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RE: The UniProt database in RDF format

From: <Eric.Neumann@aventis.com>
Date: Wed, 21 Jul 2004 17:36:09 -0400
Message-ID: <81BE96441EAC744B8F6E1E738C53F9589E14E9@sccsmxsusr05.pharma.aventis.com>
To: <wilbanks@w3.org>
Cc: <Eric.Jain@isb-sib.ch>, <public-semweb-lifesci@w3.org>


John,

Scientists still need better methods and tools for "saying" something about a particular protein target or the compound that purports to interact with it. This would allow them to intelligently "share" their findings. Simply querying a database and passing the text-annotated results elsewhere means we are probably losing knowledge, since locating a finding is limited here to matching keywords or by serendipitously bumping into the annotated object.

Scientists would like to be able to say (using RDF): 

JaneSmyth proposes: 
	{ ph48372 interacts with CDK4 isoform 3, which is involved in melanoma predisposition as part of the INK4a pathway }

Facts regarding CDK4 isoform 3 may come from Uniprot, but in addition the relation proposed is an aggregation of chemistry and disease/pathway processes appended by the scientist using RDF. If one can make such statements, store, and share them with colleagues within the right context, we will have advanced pure informatics to knowledge capture.  

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


-----Original Message-----
From: John Wilbanks [mailto:wilbanks@w3.org]
Sent: Wednesday, July 21, 2004 2:58 PM
To: Neumann, Eric PH/US
Cc: Eric.Jain@isb-sib.ch; public-semweb-lifesci@w3.org
Subject: Re: The UniProt database in RDF format


Eric,

Please allow me to follow on in thanks!  I have passed this link around 
inside the W3C and we will be taking a long look at this release, and 
will certainly put together a list of comments and responses...

On a first pass, I did have a quick question - what do you mean by "a 
mechanism for grouping together a set of statements in a file would be 
welcome" (this is in the XML syntax portion of the backgrounder)?   I've 
got some folks here eager to decode that one :-)

jtw

Eric.Neumann@aventis.com wrote:

>Eric,
>
>Thak you very much for your contribution! I am very excited to see the Uniprot project available in RDF/OWL format, along with your documentation. I think this opens the possibility of working with public bioinformatic data not only in traditional ways, but also through new knowledge discovery collaborations. I specifically look forwards to seeing examples of researchers making statements or hypotheses about protein functions and roles using your data, and being able semantically to tie them to pathway, transcriptomic, chemistry, and disease knowledge!   
>
>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
>
>
>-----Original Message-----
>From: public-semweb-lifesci-request@w3.org
>[mailto:public-semweb-lifesci-request@w3.org]On Behalf Of Eric Jain
>Sent: Wednesday, July 21, 2004 6:24 AM
>To: public-semweb-lifesci
>Subject: RFC: The UniProt database in RDF format
>
>
>
>We are currently considering providing an RDF version of the UniProt 
>protein database. A preview is available at:
>
>   http://www.isb-sib.ch/~ejain/rdf/
>
>Feedback is welcome, in particular:
>
>* Do you see any problems with our approach?
>* Could any of the data or tools be of use to you?
>* Any issues that should be fixed or improved?
>
>
>  
>
Received on Wednesday, 21 July 2004 17:36:46 GMT

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