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Re: Choosing a use case for an Expert Query Browser

From: Susie Stephens <susie.stephens@gmail.com>
Date: Mon, 2 Nov 2009 11:48:29 -0500
Message-ID: <fcc499200911020848g210adddcs31727033b4442f46@mail.gmail.com>
To: Oshani Seneviratne <oshani@csail.mit.edu>
Cc: public-semweb-lifesci@w3.org, Rachel Sealfon <rsealfon@mit.edu>
Hi Oshani,

The Translational Medicine Ontology task is working to build an application
that demonstrates the utility of the ontology that we have created. The text
that you've pulled out highlights part of the use case that we're working to

Please feel free to participate in the task calls, or read minutes from past
calls, to learn more about the status of our work, including the conversion
of data to RDF.

We are also working to create an interface. Our preference is to have an
interface that would be very simple to use, and builds upon formats that are
familiar to physicians today. We are currently taking a look at the open
source eHR system OPENVISTA (



On Fri, Oct 30, 2009 at 8:28 PM, Oshani Seneviratne <oshani@csail.mit.edu>wrote:

> Hi all,
> We are interested in building an "expert" query browser to answer
> queries similar to the ones outlined in [1].
> We thought the following use case listed in the wiki would be a good
> one to start with:
> "Fundamental questions will be answered by the ontology at this stage
> by sourcing the data sets listed below simultaneously or in a specific
> order.
> A. What are the clinically recommended agents NICE
> B. What products are available to prescribe, and which are legally
> indicated for disease AD [DOID: 10652]? [Physicians Desk Reference]
> C. What is the SNP verdict? These agents are sourced with
> pharmacogenomics database Pharmacogenetics Research Network (PGRN) to
> determine (Data source: PharmaGKB, Michel's DB (depression))
> Will they be efficacious? Receptor positive disease?
> Will they be harmful? Toxic metabolites? Available CYP 450 or
> acetylator status? (Data source: Drugbank, Dailymed?, SIDER?)
> D. Are the resulting pharmaceutical agents covered by the patientís
> specific insurance? (In real time). Are the preceding predictive
> genetic SNP tests covered by the patientís insurance company? These
> may be recommended and indicated prior to treatment as in HIV
> medication ABACAVIR.(PGRN, PDR, NICE, Medicare, Blue Cross Blue
> Shield)
> The Physician [NCI Thesaurus: Physician] checks with pharmacist, or
> consults drug information literature to avoid potential drug
> interactions"
> We were wondering about the availability of the data sources mentioned
> in this particular use case: has somebody exported those to RDF? Or
> are there any efforts underway?
> Or else, is there any other use case for which we can use the relevant
> ontologies which already has data in RDF?
> Also, we are wondering what specific use cases would be most relevant
> to the community at the moment?
> [1] http://esw.w3.org/topic/HCLSIG/PharmaOntology/UseCases
> Thanks,
> Oshani and Rachel
Received on Monday, 2 November 2009 16:49:02 UTC

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