- From: Erick Antezana <erick.antezana@gmail.com>
- Date: Sat, 7 Apr 2012 08:16:15 +0200
- 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 UTC