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Re: [TMO] Re: Choosing a use case for an Expert Query Browser

From: Susie Stephens <susie.stephens@gmail.com>
Date: Tue, 10 Nov 2009 08:14:08 -0500
Message-ID: <fcc499200911100514v7724377elf767c53562836ecf@mail.gmail.com>
To: Oshani Seneviratne <oshani@csail.mit.edu>
Cc: public-semweb-lifesci@w3.org, Rachel Sealfon <rsealfon@mit.edu>, "Eric Prud'hommeaux" <eric@w3.org>
Please feel free to participate in the TMO calls if you would like to
discuss use cases (http://esw.w3.org/topic/HCLSIG/PharmaOntology).

Susie

On Mon, Nov 9, 2009 at 3:28 PM, Oshani Seneviratne <oshani@csail.mit.edu>wrote:

> Hi Susie et al,
>
> Thanks a lot for the comments.
>
> Rachel and I have been working on a prototype last week, and we have a
> simple implementation that takes in a keyword (such as 'coronary
> artery disease') and queries diseasome for diseases that mention that
> keyword, and dailymed for drugs that treat that particular disease. We
> are yet to provide a nice UI, but the basic functionality is there.
> We were wondering if this satisfies any use case (or a part of any use
> case) mentioned in the TMO wiki?
>
> We are also thinking of linking to other data sources, incrementally
> refine the query and/or to augment the query results. For example, one
> addition we are thinking of doing, is to get linkedct data on clinical
> trials that have treated this particular disease. Do you think this is
> a good addition? Also, are there any data sources that might be of
> interest to physicians?
>
> BTW, the source code of our project is available at:
> http://code.google.com/p/querymed/
> It's still in very early stages, but feel free to check it out if you
> are interested.
>
> Thanks,
> Oshani
>
> On Wed, Nov 4, 2009 at 8:59 AM, Susie Stephens <susie.stephens@gmail.com>
> wrote:
> > Hi Oshani,
> >
> > I definitely agree that a web interface is the way to go. But do want a
> > realistic interface, so want to use existing systems as a reference point
> as
> > to what is likely to work well. Physicians have a reputation for being
> > technically illiterate, so we want to build something that's very simple
> to
> > use.
> >
> > A couple of small comments on your text.
> > 1. At the moment, people want to bridge silos of data, rather than do
> > inferencing.
> > 2. OBO is a very common format for ontologies in biomedicine.
> >
> > Cheers,
> > Susie
> >
> > On Mon, Nov 2, 2009 at 3:50 PM, Oshani Seneviratne <oshani@csail.mit.edu
> >
> > wrote:
> >>
> >> 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
> >> document:
> >> http://querymed.googlecode.com/svn/trunk/docs/proposal.pdf
> >> We'd appreciate if you can go through this, and let us know if this is
> >> what is really needed.
> >>
> >> Thanks!
> >> Oshani
> >>
> >> 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 Tuesday, 10 November 2009 13:14:49 GMT

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