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Re: Chemistry and the Semantic Web

From: John Wilbanks <wilbanks@w3.org>
Date: Fri, 02 Jul 2004 13:47:33 -0400
Message-ID: <40E59FB5.7050504@w3.org>
Cc: public-semweb-lifesci@w3.org

Oracle's NDM is actually in active development as an RDF store.  Wearing 
my W3C hat, I just spoke at their Life Sciences User Group meeting in 
the NDM workshop...  They're actively looking for use cases on how to 
deploy NDM in an RDF setting in lifesciences and I'll alert Susie 
Stephens to this thread.

jtw

-- 
John Wilbanks
W3C Fellow
Semantic Web - Life Sciences
http://www.w3.org/People/all#wilbanks
wilbanks@w3.org
617-253-5845 (direct)
617-838-6333 (mobile; best voicemail #)
--



Joanne S. Luciano wrote:

> 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, 7 July 2004 14:51:07 GMT

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