Choosing a use case for an Expert Query Browser

[Oshani Seneviratne-3]

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 patient’s
specific insurance? (In real time). Are the preceding predictive
genetic SNP tests covered by the patient’s 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

[Susie Stephens-3]

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@...> 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 patient’s
specific insurance? (In real time). Are the preceding predictive
genetic SNP tests covered by the patient’s 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

[Oshani Seneviratne-3]

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@...> 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@...>
> 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 patient’s
>> specific insurance? (In real time). Are the preceding predictive
>> genetic SNP tests covered by the patient’s 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
>>
>
>

[Oshani Seneviratne-3]

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@...> 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@...>
> 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@...> 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@...>
>> > 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 patient’s
>> >> specific insurance? (In real time). Are the preceding predictive
>> >> genetic SNP tests covered by the patient’s 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
>> >>
>> >
>> >
>
>

[Susie Stephens-3]

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@...> 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@...> 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@...>
> 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@...> 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@...>
>> > 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 patient’s
>> >> specific insurance? (In real time). Are the preceding predictive
>> >> genetic SNP tests covered by the patient’s 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
>> >>
>> >
>> >
>
>