From: binchenindi...@gmail.com [mailto:binchenindi...@gmail.com] On Behalf Of
bin chen
Sent: Tuesday, April 10, 2012 11:03 AM
To: Bhat, Talapady N.
Cc: Erick Antezana; public-semweb-lifesci; Plant, Anne L. Dr.; Elliott, John T.
Subject: Re: reasoning on gene ontology
Thanks all for the response
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. wrote
sci; 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 web
nsr>
- Original Message -
*From:* Chris Mungall <mailto:cjmung...@lbl.gov>
*To:* bin chen <mailto:binc...@indiana.edu>
*Cc:* public-semweb-lifesci <mailto:public-semweb-lifesci@w3.org>
*Sent:* Friday, April 06, 2012 4:20 PM
*Subject:* Re: r
Hi Bin,
I have been playing around the GO and looking for interesting cases too. I
believe the reasoner could help for the following tasks:
1- Terms retrieval/search, as you pointed out, SW queries are more powerful
and intuitive than relational databases one.
2- Ontology re-factoring: When new
2010.
You can find versions of these papers on my Web site via
http://www.cs.man.ac.uk/~stevensr
- Original Message -
From: Chris Mungall
To: bin chen
Cc: public-semweb-lifesci
Sent: Friday, April 06, 2012 4:20 PM
Subject: Re: reasoning on gene ontology
Hi Bin,
at, 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
Hi,
You may be interested in the system and examples online at the site below.
In particular:
www.reengineeringllc.com/demo_agents/GeneSequenceOntology3.agent
Apologies if you have seen this before, and thanks for comments.
-- Adrian
Interne
emented 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: binchenindi...@gmail.com [mailto:binchenindi...@gmail.com] On
ral 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: binchenindi...@gmail.com [mailto:binchenindi...@gmail.com] On Behalf
> Of bin ch
Hi Bin,
We use OWL reasoning extensively within the GO consortium, primarily
for automated classification of new terms, and for validation of the
ontology and gene associations. For some more background, see
PMID:20152934 and PMID:20973947 (note that in those papers we used
some custom reasoning t
shown below
http://xpdb.nist.gov/chemblast/pdb.pl
Let me know if you have any comments
T N Bhat
From: binchenindi...@gmail.com [mailto:binchenindi...@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
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
ha
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