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Re: reasoning on gene ontology

From: Erick Antezana <erick.antezana@gmail.com>
Date: Fri, 6 Apr 2012 17:43:14 +0200
Message-ID: <CA+u43f0FKgd1PXee=DzJAS=Rr-ZXNEdCR2o64LpgPOydkWgBNQ@mail.gmail.com>
To: "Bhat, Talapady N." <talapady.bhat@nist.gov>
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>
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 15:43:44 GMT

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