-3307 Eric.Neumann@Aventis.com
Received on Wednesday, 30 June 2004 09:00:05 UTC