W3C home > Mailing lists > Public > public-semweb-lifesci@w3.org > April 2012

RE: reasoning on gene ontology

From: Bhat, Talapady N. <talapady.bhat@nist.gov>
Date: Mon, 9 Apr 2012 09:42:50 -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: <7E80450DE7474E4881E405C742AC0DEA1271F7A6AB@MBCLUSTER.xchange.nist.gov>
Hi,
Bioroot Technology: Bioroot database was originally built in Oracle but the public server uses MySQL.
All scripts are written in Perl for both instances.
Lots of independent perl modules that fetch specific data are used in this webpage. Many of them can in principle work as Webservice.
For instance : On typing Canc into the text box the autocomplete generates a list of matched terms such as cancer, cancel, cancerFax and so on. This part is not available at this time as web service. However, on completing the query for cancer a table is generated with lists of the ontology and the frequency of count for terms that sounds like 'cancer'.  In this table the terms are hyper linked as http://xpdb.nist.gov/bioroot/bioroot.pl?allTrees=1&termid=378240&wrd=cancer&foundin=::23::6::26::88::
The values for parameter =foundin are the ontology Id where the term is found. This link lets one get the specific rows of the ontology and it can be accessed on its own as Web service.

If there is sufficient interest for providing links for the first part of the query as Web service, I will be glad to work on that. However, too many simultaneous Web service query for the first part may overload our server. For most part of users needs I believe that the first part can be accomplished using the manual set up established now. I can be wrong, I am not sure though.

If one wants to have a list of highly re-used terms among all these ontology one may tic-mark the 'List highly re-used short terms' and then use the hyper links to access those instances

Thanks

T N Bhat

-----Original Message-----
From: Erick Antezana [mailto:erick.antezana@gmail.com] 
Sent: Saturday, April 07, 2012 2:16 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,

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 Monday, 9 April 2012 13:43:17 GMT

This archive was generated by hypermail 2.3.1 : Tuesday, 26 March 2013 18:01:06 GMT