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Posted to dev@ctakes.apache.org by "Hari, Sekhar" <se...@cgi.com> on 2019/03/18 16:42:29 UTC

Therapeutic are - Drug mapping

Hi -

Is there a publicly available database or API that can provide mapping between a therapeutic area and drugs? For example: all the FDA approved drugs in use for the therapeutic area "Cardiovascular".

Thanks
Sekhar H.

Re: Therapeutic are - Drug mapping [EXTERNAL]

Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.

Hi Sekhar,

I think that the treatment relations that might interest you most would be "manages", "treats", "prevents".  Then follow the "isa" relations up until you find a root area (disease / finding) of interest.

Walking the semantic web can be a little challenging, as not every node that has a relationship will list it explicitly.  For instance, aspirin is used for a lot of things, but might have zero "manages" relations.  Instead, an ancestor of aspirin like "non-steroidal drug" might have the relations.

Unless you have some experience with graphs and the umls then it might be better for you to use some other existing dataset or api.

good luck,
Sean
________________________________________
From: Hari, Sekhar <se...@cgi.com>
Sent: Tuesday, March 19, 2019 7:17 AM
To: dev@ctakes.apache.org
Subject: RE: Therapeutic are - Drug mapping [EXTERNAL]

Thanks Sean! Looks a little complex to navigate the relationships. Can you please cite the most appropriate terms in this relationship that may point to therapeutic area?

Thanks
Sekhar Hari | AI Program Lead | Health Sciences R&D | Asia Pacific Solutions Delivery Center
+91 814 7027 779 (C)


-----Original Message-----
From: Finan, Sean <Se...@childrens.harvard.edu>
Sent: Monday, March 18, 2019 11:09 PM
To: dev@ctakes.apache.org
Subject: Re: Therapeutic are - Drug mapping [EXTERNAL]

Hi Sekhar,

Perhaps through relationships in the umls you could arrive at such groupings.

https://urldefense.proofpoint.com/v2/url?u=https-3A__www.nlm.nih.gov_research_umls_META3-5Fcurrent-5Frelations.html&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=oRbKp1vdCyFhiA0FxL1-jWiPVkUi0tMecCn2kcoe1Vo&s=c9-O3_dlDm1ttSNgIgfUpUv2PpXIMDqG7jGNgjHysd8&e=

https://urldefense.proofpoint.com/v2/url?u=https-3A__www.ncbi.nlm.nih.gov_books_NBK9679_figure_ch05.F3_&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=oRbKp1vdCyFhiA0FxL1-jWiPVkUi0tMecCn2kcoe1Vo&s=nOPrRn_ujda8UOvwedQKkE32wmRNGqSJv0zA9cRcZnw&e=

Sean
________________________________________
From: Hari, Sekhar <se...@cgi.com>
Sent: Monday, March 18, 2019 12:42 PM
To: dev@ctakes.apache.org
Subject: Therapeutic are - Drug mapping [EXTERNAL]

Hi -

Is there a publicly available database or API that can provide mapping between a therapeutic area and drugs? For example: all the FDA approved drugs in use for the therapeutic area "Cardiovascular".

Thanks
Sekhar H.

RE: Therapeutic are - Drug mapping [EXTERNAL]

Posted by "Hari, Sekhar" <se...@cgi.com>.

Thanks Sean! Looks a little complex to navigate the relationships. Can you please cite the most appropriate terms in this relationship that may point to therapeutic area?

Thanks
Sekhar Hari | AI Program Lead | Health Sciences R&D | Asia Pacific Solutions Delivery Center
+91 814 7027 779 (C)


-----Original Message-----
From: Finan, Sean <Se...@childrens.harvard.edu> 
Sent: Monday, March 18, 2019 11:09 PM
To: dev@ctakes.apache.org
Subject: Re: Therapeutic are - Drug mapping [EXTERNAL]

Hi Sekhar,

Perhaps through relationships in the umls you could arrive at such groupings.

https://www.nlm.nih.gov/research/umls/META3_current_relations.html

https://www.ncbi.nlm.nih.gov/books/NBK9679/figure/ch05.F3/

Sean
________________________________________
From: Hari, Sekhar <se...@cgi.com>
Sent: Monday, March 18, 2019 12:42 PM
To: dev@ctakes.apache.org
Subject: Therapeutic are - Drug mapping [EXTERNAL]

Hi -

Is there a publicly available database or API that can provide mapping between a therapeutic area and drugs? For example: all the FDA approved drugs in use for the therapeutic area "Cardiovascular".

Thanks
Sekhar H.

Re: Therapeutic are - Drug mapping [EXTERNAL]

Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.

Hi Sekhar,

Perhaps through relationships in the umls you could arrive at such groupings.

https://www.nlm.nih.gov/research/umls/META3_current_relations.html

https://www.ncbi.nlm.nih.gov/books/NBK9679/figure/ch05.F3/

Sean
________________________________________
From: Hari, Sekhar <se...@cgi.com>
Sent: Monday, March 18, 2019 12:42 PM
To: dev@ctakes.apache.org
Subject: Therapeutic are - Drug mapping [EXTERNAL]

Hi -

Is there a publicly available database or API that can provide mapping between a therapeutic area and drugs? For example: all the FDA approved drugs in use for the therapeutic area "Cardiovascular".

Thanks
Sekhar H.

Re: Therapeutic are - Drug mapping [EXTERNAL]

Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.

Hi Sekhar, Jessie,

I am intrigued by RxMix this app!

Thanks,
Sean
________________________________________
From: Hari, Sekhar <se...@cgi.com>
Sent: Tuesday, March 19, 2019 10:34 AM
To: jessie.tenenbaum@duke.edu
Cc: dev@ctakes.apache.org
Subject: RE: Therapeutic are - Drug mapping [EXTERNAL]Jessie

Update: I found a locally installable docker namely 'RxNav-in-a-box' that can be used for such queries in an unlimited way. But unsure if the docker also contain the entire RxClass data.

Thanks
Sekhar Hari | AI Program Lead | Health Sciences R&D | Asia Pacific Solutions Delivery Center
+91 814 7027 779 (C)

-----Original Message-----
From: Hari, Sekhar <se...@cgi.com>
Sent: Tuesday, March 19, 2019 7:53 PM
To: jessie.tenenbaum@duke.edu
Cc: dev@ctakes.apache.org
Subject: RE: Therapeutic are - Drug mapping

Thanks Jessie! It worked really well through the RxClass API (classContext function). Is there a way to install the RxClass APIs locally in a VM instead of calling through the web? I think there is a limitation of 20 requests per second if called through a web API.

Thanks
Sekhar Hari | AI Program Lead | Health Sciences R&D | Asia Pacific Solutions Delivery Center
+91 814 7027 779 (C)

-----Original Message-----
From: Jessie Tenenbaum, Ph.D. <je...@duke.edu>
Sent: Tuesday, March 19, 2019 4:02 AM
To: dev@ctakes.apache.org
Subject: RE: Therapeutic are - Drug mapping

Some combination of RxMix (https://urldefense.proofpoint.com/v2/url?u=https-3A__mor.nlm.nih.gov_RxMix_&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=T6tULK8a30JsVCcRBMkn6AftMMszbL6MOdsb9ozNWKQ&s=TLs9YTrBH4pPFIC0eD6QksHWBeFxm0xf0_gH0ui8_dg&e=) and RxClass may be what you need.

________________________________________________________________________

Jessica Tenenbaum, PhD, FACMI | jessie.tenenbaum@duke.edu<ma...@duke.edu> | (919) 684-7308

-----Original Message-----

From: Hari, Sekhar [mailto:sekhar.hari@cgi.com]

Sent: Monday, March 18, 2019 12:42 PM

To: dev@ctakes.apache.org<ma...@ctakes.apache.org>

Subject: Therapeutic are - Drug mapping

Hi -

Is there a publicly available database or API that can provide mapping between a therapeutic area and drugs? For example: all the FDA approved drugs in use for the therapeutic area "Cardiovascular".

Thanks

Sekhar H.

RE: Therapeutic are - Drug mapping

Posted by "Hari, Sekhar" <se...@cgi.com>.

Update: I found a locally installable docker namely 'RxNav-in-a-box' that can be used for such queries in an unlimited way. But unsure if the docker also contain the entire RxClass data.
 
Thanks
Sekhar Hari | AI Program Lead | Health Sciences R&D | Asia Pacific Solutions Delivery Center
+91 814 7027 779 (C)


-----Original Message-----
From: Hari, Sekhar <se...@cgi.com> 
Sent: Tuesday, March 19, 2019 7:53 PM
To: jessie.tenenbaum@duke.edu
Cc: dev@ctakes.apache.org
Subject: RE: Therapeutic are - Drug mapping

Thanks Jessie! It worked really well through the RxClass API (classContext function). Is there a way to install the RxClass APIs locally in a VM instead of calling through the web? I think there is a limitation of 20 requests per second if called through a web API.


Thanks
Sekhar Hari | AI Program Lead | Health Sciences R&D | Asia Pacific Solutions Delivery Center
+91 814 7027 779 (C)



-----Original Message-----
From: Jessie Tenenbaum, Ph.D. <je...@duke.edu>
Sent: Tuesday, March 19, 2019 4:02 AM
To: dev@ctakes.apache.org
Subject: RE: Therapeutic are - Drug mapping



Some combination of RxMix (https://mor.nlm.nih.gov/RxMix/) and RxClass may be what you need.



________________________________________________________________________

Jessica Tenenbaum, PhD, FACMI | jessie.tenenbaum@duke.edu<ma...@duke.edu> | (919) 684-7308



-----Original Message-----

From: Hari, Sekhar [mailto:sekhar.hari@cgi.com]

Sent: Monday, March 18, 2019 12:42 PM

To: dev@ctakes.apache.org<ma...@ctakes.apache.org>

Subject: Therapeutic are - Drug mapping



Hi -



Is there a publicly available database or API that can provide mapping between a therapeutic area and drugs? For example: all the FDA approved drugs in use for the therapeutic area "Cardiovascular".



Thanks

Sekhar H.

RE: Therapeutic are - Drug mapping

Posted by "Hari, Sekhar" <se...@cgi.com>.

Thanks Jessie! It worked really well through the RxClass API (classContext function). Is there a way to install the RxClass APIs locally in a VM instead of calling through the web? I think there is a limitation of 20 requests per second if called through a web API.


Thanks
Sekhar Hari | AI Program Lead | Health Sciences R&D | Asia Pacific Solutions Delivery Center
+91 814 7027 779 (C)



-----Original Message-----
From: Jessie Tenenbaum, Ph.D. <je...@duke.edu>
Sent: Tuesday, March 19, 2019 4:02 AM
To: dev@ctakes.apache.org
Subject: RE: Therapeutic are - Drug mapping



Some combination of RxMix (https://mor.nlm.nih.gov/RxMix/) and RxClass may be what you need.



________________________________________________________________________

Jessica Tenenbaum, PhD, FACMI | jessie.tenenbaum@duke.edu<ma...@duke.edu> | (919) 684-7308



-----Original Message-----

From: Hari, Sekhar [mailto:sekhar.hari@cgi.com]

Sent: Monday, March 18, 2019 12:42 PM

To: dev@ctakes.apache.org<ma...@ctakes.apache.org>

Subject: Therapeutic are - Drug mapping



Hi -



Is there a publicly available database or API that can provide mapping between a therapeutic area and drugs? For example: all the FDA approved drugs in use for the therapeutic area "Cardiovascular".



Thanks

Sekhar H.

RE: Therapeutic are - Drug mapping

Posted by "Jessie Tenenbaum, Ph.D." <je...@duke.edu>.

Some combination of RxMix (https://mor.nlm.nih.gov/RxMix/) and RxClass may be what you need.

________________________________________________________________________
Jessica Tenenbaum, PhD, FACMI | jessie.tenenbaum@duke.edu | (919) 684-7308

-----Original Message-----
From: Hari, Sekhar [mailto:sekhar.hari@cgi.com] 
Sent: Monday, March 18, 2019 12:42 PM
To: dev@ctakes.apache.org
Subject: Therapeutic are - Drug mapping

Hi -

Is there a publicly available database or API that can provide mapping between a therapeutic area and drugs? For example: all the FDA approved drugs in use for the therapeutic area "Cardiovascular".

Thanks
Sekhar H.