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RE: Uniprot RDF in RDF Gateway

From: Luo, James (NIH/NCI) <luoja@mail.nih.gov>
Date: Thu, 12 May 2005 15:13:05 -0400
Message-ID: <CE0E73903DB53F43B4B0938747F34F8A8DF82C@nihexchange7.nih.gov>
To: "'jluciano@predmed.com'" <jluciano@predmed.com>, 'Eric Jain' <Eric.Jain@isb-sib.ch>, 'Geoff Chappell' <gchappell@intellidimension.com>
Cc: public-semweb-lifesci@w3.org

UniProt itself has GO IDs. You can go to UniProt site 
ftp://ftp.ebi.ac.uk/pub/databases/uniprot/knowledgebase/

The file to get for GO ids is
uniprot_sprot.dat.gz

James 


===================================================
James Luo, Ph.D.
Sr. Bioinformatics Scientist / Lead Data Architect
Contractor
Email:  luoja@mail.nih.gov
Phone: 301-402-1621(o), 301-943-8856(c); Fax: 301-480-4222
National Cancer Institute Center for BioInformatics, NIH / AITC, SAIC

-----Original Message-----
From: Joanne Luciano [mailto:jluciano@predmed.com] 
Sent: Thursday, May 12, 2005 2:22 PM
To: 'Eric Jain'; 'Geoff Chappell'
Cc: public-semweb-lifesci@w3.org
Subject: RE: Uniprot RDF in RDF Gateway


Maybe you guys know...

Is there a way to link UniProt IDs and GO (Gene Ontology) IDs?
Is there a database that has both?

Eric, can this be done indirectly through the KEGG/RDF work you did?

Thanks,

Joanne 

> -----Original Message-----
> From: public-semweb-lifesci-request@w3.org 
> [mailto:public-semweb-lifesci-request@w3.org] On Behalf Of Eric Jain
> Sent: Thursday, May 12, 2005 1:49 PM
> To: Geoff Chappell
> Cc: public-semweb-lifesci@w3.org
> Subject: Re: Uniprot RDF in RDF Gateway
> 
> 
> Geoff Chappell wrote:
> > I imagined this was probably the case. It might be worth 
> highlighting 
> > for folks on your site
> 
> Yes, good idea.
> 
> 
> > Yeah, it's unfortunate there isn't a meaningful common 
> superclass of 
> > those (since the they all describe ranges on the timeline). 
> I suppose 
> > you could make the range the union of the three types.
> 
> We used this approach in the XML Schema for the plain XML 
> version of our data [http://www.uniprot.org/support/docs/uniprot.xsd].
> 
> Unfortunately Protege (which is used to maintain the 
> ontology) doesn't seem to support custom data types, and I 
> suspect other RDF tools may have problems, too...
> 
> 
> 
> 
Received on Friday, 13 May 2005 06:00:28 UTC

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