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RE: The UniProt database in RDF format

From: Pat Hayes <phayes@ihmc.us>
Date: Wed, 21 Jul 2004 17:25:15 -0700
Message-Id: <p06001f2bbd24b861b173@[]>
To: <Eric.Neumann@aventis.com>, wilbanks@w3.org
Cc: public-semweb-lifesci@w3.org

>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 
>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 

Right on.

FWIW, I have heard customers from at least three 
other communities (military, intelligence, 
commercial database) make the same point, and put 
this ability at the top of their needs list. A 
recent NGIA BAA (#HM1582-04-BAA-0005 ) offers to 
fund research on exactly this (not in 
bioinformatics, but the functionality transcends 

Pat Hayes

>Eric Neumann, Ph.D.
>Global Head of Knowledge Management
>Aventis - DI&A
>Tel:   908-231-3510
>Fax:  908-231-3307
>-----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
>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 :-)
>Eric.Neumann@aventis.com wrote:
>>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 
>>Eric Neumann, Ph.D.
>>Global Head of Knowledge Management
>>Aventis - DI&A
>>Tel:   908-231-3510
>>Fax:  908-231-3307
>>-----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?

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Received on Wednesday, 21 July 2004 20:27:02 UTC

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