Re: SNOW SHRINE metadata

Wisconsin, we added 80 or so labs to our ontology and Yesh is just now deploying to our release site so check with him and he will assure we have our 20180330 release. Jim From: Klann, Jeffrey G. <jeff.kl...@mgh.harvard.edu> Sent: Tuesday, April 3, 2018

Re: SHRINE\SCILHS metadata enhancements and maintenance plan proposed by Nebraska

Sounds great! Quick note, our ontology is currently in release 3.1, not 2.2: https://github.com/ARCH-commons/arch-ontology/blob/master/README.md I see that some of our READMEs on GitHub are outdated, but version #s in the ontology are correct. Thanks, Jeff Jeffrey Klann, PhD Instructor of

Re: Med ontology missing NDC question

Is the property commutative? As in, (the great and powerful (Lori Phillips and Jeff Klann)) or ((the great and powerful Lori Phillips) and Jeff Klann)? There are a massive number of retired NDC codes that we did not have any way of grabbing systematically when we built the ontology, and we

Re: [gpc-informatics] #280: Medication ontology orgainzed by ingredient

0029066\N029067\3554\197623\00106117530\|concept_cd|PCORI\MEDICATION Jay Pedersen, M.A. Department of Pathology/Microbiology University of Nebraska Medical Center 985900 Nebraska Medical Center Omaha NE 68198-5900 402-559-9487 (office) 402-739-3496 (mobile) ___

Re: [gpc-informatics] #280: Medication ontology orgainzed by ingredient

C: 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 (office) 402-739-3496 (mobile) From: Klann, Jeffrey G. <jeff.kl...@mgh.

Re: [gpc-informatics] #280: Medication ontology orgainzed by ingredient

ebraska Medical Center 985900 Nebraska Medical Center Omaha NE 68198-5900 402-559-9487 (office) 402-739-3496 (mobile) From: Dan Connolly <dconno...@kumc.edu> Sent: Monday, April 24, 2017 8:56:13 PM To: Pedersen, Jay G Cc: Hubert Hickman; Russ Waitman; gpc-dev@l

Re: [gpc-informatics] #280: Medication ontology orgainzed by ingredient

Yes, I have not seen it either. Please point us to it, thanks. On 4/24/17, 11:59 AM, "GPC Informatics" wrote: #280: Medication ontology orgainzed by ingredient -+ Reporter: preeder | Owner:

Re: [gpc-informatics] #280: Medication ontology orgainzed by ingredient

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, Apri

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

Epic ERX->RxNorm mappings

Dan et al, We found your HERON ETL code and a note that Epic now has an ERX->RxNorm mapping table (https://informatics.gpcnetwork.org/trac/Project/ticket/391 ). Where does one find this table? (Yes, this probably applies only to Epic customers, and yes I have a UserWeb account.) Thanks, Jeff

Re: specific major/minor/bug-fix SHRINE version of SCILHS network

<rwait...@kumc.edu>, 'Wanta Keith M' <kwa...@uwhealth.org>, "GPC-DEV@LISTSERV.KUMC.EDU" <GPC-DEV@LISTSERV.KUMC.EDU> Cc: "Klann, Jeffrey G." <jeff.kl...@mgh.harvard.edu>, Shawn Murphy <snmur...@partners.org> Subject: Re: specific major/minor/bug-fix SH

Re: #455: SCILHS CDM compliant with ONC standard coding?

________ >From: Klann, Jeffrey G. [jeff.kl...@mgh.harvard.edu] >Sent: Monday, April 25, 2016 2:34 PM >To: Dan Connolly; gpc-dev@listserv.kumc.edu; campb...@unmc.edu >Cc: Murphy, Shawn N. >Subject: Re: #455: SCILHS CDM compliant with ONC standard coding? > >Co

Re: #455: SCILHS CDM compliant with ONC standard coding?

Cool. Some initial reactions: This intuitively feels very useful, but what¹s the intended use case? In SCILHS, whatever c_basecodes we provide in the default ontology are mostly overwritten by local sites with their local terminologies, especially in demographics and vitals. I don¹t have a full

Re: CDM v3 dependency on SCILHS code (#266, #381) RE: Agenda for GPC-DEV call tomorrow

Yes, Dan is correct. CDMv3 and transform for MSSQL is available in our Google Drive, sans Death, PRO, and Clinical_Trials. Oracle version will be out before the holidays. Working on transform bug fixes and speed optimizations at present. Email me individually for access. I am working on moving

RE: CDM refresh

for MSSQL now (Oracle forthcoming). Death, PRO, and Clinical_Trial tables are not yet supported. Thanks, Jeffrey Klann, PhD Instructor of Medicine, Harvard Medical School From: Dan Connolly [mailto:dconno...@kumc.edu] Sent: Tuesday, October 27, 2015 5:19 PM To: Stroup, Jeff; Klann, Jeffrey G. Cc

RE: [gpc-informatics] #191: represent PCORI CDM 2.x terminology as i2b2 metadata

: 617-643-5879 email: jkl...@partners.org -Original Message- From: GPC Informatics [mailto:d...@madmode.com] Sent: Thursday, August 27, 2015 1:00 PM To: dconno...@kumc.edu; nate.apa...@cerner.com; verhagen.lau...@mcrf.mfldclin.edu Cc: gpc-dev@listserv.kumc.edu; Klann, Jeffrey G

RE: PCORI CDM V3 vote

; 'Campbell, James R'; GPC-DEV@LISTSERV.KUMC.EDU; 'McClay, James C (jmcc...@unmc.edu)' Cc: Murphy, Shawn N.; Rachel Hess (rachel.h...@hsc.utah.edu); Klann, Jeffrey G. Subject: RE: PCORI CDM V3 vote Thanks for sharing the PaTH perspective Chuck. As previously mentioned, GPC code for this has been up

Re: SNOMED in i2b2

of Russ Waitman [rwait...@kumc.edumailto:rwait...@kumc.edu] Sent: Thursday, November 27, 2014 8:55 AM To: Charles Borromeo Cc: Klann, Jeffrey G.; Visweswaran, Shyam; trent.rosenbl...@vanderbilt.edumailto:trent.rosenbl...@vanderbilt.edu; Lori C. LCPHILLIPS@PARTNERS. ORG Phillips; Shawn N. Murphy

Re: [gpc-informatics] #109: mapping to PCORI CDM (aka mini-sentinel data model)

From: Klann, Jeffrey G. [jeff.kl...@mgh.harvard.edu] Sent: Monday, June 09, 2014 10:23 PM To: gpc-dev@listserv.kumc.edu; Russ Waitman; Dan Connolly Cc: Matthew Hoag; Nathan Graham; campb...@unmc.edu; Murphy, Shawn N. Subject: Re: [gpc-informatics] #109: mapping to PCORI CDM

Re: [gpc-informatics] #109: mapping to PCORI CDM (aka mini-sentinel data model)

Hi Dan, Some comments: On A - I agree, we¹re nearing a workable ontology. Per our discussion today, I gather that query compatibility across our networks is of utmost importance. So we need to synchronize our fullnames and basecodes in the PCORnet ontology. I started looking at differences

Re: [gpc-informatics] #109: mapping to PCORI CDM (aka mini-sentinel data model)

BUG: Modifiers get the same table name and column name as concepts. I don't understand that one. I'll have to follow up for details. i2b2 is flexible, but generally for modifiers the c_tablename column is ŒMODIFIER_DIMENSION¹ and the c_columname is Œmodifier_path¹. BUG: Need to remove