Hi,
We are using the VA drug classes (NDF-RT) for building Medications metadata for
SCILHS.
The medications metadata can be seen in the following folders in BABEL:
UNMC: SCILHS
Medications
RxNorm code (by VA Drug Class)
Drugs by Ingredient
I am guessing that you were looking at the following folder (which does use the
ATC hierarchy):
UNMC: Medications (UNMC)
Jay Pedersen, M.A.
Department of Pathology/Microbiology
University of Nebraska Medical Center
985900 Nebraska Medical Center
Omaha NE 68198-5900
402-559-9487<tel:402-559-9593> (office)
402-739-3496<tel:402-350-7851> (mobile)
________________________________
From: Klann, Jeffrey G. <[email protected]>
Sent: Wednesday, April 12, 2017 3:35:31 PM
To: Campbell, James R; [email protected]; Pedersen, Jay G;
[email protected]; [email protected]; [email protected]
Cc: [email protected]
Subject: Re: [gpc-informatics] #280: Medication ontology orgainzed by ingredient
Great, I see that Dan opened a ticket about BABELing. Not sure where you’re
pushing it but please let me know when you have and we’ll be glad to take a
look.
It looks like you are using ATC, not NDF-RT (VA)?
Also, if you are including all retired RxNorm codes, how do you arrange the
ontology in the case where two RxNorm codes refer to exactly the same drug?
Thanks,
Jeff Klann, PhD
On 4/12/17, 9:46 AM, "Campbell, James R" <[email protected]> wrote:
Jeff
I assume you are trying to review on BABEL? I will leave indexing and
efficiency there to KU's discretion.
Jay is pushing a copy along with documentation up to your GITHUB site for
you and the SCILHS community to comment. We have set the procedures and
software arranged with NLM and we will take responsibility for refreshing the
metadata every six months for SCILHS (and GPC) if you approve. The VA/class
top level ontology is basically what you have done with the minor exception of
renaming some of the ingredient level nodes where the VA has not deployed all
formulations of that ingredient class (like CARDIOVASCULAR -BETA BLOCKERS-
TIMOLOL where the eye preps of timolol are not included as subtypes for
searching.
The need to have a metadata set that would index all US drugs is the reason
that we added the second alpha ingredient list. Speaking with NLM, NO drug
classification - ATC, VA or whatever -is inclusive of all US pharmacopoeia.
Ken Mandl co-authored a paper with Olivier Bodenreider discussing that very
issue.
I would be very interested in your thoughts about this metadata when you
get a chance to review
Jim
-----Original Message-----
From: Klann, Jeffrey G. [mailto:[email protected]]
Sent: Tuesday, April 11, 2017 10:37 PM
To: [email protected]; Pedersen, Jay G <[email protected]>;
Campbell, James R <[email protected]>; [email protected];
[email protected]; [email protected]
Cc: [email protected]
Subject: Re: [gpc-informatics] #280: Medication ontology orgainzed by
ingredient
It is *extremely* slow to browse. Can you check your indexes? I’d like to
explore your hard work but it’s unusable right now.
( I tried a few random other trees and they were also unbrowsably-slow. Is
there an epidemic of bad indexes on babel? )
Thanks,
Jeffrey Klann, PhD
Instructor of Medicine, Harvard Medical School Instructor in Investigation,
Massachusetts General Hospital
On 4/11/17, 12:00 PM, "GPC Informatics" <[email protected]> wrote:
#280: Medication ontology orgainzed by ingredient
-------------------------+----------------------------
Reporter: preeder | Owner: jay.pedersen
Type: enhancement | Status: assigned
Priority: major | Milestone: snow-shrine-2
Component: data-stds | Resolution:
Keywords: | Blocked By:
Blocking: |
-------------------------+----------------------------
Comment (by dconnolly):
Replying to [comment:19 campbell]:
> SCILHS/Medication metadata issues addressed with load to BABEL
toiday:
Which folder has the updated medication metadata? is it **UNMC:
Medications (UNMC)**?
> • (therefore) with VA drug classes as sole top-level ontology,
not
all clinical formulations or packages can be deployed
So this is a wholesale re-organization of the ontology?
If you can share the code you used to build it, please do.
--
Ticket URL:
<http://informatics.gpcnetwork.org/trac/Project/ticket/280#comment:20>
gpc-informatics <http://informatics.gpcnetwork.org/>
Greater Plains Network - Informatics
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