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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.


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?



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

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Received on Friday, 1 July 2005 21:04:59 UTC

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