- From: <Larry.Hunter@uchsc.edu>
- Date: Fri, 1 Jul 2005 15:03:17 -0600
- 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 UTC