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Re: Choosing a use case for an Expert Query Browser

From: Oshani Seneviratne <oshani@csail.mit.edu>
Date: Mon, 2 Nov 2009 15:50:31 -0500
Message-ID: <a477174c0911021250u3a9261act5f380ecb4f4353de@mail.gmail.com>
To: Susie Stephens <susie.stephens@gmail.com>
Cc: public-semweb-lifesci@w3.org, Rachel Sealfon <rsealfon@mit.edu>
Hi Susie,

Yes, Rachel and I are planning on participating in the telecons from
this week. We hope that it will be useful for us to better understand
the requirements of the community.

As for the interface, we would like it to implement a web interface,
and not a standalone windows application like OPENVISTA (so that it
can be used by anybody without having to stick to one platform). But
we haven't begun any real coding, and if it's a system like that, that
is really required, we will consider it.

As per one of the requirements of the class project, Rachel and I
drafted a project proposal based on what we think is a useful system
to build after a discussion we had with EricP. Here's a link to the
We'd appreciate if you can go through this, and let us know if this is
what is really needed.


On Mon, Nov 2, 2009 at 11:48 AM, Susie Stephens
<susie.stephens@gmail.com> wrote:
> 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
> implement.
> 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
> (http://sourceforge.net/projects/openvista/penVista).
> Cheers,
> Susie
> 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 20:51:04 UTC

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