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" <campb...@unmc.edu> 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:jeff.kl...@mgh.harvard.edu]
Sent: Tuesday, April 11, 2017 10:37 PM
To: gpc-dev@listserv.kumc.edu; Pedersen, Jay G <jay.peder...@unmc.edu>;
Campbell, James R <campb...@unmc.edu>; huhick...@nebraskamed.com;
dconno...@kumc.edu; rwait...@kumc.edu
Cc: mprit...@kumc.edu
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" <d...@madmode.com> 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
The information in this e-mail is intended only for the person to whom it
is addressed. If you believe this e-mail was sent to you in error and the
e-mail contains patient information, please contact the Partners Compliance
HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to
you in error but does not contain patient information, please contact the
sender and properly dispose of the e-mail.
The information in this e-mail may be privileged and confidential, intended
only for the use of the addressee(s) above. Any unauthorized use or disclosure
of this information is prohibited. If you have received this e-mail by mistake,
please delete it and immediately contact the sender.
_______________________________________________
Gpc-dev mailing list
Gpc-dev@listserv.kumc.edu
http://listserv.kumc.edu/mailman/listinfo/gpc-dev
