Jay In followup to our discussion yesterday, post the i2b2 metadata to the website of Jeff’s choosing for his analysis Jim
From: Klann, Jeffrey G. [mailto:jeff.kl...@mgh.harvard.edu] Sent: Thursday, May 11, 2017 3:39 PM To: Pedersen, Jay G <jay.peder...@unmc.edu>; Campbell, James R <campb...@unmc.edu>; gpc-dev@listserv.kumc.edu; huhick...@nebraskamed.com; dconno...@kumc.edu; rwait...@kumc.edu Cc: mprit...@kumc.edu Subject: Re: [gpc-informatics] #280: Medication ontology orgainzed by ingredient Jay, have you posted this ontology anywhere we could download it and take a look? Thanks, Jeffrey Klann, PhD Instructor of Medicine, Harvard Medical School Director, SCILHS Query Core From: "Pedersen, Jay G" <jay.peder...@unmc.edu<mailto:jay.peder...@unmc.edu>> Date: Wednesday, April 12, 2017 at 5:03 PM To: Jeffrey KLANN <jeff.kl...@mgh.harvard.edu<mailto:jeff.kl...@mgh.harvard.edu>>, "Campbell, James R" <campb...@unmc.edu<mailto:campb...@unmc.edu>>, "gpc-dev@listserv.kumc.edu<mailto:gpc-dev@listserv.kumc.edu>" <gpc-dev@listserv.kumc.edu<mailto:gpc-dev@listserv.kumc.edu>>, "huhick...@nebraskamed.com<mailto:huhick...@nebraskamed.com>" <huhick...@nebraskamed.com<mailto:huhick...@nebraskamed.com>>, "dconno...@kumc.edu<mailto:dconno...@kumc.edu>" <dconno...@kumc.edu<mailto:dconno...@kumc.edu>>, "rwait...@kumc.edu<mailto:rwait...@kumc.edu>" <rwait...@kumc.edu<mailto:rwait...@kumc.edu>> Cc: "mprit...@kumc.edu<mailto:mprit...@kumc.edu>" <mprit...@kumc.edu<mailto:mprit...@kumc.edu>> Subject: Re: [gpc-informatics] #280: Medication ontology orgainzed by ingredient 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. <jeff.kl...@mgh.harvard.edu<mailto:jeff.kl...@mgh.harvard.edu>> Sent: Wednesday, April 12, 2017 3:35:31 PM To: Campbell, James R; gpc-dev@listserv.kumc.edu<mailto:gpc-dev@listserv.kumc.edu>; Pedersen, Jay G; huhick...@nebraskamed.com<mailto:huhick...@nebraskamed.com>; dconno...@kumc.edu<mailto:dconno...@kumc.edu>; rwait...@kumc.edu<mailto:rwait...@kumc.edu> Cc: mprit...@kumc.edu<mailto:mprit...@kumc.edu> 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" <campb...@unmc.edu<mailto: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<mailto:gpc-dev@listserv.kumc.edu>; Pedersen, Jay G <jay.peder...@unmc.edu<mailto:jay.peder...@unmc.edu>>; Campbell, James R <campb...@unmc.edu<mailto:campb...@unmc.edu>>; huhick...@nebraskamed.com<mailto:huhick...@nebraskamed.com>; dconno...@kumc.edu<mailto:dconno...@kumc.edu>; rwait...@kumc.edu<mailto:rwait...@kumc.edu> Cc: mprit...@kumc.edu<mailto: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<mailto: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. 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