W3C home > Mailing lists > Public > public-semweb-lifesci@w3.org > July 2005

protein identification problem

From: <Larry.Hunter@uchsc.edu>
Date: Fri, 1 Jul 2005 15:03:17 -0600
Message-ID: <17093.44949.770000.606586@fast.uchsc.edu>
To: Ken I Fukuda <fukuda-cbrc@aist.go.jp>
Cc: public-semweb-lifesci@w3.org


 > An ontology for generic/concrete protein names, called
 > "MoleculeRole Ontology" is available from
 > http://www.inoh.org/ontology-viewer/.
 > Actually, it is a DAG structured controled vocabulary (CV).
 > The current version covers about 4400 Uniprot IDs which means
 > that the CV defines generic/concrete protein relations for
 > more than 4400 concrete proteins.

Ken,

This is clearly a very useful thing to be doing.  

Can you explain how your work relates to the PIR Superfamily ontology,
PIRSF (http://pir.georgetown.edu/pirsf/) which is included in uniprot?

Is this just based on sequence similarity, or is there more to it than
that?   Do you have a sense of how well your ontology corresponds to
generic protein references in a sample of the literature?  Also, it
seems as if the leaf nodes in your ontology mostly correspond to
species differences, rather than splice variants, paralogs or other
within species generic uses.  Is that right?

Larry

-- 

Lawrence Hunter, Ph.D.
Director, Center for Computational Pharmacology
Associate Professor of Pharmacology, PMB & Computer Science

phone: +1 303 724 3574           
cell:  +1 303 324 0355
fax:   +1 303 724 3648
email: Larry.Hunter@uchsc.edu    
URL: http://compbio.uchsc.edu/hunter

US mail: PO Box 6511, MS 8303, Aurora, CO 80045-0511 USA
Express Delivery:  12801 E. 17th Ave, RC-1 South Rm L18-6101, Aurora, CO 80045

PGP key on public keyservers     
Received on Friday, 1 July 2005 21:04:59 GMT

This archive was generated by hypermail 2.3.1 : Tuesday, 26 March 2013 18:00:40 GMT