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Re: reasoning on gene ontology

From: bin chen <binchen@indiana.edu>
Date: Tue, 10 Apr 2012 11:03:14 -0400
Message-ID: <CADwUy41b1vDB0KdUU2UQkiSA-d+KhKLnpRGg=dU--NeKOOj2=g@mail.gmail.com>
To: "Bhat, Talapady N." <talapady.bhat@nist.gov>
Cc: Erick Antezana <erick.antezana@gmail.com>, public-semweb-lifesci <public-semweb-lifesci@w3.org>, "Plant, Anne L. Dr." <anne.plant@nist.gov>, "Elliott, John T." <john.elliott@nist.gov>
Thanks all for the response. Very useful references. I hope to see more
work on reasoning on gene ontology and other ontologies especially pathway
ontology to maximize the usage of semantics beyond annotation
and integration.

Cheers,
Bin

On Mon, Apr 9, 2012 at 9:42 AM, Bhat, Talapady N. <talapady.bhat@nist.gov>wrote:

> 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
>



-- 
Bin Chen
PHD student, Informatics,
Indiana University at Bloomington
http://cheminfo.informatics.indiana.edu/~binchen
Received on Tuesday, 10 April 2012 15:04:09 GMT

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