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RE: reasoning on gene ontology

From: Bhat, Talapady N. <talapady.bhat@nist.gov>
Date: Fri, 6 Apr 2012 09:29:31 -0400
To: bin chen <binchen@indiana.edu>, public-semweb-lifesci <public-semweb-lifesci@w3.org>
CC: "Bhat, Talapady N." <talapady.bhat@nist.gov>, "Plant, Anne L. Dr." <anne.plant@nist.gov>, "Elliott, John T." <john.elliott@nist.gov>
Message-ID: <7E80450DE7474E4881E405C742AC0DEA1271F7A131@MBCLUSTER.xchange.nist.gov>
Hi,
Because you mentioned about ontology (GO) in the context of relational databases I thought you may be interested in looking into our site where we incorporated over 99 large ontology into a relational database. Most of these large ontology were originally obtained from GO.
http://xpdb.nist.gov/bioroot/bioroot.pl
The above Web resource allows a user to selectively query and download custom made section of any of the ontology for his/her needs in simple Excel format
Below is a link to a recent BMC paper where we discuss a new approach for building and reasoning ontology in a federated set up.
http://www.biomedcentral.com/1471-2105/12/487

An example of this approach for cell image data is in http://sbd.nist.gov/image/cell_image.html


Similar approach for building and reasoning rule-based ontology for chemical structures are implemented for several million compound in the URL shown below
http://xpdb.nist.gov/chemblast/pdb.pl

Let me know if you have any comments

T N Bhat


From: binchenindiana@gmail.com [mailto:binchenindiana@gmail.com] On Behalf Of bin chen
Sent: Thursday, April 05, 2012 4:10 PM
To: public-semweb-lifesci
Subject: reasoning on gene ontology

Hi,

Does anyone perform some reasoning using gene ontology? Any intereting story to share? I recently ran reasoning based on extended GO relations [1], and found that the triples doubled after reasoning. I was also aware of some queries are not able to be performed in relational database. but I havenot found very interesing cases to utlize the inferred results. Any reference? Thanks.

Best, Bin
[1]  http://www.geneontology.org/GO.ontology-ext.relations.shtml

--
Bin Chen
PHD student, Informatics,
Indiana University at Bloomington
http://cheminfo.informatics.indiana.edu/~binchen
Received on Friday, 6 April 2012 13:30:04 GMT

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