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Re: reasoning on gene ontology

From: Erick Antezana <erick.antezana@gmail.com>
Date: Sat, 7 Apr 2012 08:16:15 +0200
Message-ID: <CA+u43f1M+6eC9QxUZmtsB64joHqwQHtrpSP1ZmiB22qd64z_UA@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,

I would be interested in the looking at the schema of BIOROOT as well
as knowing a bit more about the technology behing it (lucene? java?
oracle?). On the other hand, do you have any plans to provide some
webservices to fetch data?

cheers,
Erick

On 6 April 2012 18:30, Bhat, Talapady N. <talapady.bhat@nist.gov> wrote:
> 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 Saturday, 7 April 2012 06:16:44 GMT

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