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RE: reasoning on gene ontology

From: Bhat, Talapady N. <talapady.bhat@nist.gov>
Date: Fri, 6 Apr 2012 12:30:09 -0400
To: Erick Antezana <erick.antezana@gmail.com>
CC: bin chen <binchen@indiana.edu>, public-semweb-lifesci <public-semweb-lifesci@w3.org>, "Plant, Anne L. Dr." <anne.plant@nist.gov>, "Elliott, John T." <john.elliott@nist.gov>, "Bhat, Talapady N." <talapady.bhat@nist.gov>
Message-ID: <7E80450DE7474E4881E405C742AC0DEA1271F7A301@MBCLUSTER.xchange.nist.gov>
Hi,
Sure I can give the database schema. 

The database has been updated last Oct.

Giving the database dump is complicated for several reasons. 1) It is really huge; 2) We are yet to publish some of the work in a real journal article, 3) Some of the ontologies may require re-authorization from their original source to redistribute. (4) More than all I have not thought about this question yet and also I need to talk to my colleagues here. 

I mentioned mainly three databases which one you are really interested in your question and what is your need for a database dump are also important factors for us to decide on this.

Thanks

T N Bhat


-----Original Message-----
From: Erick Antezana [mailto:erick.antezana@gmail.com] 
Sent: Friday, April 06, 2012 11:43 AM
To: Bhat, Talapady N.
Cc: bin chen; public-semweb-lifesci; Plant, Anne L. Dr.; Elliott, John T.
Subject: Re: reasoning on gene ontology

Hi,

is it possible to get the relational database schema you use? and a database dump?

how often do you update your system?

cheers,
Erick

On 6 April 2012 15:29, Bhat, Talapady N. <talapady.bhat@nist.gov> wrote:
> 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 16:30:34 GMT

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