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

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

2018-04-10 Thread Debbie Yoshihara

Excellent!!


--- Debbie


Debbie Yoshihara
Informatics Specialist
Biomedical Informatics Services - SMPH-IT
Institute for Clinical and Translational Research (ICTR)
School of Medicine and Public Health, UW-Madison
matrixed employee of UW Health



From: Gpc-dev <gpc-dev-boun...@listserv.kumc.edu> on behalf of GPC Informatics 
<d...@madmode.com>
Sent: Tuesday, April 10, 2018 3:08:19 PM
To: campb...@unmc.edu; huhick...@nebraskamed.com; dconno...@kumc.edu; 
rwait...@kumc.edu; jay.peder...@unmc.edu; bradley-mcdow...@uiowa.edu
Cc: mprit...@kumc.edu; gpc-dev@listserv.kumc.edu; jeff.kl...@mgh.harvard.edu
Subject: Re: [gpc-informatics] #280: Medication ontology orgainzed by ingredient

#280: Medication ontology orgainzed by ingredient
-+
 Reporter:  preeder  |   Owner:  campbell
 Type:  enhancement  |  Status:  assigned
 Priority:  major|   Milestone:  snow-shrine-3
Component:  data-stds|  Resolution:
 Keywords:  all-sites|  Blocked By:  568, 592
 Blocking:  411  |
-+

Comment (by jay.pedersen):

 UNMC has published an expanded Medications ontology for SHRINE, including
 historically comprehensive RxNorm coding, as of March 2018.

 This release is published at the following site, and requires a UMLS
 license to download.  The license is free within the US:

 https://unmc.edu/pathology/informatics/tdc

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

2018-04-10 Thread GPC Informatics

#280: Medication ontology orgainzed by ingredient
-+
 Reporter:  preeder  |   Owner:  campbell
 Type:  enhancement  |  Status:  closed
 Priority:  major|   Milestone:  snow-shrine-3
Component:  data-stds|  Resolution:  fixed
 Keywords:  all-sites|  Blocked By:  568, 592
 Blocking:  411  |
-+
Changes (by jay.pedersen):

 * status:  assigned => closed
 * resolution:   => fixed


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

2018-02-19 Thread GPC Informatics

#280: Medication ontology orgainzed by ingredient
-+
 Reporter:  preeder  |   Owner:  campbell
 Type:  enhancement  |  Status:  assigned
 Priority:  major|   Milestone:  snow-shrine-3
Component:  data-stds|  Resolution:
 Keywords:  all-sites|  Blocked By:  568, 592
 Blocking:  411  |
-+

Comment (by dconnolly):

 I looked into what OHSDI does. It's pretty interesting:

  -
 [http://www.ohdsi.org/web/wiki/doku.php?id=documentation:vocabulary:drug
 Standardized Vocabularies Drug Domain]

 Here's hoping for time to ask them if they have a hierarchical form or
 experience putting it into i2b2.

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

2017-10-03 Thread GPC Informatics

#280: Medication ontology orgainzed by ingredient
-+
 Reporter:  preeder  |   Owner:  campbell
 Type:  enhancement  |  Status:  assigned
 Priority:  major|   Milestone:  snow-shrine-2
Component:  data-stds|  Resolution:
 Keywords:  all-sites|  Blocked By:  568, 592
 Blocking:  411  |
-+

Comment (by brad_mcdowell):

 The dropbox link in comment:26 won't work for me (says the file has either
 been moved or made private). Could someone attach the file to this ticket?
 Thanks!

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

2017-09-26 Thread GPC Informatics

#280: Medication ontology orgainzed by ingredient
-+
 Reporter:  preeder  |   Owner:  campbell
 Type:  enhancement  |  Status:  assigned
 Priority:  major|   Milestone:  snow-shrine-2
Component:  data-stds|  Resolution:
 Keywords:  all-sites|  Blocked By:  568, 592
 Blocking:  411  |
-+

Comment (by dconnolly):

 Thanks, Jay and UNMC folks. Those 478,729 NDC codes cover 99% of the ~200M
 medication facts in grouse.

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

2017-09-26 Thread GPC Informatics

#280: Medication ontology orgainzed by ingredient
-+
 Reporter:  preeder  |   Owner:  campbell
 Type:  enhancement  |  Status:  assigned
 Priority:  major|   Milestone:  snow-shrine-2
Component:  data-stds|  Resolution:
 Keywords:  all-sites|  Blocked By:  568, 592
 Blocking:  411  |
-+

Comment (by jay.pedersen):

 The link to the zip file of SCILHS MEDICATION metadata from comment 26 is
 no longer valid.  The following is the current link:

 https://www.dropbox.com/s/oc56lvqi7jvftp8/scilhs_meds_mods.zip?dl=0

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

2017-05-31 Thread GPC Informatics

#280: Medication ontology orgainzed by ingredient
-+
 Reporter:  preeder  |   Owner:  campbell
 Type:  enhancement  |  Status:  assigned
 Priority:  major|   Milestone:  snow-shrine-2
Component:  data-stds|  Resolution:
 Keywords:  all-sites|  Blocked By:  568, 592
 Blocking:   |
-+

Comment (by campbell):

 Extract from UNMC Clarity found 6,134,787 medication administration events
 coded in NDC and reported since 2012 with roughly 1.43M episodes per year.
 An episode is defined as a continuous series of administration events
 bounded by a START_DATE and STOP_DATE for a single drug ordered within an
 individual medication order.  There were 7717 distinct NDC codes
 referenced in these events.  181 NDC codes were not in our SCILHS
 metadata, some of which are erroneous but some apparently missed in our
 metadata build.  I found only 5589 investigational drug events which were
 coded by our pharmacy using homegrown codes.

 We will push these Medication Administration events into CDMV31.PROCEDURES
 using the NDC codes.
 Jim

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

2017-05-22 Thread GPC Informatics

#280: Medication ontology orgainzed by ingredient
-+
 Reporter:  preeder  |   Owner:  campbell
 Type:  enhancement  |  Status:  assigned
 Priority:  major|   Milestone:  snow-shrine-2
Component:  data-stds|  Resolution:
 Keywords:  all-sites|  Blocked By:  568, 592
 Blocking:   |
-+
Changes (by dconnolly):

 * owner:  jay.pedersen => campbell


Comment:

 JRC, Jay, does UNMC load MAR info into PROCEDURES?

 As to a pointer to the ontology...
 > The following is a link to a zip file which contains UNMC's created
 version of the SCILHS Medication metadata.
 > https://dl.dropboxusercontent.com/u/5167630/scilhs_medication.zip

 -- [http://listserv.kumc.edu/pipermail/gpc-dev/2017q2/003949.html Pedersen
 13 May]

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

2017-05-15 Thread Klann, Jeffrey G.

Cool, thanks, I’ve got it loaded up. Can you say a bit more about how the 
RxNorm code folders are organized? It appears that 50k RxNorm codes appear in a 
different place in the ontology than ours, so there must be a different 
organizing principle, I just haven’t figured it out yet. ☺

Thanks!

Jeffrey Klann, PhD
Instructor of Medicine, Harvard Medical School
Director, SCILHS Query Core


From: "Pedersen, Jay G" <jay.peder...@unmc.edu>
Date: Saturday, May 13, 2017 at 1:56 PM
To: "Campbell, James R" <campb...@unmc.edu>, Jeffrey KLANN 
<jeff.kl...@mgh.harvard.edu>, "gpc-dev@listserv.kumc.edu" 
<gpc-dev@listserv.kumc.edu>, "huhick...@nebraskamed.com" 
<huhick...@nebraskamed.com>, "dconno...@kumc.edu" <dconno...@kumc.edu>, 
"rwait...@kumc.edu" <rwait...@kumc.edu>
Cc: "mprit...@kumc.edu" <mprit...@kumc.edu>
Subject: Re: [gpc-informatics] #280: Medication ontology orgainzed by ingredient


Hi,



The following is a link to a zip file which contains UNMC's created version of 
the SCILHS Medication metadata.



https://dl.dropboxusercontent.com/u/5167630/scilhs_medication.zip



The metadata file, just for Medication, is 680 Megabytes in size, the zip file 
is 44 MB.



This contains the \PCORI\MEDICATION\ rows.



Here are the first few rows from the Medications metadata file (note that the 
paths use NDF-RT and NDC codes in the RXNORM_CUI paths):


C_FULLNAME|C_HLEVEL|C_NAME|C_BASECODE|C_VISUALATTRIBUTES|M_APPLIED_PATH|C_SYNONYM_CD|C_TABLENAME|C_COLUMNNAME|C_COLUMNDATATYPE|C_OPERATOR|C_DIMCODE|C_FACTTABLECOLUMN|C_TOOLTIP|C_TOTALNUM|FACT_COUNT|SOURCESYSTEM_CD
\PCORI\MEDICATION\|1|Medications|RXNORM_ROOT|FA 
|@|N|concept_dimension|concept_path|T|like|\PCORI\MEDICATION\|concept_cd|PCORI\MEDICATION|0|0|rxnav.nlm.nih.gov
\PCORI\MEDICATION\RXNORM_CUI\|2|RxNorm Code (by VA Drug 
Class)|NDFRT:N010574|FA 
|@|N|concept_dimension|concept_path|T|like|\PCORI\MEDICATION\RXNORM_CUI\|concept_cd|PCORI\MEDICATION\RXNORM_CUI|0|0|rxnav.nlm.nih.gov
\PCORI\MEDICATION\RXNORM_CUI\N029066\|3|Antidotes,deterrents and poison 
control|NDFRT:N029066|FA 
|@|N|concept_dimension|concept_path|T|like|\PCORI\MEDICATION\RXNORM_CUI\N029066\|concept_cd|PCORI\MEDICATION\RXNORM_CUI\N029066|0|0|rxnav.nlm.nih.gov
\PCORI\MEDICATION\RXNORM_CUI\N029066\N029067\|4|Alcohol 
deterrents|NDFRT:N029067|FA 
|@|N|concept_dimension|concept_path|T|like|\PCORI\MEDICATION\RXNORM_CUI\N029066\N029067\|concept_cd|PCORI\MEDICATION\RXNORM_CUI\N029066\N029067|0|0|rxnav.nlm.nih.gov
\PCORI\MEDICATION\RXNORM_CUI\N029066\N029067\3554\|5|Disulfiram (VA 
subset)|RXNORM:3554|FA 
|@|N|concept_dimension|concept_path|T|like|\PCORI\MEDICATION\RXNORM_CUI\N029066\N029067\3554\|concept_cd|PCORI\MEDICATION\RXNORM_CUI\N029066\N029067\3554|0|0|rxnav.nlm.nih.gov
\PCORI\MEDICATION\RXNORM_CUI\N029066\N029067\3554\197623\|6|Disulfiram 
250 MG Oral Tablet|RXNORM:197623|FA 
|@|N|concept_dimension|concept_path|T|like|\PCORI\MEDICATION\RXNORM_CUI\N029066\N029067\3554\197623\|concept_cd|PCORI\MEDICATION\RXNORM_CUI\N029066\N029067\3554\197623|0|0|rxnav.nlm.nih.gov
\PCORI\MEDICATION\RXNORM_CUI\N029066\N029067\3554\197623\00046080952\|7|(00046080952)
 Disulfiram 250 MG Oral Tablet|NDC:00046080952|LA 
|@|N|concept_dimension|concept_path|T|like|\PCORI\MEDICATION\RXNORM_CUI\N029066\N029067\3554\197623\00046080952\|concept_cd|PCORI\MEDICATION\RXNORM_CUI\N029066\N029067\3554\197623\00046080952|0|0|rxnav.nlm.nih.gov
\PCORI\MEDICATION\RXNORM_CUI\N029066\N029067\3554\197623\00046080981\|7|(00046080981)
 Disulfiram 250 MG Oral Tablet|NDC:00046080981|LA 
|@|N|concept_dimension|concept_path|T|like|\PCORI\MEDICATION\RXNORM_CUI\N029066\N029067\3554\197623\00046080981\|concept_cd|PCORI\MEDICATION\RXNORM_CUI\N029066\N029067\3554\197623\00046080981|0|0|rxnav.nlm.nih.gov
\PCORI\MEDICATION\RXNORM_CUI\N029066\N029067\3554\197623\00054035613\|7|Disulfiram
 (Disulfiram) 30 TABLET in 1 BOTTLE (0054-0356-13)|NDC:00054035613|LA 
|@|N|concept_dimension|concept_path|T|like|\PCORI\MEDICATION\RXNORM_CUI\N029066\N029067\3554\197623\00054035613\|concept_cd|PCORI\MEDICATION\RXNORM_CUI\N029066\N029067\3554\197623\00054035613|0|0|rxnav.nlm.nih.gov
\PCORI\MEDICATION\RXNORM_CUI\N029066\N029067\3554\197623\00054035625\|7|Disulfiram
 (Disulfiram) 100 TABLET in 1 BOTTLE (0054-0356-25)|NDC:00054035625|LA 
|@|N|concept_dimension|concept_path|T|like|\PCORI\MEDICATION\RXNORM_CUI\N029066\N029067\3554\197623\00054035625\|concept_cd|PCORI\MEDICATION\RXNORM_CUI\N029066\N029067\3554\197623\00054035625|0|0|rxnav.nlm.nih.gov
\PCORI\MEDICATION\RXNORM_CUI\N029066\N029067\3554\197623\00093503501\|7|Disulfiram
 (Disulfiram) 100 TABLET in 1 BOTTLE (0093-5035-01)|NDC:00093503501|LA 
|@|N|concept_dimension|concept_path|T|like|\PCORI\MED

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

2017-05-13 Thread Pedersen, Jay G

Hi,


The following is a link to a zip file which contains UNMC's created version of 
the SCILHS Medication metadata.


https://dl.dropboxusercontent.com/u/5167630/scilhs_medication.zip


The metadata file, just for Medication, is 680 Megabytes in size, the zip file 
is 44 MB.


This contains the \PCORI\MEDICATION\ rows.


Here are the first few rows from the Medications metadata file (note that the 
paths use NDF-RT and NDC codes in the RXNORM_CUI paths):


C_FULLNAME|C_HLEVEL|C_NAME|C_BASECODE|C_VISUALATTRIBUTES|M_APPLIED_PATH|C_SYNONYM_CD|C_TABLENAME|C_COLUMNNAME|C_COLUMNDATATYPE|C_OPERATOR|C_DIMCODE|C_FACTTABLECOLUMN|C_TOOLTIP|C_TOTALNUM|FACT_COUNT|SOURCESYSTEM_CD

\PCORI\MEDICATION\|1|Medications|RXNORM_ROOT|FA 
|@|N|concept_dimension|concept_path|T|like|\PCORI\MEDICATION\|concept_cd|PCORI\MEDICATION|0|0|rxnav.nlm.nih.gov
\PCORI\MEDICATION\RXNORM_CUI\|2|RxNorm Code (by VA Drug 
Class)|NDFRT:N010574|FA 
|@|N|concept_dimension|concept_path|T|like|\PCORI\MEDICATION\RXNORM_CUI\|concept_cd|PCORI\MEDICATION\RXNORM_CUI|0|0|rxnav.nlm.nih.gov
\PCORI\MEDICATION\RXNORM_CUI\N029066\|3|Antidotes,deterrents and poison 
control|NDFRT:N029066|FA 
|@|N|concept_dimension|concept_path|T|like|\PCORI\MEDICATION\RXNORM_CUI\N029066\|concept_cd|PCORI\MEDICATION\RXNORM_CUI\N029066|0|0|rxnav.nlm.nih.gov
\PCORI\MEDICATION\RXNORM_CUI\N029066\N029067\|4|Alcohol 
deterrents|NDFRT:N029067|FA 
|@|N|concept_dimension|concept_path|T|like|\PCORI\MEDICATION\RXNORM_CUI\N029066\N029067\|concept_cd|PCORI\MEDICATION\RXNORM_CUI\N029066\N029067|0|0|rxnav.nlm.nih.gov
\PCORI\MEDICATION\RXNORM_CUI\N029066\N029067\3554\|5|Disulfiram (VA 
subset)|RXNORM:3554|FA 
|@|N|concept_dimension|concept_path|T|like|\PCORI\MEDICATION\RXNORM_CUI\N029066\N029067\3554\|concept_cd|PCORI\MEDICATION\RXNORM_CUI\N029066\N029067\3554|0|0|rxnav.nlm.nih.gov
\PCORI\MEDICATION\RXNORM_CUI\N029066\N029067\3554\197623\|6|Disulfiram 
250 MG Oral Tablet|RXNORM:197623|FA 
|@|N|concept_dimension|concept_path|T|like|\PCORI\MEDICATION\RXNORM_CUI\N029066\N029067\3554\197623\|concept_cd|PCORI\MEDICATION\RXNORM_CUI\N029066\N029067\3554\197623|0|0|rxnav.nlm.nih.gov
\PCORI\MEDICATION\RXNORM_CUI\N029066\N029067\3554\197623\00046080952\|7|(00046080952)
 Disulfiram 250 MG Oral Tablet|NDC:00046080952|LA 
|@|N|concept_dimension|concept_path|T|like|\PCORI\MEDICATION\RXNORM_CUI\N029066\N029067\3554\197623\00046080952\|concept_cd|PCORI\MEDICATION\RXNORM_CUI\N029066\N029067\3554\197623\00046080952|0|0|rxnav.nlm.nih.gov
\PCORI\MEDICATION\RXNORM_CUI\N029066\N029067\3554\197623\00046080981\|7|(00046080981)
 Disulfiram 250 MG Oral Tablet|NDC:00046080981|LA 
|@|N|concept_dimension|concept_path|T|like|\PCORI\MEDICATION\RXNORM_CUI\N029066\N029067\3554\197623\00046080981\|concept_cd|PCORI\MEDICATION\RXNORM_CUI\N029066\N029067\3554\197623\00046080981|0|0|rxnav.nlm.nih.gov
\PCORI\MEDICATION\RXNORM_CUI\N029066\N029067\3554\197623\00054035613\|7|Disulfiram
 (Disulfiram) 30 TABLET in 1 BOTTLE (0054-0356-13)|NDC:00054035613|LA 
|@|N|concept_dimension|concept_path|T|like|\PCORI\MEDICATION\RXNORM_CUI\N029066\N029067\3554\197623\00054035613\|concept_cd|PCORI\MEDICATION\RXNORM_CUI\N029066\N029067\3554\197623\00054035613|0|0|rxnav.nlm.nih.gov
\PCORI\MEDICATION\RXNORM_CUI\N029066\N029067\3554\197623\00054035625\|7|Disulfiram
 (Disulfiram) 100 TABLET in 1 BOTTLE (0054-0356-25)|NDC:00054035625|LA 
|@|N|concept_dimension|concept_path|T|like|\PCORI\MEDICATION\RXNORM_CUI\N029066\N029067\3554\197623\00054035625\|concept_cd|PCORI\MEDICATION\RXNORM_CUI\N029066\N029067\3554\197623\00054035625|0|0|rxnav.nlm.nih.gov
\PCORI\MEDICATION\RXNORM_CUI\N029066\N029067\3554\197623\00093503501\|7|Disulfiram
 (Disulfiram) 100 TABLET in 1 BOTTLE (0093-5035-01)|NDC:00093503501|LA 
|@|N|concept_dimension|concept_path|T|like|\PCORI\MEDICATION\RXNORM_CUI\N029066\N029067\3554\197623\00093503501\|concept_cd|PCORI\MEDICATION\RXNORM_CUI\N029066\N029067\3554\197623\00093503501|0|0|rxnav.nlm.nih.gov
\PCORI\MEDICATION\RXNORM_CUI\N029066\N029067\3554\197623\00106117530\|7|(00106117530)
 Disulfiram 250 MG Oral Tablet|NDC:00106117530|LA 
|@|N|concept_dimension|concept_path|T|like|\PCORI\MEDICATION\RXNORM_CUI\N029066\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)

From: Campbell, James R
Sent: Saturday, May 13, 2017 11:34:34 AM
To: Klann, Jeffrey G.; Pedersen, Jay G; 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
In followup to our

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

2017-05-13 Thread Campbell, James R

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 (office)
402-739-3496 (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>>; Camp

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

2017-05-11 Thread Klann, Jeffrey G.

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>
Date: Wednesday, April 12, 2017 at 5:03 PM
To: Jeffrey KLANN <jeff.kl...@mgh.harvard.edu>, "Campbell, James R" 
<campb...@unmc.edu>, "gpc-dev@listserv.kumc.edu" <gpc-dev@listserv.kumc.edu>, 
"huhick...@nebraskamed.com" <huhick...@nebraskamed.com>, "dconno...@kumc.edu" 
<dconno...@kumc.edu>, "rwait...@kumc.edu" <rwait...@kumc.edu>
Cc: "mprit...@kumc.edu" <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 (office)
402-739-3496 (mobile)


From: Klann, Jeffrey G. <jeff.kl...@mgh.harvard.edu>
Sent: Wednesday, April 12, 2017 3:35:31 PM
To: Campbell, James R; gpc-dev@listserv.kumc.edu; Pedersen, Jay G; 
huhick...@nebraskamed.com; dconno...@kumc.edu; rwait...@kumc.edu
Cc: 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> 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]:
 > S

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

2017-04-25 Thread Dan Connolly

Note that you're going to need a github account to write to anything that Jeff 
sets up for you; so you might as well just fork 
https://github.com/SCILHS/scilhs-ontology and add the code to your fork. If you 
want to contribute it back upstream, the norm is to do a pull request.

If you prefer to just attach a .zip file to a  message to gpc-dev, that would 
be a place to  start.

--
Dan


From: Pedersen, Jay G [jay.peder...@unmc.edu]
Sent: Monday, April 24, 2017 10:06 PM
To: Klann, Jeffrey G.; Dan Connolly
Cc: Hubert Hickman; Russ Waitman; gpc-dev@listserv.kumc.edu; Michael Prittie; 
Campbell, James R
Subject: Re: [gpc-informatics] #280: Medication ontology orgainzed by ingredient


Hi,


A "contrib" repo in SCILHS works for me.  It gives me a place to put this ... 
and a place for you to take a look at it, etc.

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.harvard.edu>
Sent: Monday, April 24, 2017 9:58:00 PM
To: Pedersen, Jay G; Dan Connolly
Cc: Hubert Hickman; Russ Waitman; gpc-dev@listserv.kumc.edu; Michael Prittie; 
Campbell, James R
Subject: Re: [gpc-informatics] #280: Medication ontology orgainzed by ingredient

Might make more sense for you guys to have your own GitHub for the time being, 
and we could link to it. Or if you prefer, I’d be happy to set up a “contrib” 
repo in SCILHS that you could commit to.

Thanks,
Jeff Klann

From: "Pedersen, Jay G" <jay.peder...@unmc.edu>
Date: Monday, April 24, 2017 at 10:28 PM
To: Dan Connolly <dconno...@kumc.edu>
Cc: Hubert Hickman <huhick...@nebraskamed.com>, Russ Waitman 
<rwait...@kumc.edu>, "gpc-dev@listserv.kumc.edu" <gpc-dev@listserv.kumc.edu>, 
Jeffrey KLANN <jeff.kl...@mgh.harvard.edu>, Michael Prittie 
<mprit...@kumc.edu>, "Campbell, James R" <campb...@unmc.edu>
Subject: Re: [gpc-informatics] #280: Medication ontology orgainzed by ingredient


Hi,



I wasn't sure where to put the code in github.  I believe we are glad to share 
the code, which is written in

python and uses web services from the NLM and an input file with history 
information of RxNorm codes received from the NLM.



Where would be the appropriate spot to put that?  I thought it was supposed to 
go to the SCILHS github.


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: 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@listserv.kumc.edu; Klann, Jeffrey G.; 
Michael Prittie; Campbell, James R
Subject: Re: [gpc-informatics] #280: Medication ontology orgainzed by ingredient

Yes, it's on babel. But Jim wrote that you were sharing it via git as well. Not 
so?

On Apr 24, 2017 7:44 PM, "Pedersen, Jay G" <jay.peder...@unmc.edu> wrote:

Hi,



The Medication ontology exists in BABEL, at folder UNMC: SCILHS, in the 
Medications subfolder.



I tried it moments ago, and it still opened VERY slow.  So ... I include links 
to a couple

of pictures taken from BABEL that shows the metadata -- from the VA class level 
through

the RxNorm code level for ingredients and orderable drugs down to the NDC code 
level

for packaged drugs.



The 'VA class' hierarchy is the first subfolder of Medications, and we also have

a second which has the ingredients in alphabetical order.  We have a folder for

letters A through Z.  Taking any of these folders lists the ingredients which 
start

with that letter, and underneath of ingredients lie the orderable drugs and the

drug packages.



Links to BABEL pictures of SCILHS Medications Ontology (NOTE: there are quite a 
rows for modifiers (blue dot rows), that repeat at each level,

and can be hidden by modifying their C_VISUALATTRIBUTES if they don't apply at 
any particular site):



https://dl.dropboxusercontent.com/u/5167630/UNMC_SCILHS_MEDS_p1.png

[https://dl.dropboxusercontent.com/u/5167630/UNMC_SCILHS_MEDS_p1.png]



https://dl.dropboxusercontent.com/u/5167630/UNMC_SCILHS_MEDS_p2.png

[https://dl.dropboxusercontent.com/u/5167630/UNMC_SCILHS_MEDS_p2.png]

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.harvard.edu>
Sent: Monday, April 24, 2017 11:15:23 AM
To: gpc-dev@listserv.kumc.edu; Pedersen, Jay G; Campbell, James R; 
huhick...@nebraskamed.com; dconno...@kumc.edu; rwait...@kumc.edu
Cc: mprit...@kumc.edu
Subject

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

2017-04-24 Thread Pedersen, Jay G

Hi,


A "contrib" repo in SCILHS works for me.  It gives me a place to put this ... 
and a place for you to take a look at it, etc.

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.harvard.edu>
Sent: Monday, April 24, 2017 9:58:00 PM
To: Pedersen, Jay G; Dan Connolly
Cc: Hubert Hickman; Russ Waitman; gpc-dev@listserv.kumc.edu; Michael Prittie; 
Campbell, James R
Subject: Re: [gpc-informatics] #280: Medication ontology orgainzed by ingredient

Might make more sense for you guys to have your own GitHub for the time being, 
and we could link to it. Or if you prefer, I’d be happy to set up a “contrib” 
repo in SCILHS that you could commit to.

Thanks,
Jeff Klann

From: "Pedersen, Jay G" <jay.peder...@unmc.edu>
Date: Monday, April 24, 2017 at 10:28 PM
To: Dan Connolly <dconno...@kumc.edu>
Cc: Hubert Hickman <huhick...@nebraskamed.com>, Russ Waitman 
<rwait...@kumc.edu>, "gpc-dev@listserv.kumc.edu" <gpc-dev@listserv.kumc.edu>, 
Jeffrey KLANN <jeff.kl...@mgh.harvard.edu>, Michael Prittie 
<mprit...@kumc.edu>, "Campbell, James R" <campb...@unmc.edu>
Subject: Re: [gpc-informatics] #280: Medication ontology orgainzed by ingredient


Hi,



I wasn't sure where to put the code in github.  I believe we are glad to share 
the code, which is written in

python and uses web services from the NLM and an input file with history 
information of RxNorm codes received from the NLM.



Where would be the appropriate spot to put that?  I thought it was supposed to 
go to the SCILHS github.


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: 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@listserv.kumc.edu; Klann, Jeffrey G.; 
Michael Prittie; Campbell, James R
Subject: Re: [gpc-informatics] #280: Medication ontology orgainzed by ingredient

Yes, it's on babel. But Jim wrote that you were sharing it via git as well. Not 
so?

On Apr 24, 2017 7:44 PM, "Pedersen, Jay G" <jay.peder...@unmc.edu> wrote:

Hi,



The Medication ontology exists in BABEL, at folder UNMC: SCILHS, in the 
Medications subfolder.



I tried it moments ago, and it still opened VERY slow.  So ... I include links 
to a couple

of pictures taken from BABEL that shows the metadata -- from the VA class level 
through

the RxNorm code level for ingredients and orderable drugs down to the NDC code 
level

for packaged drugs.



The 'VA class' hierarchy is the first subfolder of Medications, and we also have

a second which has the ingredients in alphabetical order.  We have a folder for

letters A through Z.  Taking any of these folders lists the ingredients which 
start

with that letter, and underneath of ingredients lie the orderable drugs and the

drug packages.



Links to BABEL pictures of SCILHS Medications Ontology (NOTE: there are quite a 
rows for modifiers (blue dot rows), that repeat at each level,

and can be hidden by modifying their C_VISUALATTRIBUTES if they don't apply at 
any particular site):



https://dl.dropboxusercontent.com/u/5167630/UNMC_SCILHS_MEDS_p1.png

[https://dl.dropboxusercontent.com/u/5167630/UNMC_SCILHS_MEDS_p1.png]



https://dl.dropboxusercontent.com/u/5167630/UNMC_SCILHS_MEDS_p2.png

[https://dl.dropboxusercontent.com/u/5167630/UNMC_SCILHS_MEDS_p2.png]

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.harvard.edu>
Sent: Monday, April 24, 2017 11:15:23 AM
To: gpc-dev@listserv.kumc.edu; Pedersen, Jay G; Campbell, James R; 
huhick...@nebraskamed.com; dconno...@kumc.edu; rwait...@kumc.edu
Cc: mprit...@kumc.edu
Subject: 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" <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:  all-sites|  Blocked By:  568, 592
 Blocking:   |
-+

Comment (by dconno

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

2017-04-24 Thread Klann, Jeffrey G.

Might make more sense for you guys to have your own GitHub for the time being, 
and we could link to it. Or if you prefer, I’d be happy to set up a “contrib” 
repo in SCILHS that you could commit to.

Thanks,
Jeff Klann

From: "Pedersen, Jay G" <jay.peder...@unmc.edu>
Date: Monday, April 24, 2017 at 10:28 PM
To: Dan Connolly <dconno...@kumc.edu>
Cc: Hubert Hickman <huhick...@nebraskamed.com>, Russ Waitman 
<rwait...@kumc.edu>, "gpc-dev@listserv.kumc.edu" <gpc-dev@listserv.kumc.edu>, 
Jeffrey KLANN <jeff.kl...@mgh.harvard.edu>, Michael Prittie 
<mprit...@kumc.edu>, "Campbell, James R" <campb...@unmc.edu>
Subject: Re: [gpc-informatics] #280: Medication ontology orgainzed by ingredient

Hi,

I wasn't sure where to put the code in github.  I believe we are glad to share 
the code, which is written in

python and uses web services from the NLM and an input file with history 
information of RxNorm codes received from the NLM.

Where would be the appropriate spot to put that?  I thought it was supposed to 
go to the SCILHS github.

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: 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@listserv.kumc.edu; Klann, Jeffrey G.; 
Michael Prittie; Campbell, James R
Subject: Re: [gpc-informatics] #280: Medication ontology orgainzed by ingredient

Yes, it's on babel. But Jim wrote that you were sharing it via git as well. Not 
so?

On Apr 24, 2017 7:44 PM, "Pedersen, Jay G" <jay.peder...@unmc.edu> wrote:

Hi,

The Medication ontology exists in BABEL, at folder UNMC: SCILHS, in the 
Medications subfolder.

I tried it moments ago, and it still opened VERY slow.  So ... I include links 
to a couple

of pictures taken from BABEL that shows the metadata -- from the VA class level 
through

the RxNorm code level for ingredients and orderable drugs down to the NDC code 
level

for packaged drugs.

The 'VA class' hierarchy is the first subfolder of Medications, and we also have

a second which has the ingredients in alphabetical order.  We have a folder for

letters A through Z.  Taking any of these folders lists the ingredients which 
start

with that letter, and underneath of ingredients lie the orderable drugs and the

drug packages.

Links to BABEL pictures of SCILHS Medications Ontology (NOTE: there are quite a 
rows for modifiers (blue dot rows), that repeat at each level,

and can be hidden by modifying their C_VISUALATTRIBUTES if they don't apply at 
any particular site):

https://dl.dropboxusercontent.com/u/5167630/UNMC_SCILHS_MEDS_p1.png

[https://dl.dropboxusercontent.com/u/5167630/UNMC_SCILHS_MEDS_p1.png]

https://dl.dropboxusercontent.com/u/5167630/UNMC_SCILHS_MEDS_p2.png

[https://dl.dropboxusercontent.com/u/5167630/UNMC_SCILHS_MEDS_p2.png]

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.harvard.edu>
Sent: Monday, April 24, 2017 11:15:23 AM
To: gpc-dev@listserv.kumc.edu; Pedersen, Jay G; Campbell, James R; 
huhick...@nebraskamed.com; dconno...@kumc.edu; rwait...@kumc.edu
Cc: mprit...@kumc.edu
Subject: 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" <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:  all-sites|  Blocked By:  568, 592
 Blocking:   |
-+

Comment (by dconnolly):

 Campbell writes Wednesday, April 12, 2017 6:27 PM
 > Jay is pushing a copy along with documentation up to your GITHUB site
 for you and the SCILHS community to comment.

 Jay, point us to the results of that push? URL? commit hash?

--
Ticket URL: 
<http://informatics.gpcnetwork.org/trac/Project/ticket/280#comment:25>
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 Par

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

2017-04-24 Thread Pedersen, Jay G

Hi,


I wasn't sure where to put the code in github.  I believe we are glad to share 
the code, which is written in

python and uses web services from the NLM and an input file with history 
information of RxNorm codes received from the NLM.


Where would be the appropriate spot to put that?  I thought it was supposed to 
go to the SCILHS github.

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: 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@listserv.kumc.edu; Klann, Jeffrey G.; 
Michael Prittie; Campbell, James R
Subject: Re: [gpc-informatics] #280: Medication ontology orgainzed by ingredient

Yes, it's on babel. But Jim wrote that you were sharing it via git as well. Not 
so?

On Apr 24, 2017 7:44 PM, "Pedersen, Jay G" <jay.peder...@unmc.edu> wrote:

Hi,


The Medication ontology exists in BABEL, at folder UNMC: SCILHS, in the 
Medications subfolder.


I tried it moments ago, and it still opened VERY slow.  So ... I include links 
to a couple

of pictures taken from BABEL that shows the metadata -- from the VA class level 
through

the RxNorm code level for ingredients and orderable drugs down to the NDC code 
level

for packaged drugs.


The 'VA class' hierarchy is the first subfolder of Medications, and we also have

a second which has the ingredients in alphabetical order.  We have a folder for

letters A through Z.  Taking any of these folders lists the ingredients which 
start

with that letter, and underneath of ingredients lie the orderable drugs and the

drug packages.


Links to BABEL pictures of SCILHS Medications Ontology (NOTE: there are quite a 
rows for modifiers (blue dot rows), that repeat at each level,

and can be hidden by modifying their C_VISUALATTRIBUTES if they don't apply at 
any particular site):


https://dl.dropboxusercontent.com/u/5167630/UNMC_SCILHS_MEDS_p1.png

[https://dl.dropboxusercontent.com/u/5167630/UNMC_SCILHS_MEDS_p1.png]


https://dl.dropboxusercontent.com/u/5167630/UNMC_SCILHS_MEDS_p2.png

[https://dl.dropboxusercontent.com/u/5167630/UNMC_SCILHS_MEDS_p2.png]

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.harvard.edu>
Sent: Monday, April 24, 2017 11:15:23 AM
To: gpc-dev@listserv.kumc.edu; Pedersen, Jay G; Campbell, James R; 
huhick...@nebraskamed.com; dconno...@kumc.edu; rwait...@kumc.edu
Cc: mprit...@kumc.edu
Subject: 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" <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:  all-sites|  Blocked By:  568, 592
 Blocking:   |
-+

Comment (by dconnolly):

 Campbell writes Wednesday, April 12, 2017 6:27 PM
 > Jay is pushing a copy along with documentation up to your GITHUB site
 for you and the SCILHS community to comment.

 Jay, point us to the results of that push? URL? commit hash?

--
Ticket URL: 
<http://informatics.gpcnetwork.org/trac/Project/ticket/280#comment:25>
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Re: [gpc-informatics] #280: Medication ontology orgainzed by ingredient

2017-04-24 Thread Dan Connolly

Yes, it's on babel. But Jim wrote that you were sharing it via git as well. Not 
so?

On Apr 24, 2017 7:44 PM, "Pedersen, Jay G" <jay.peder...@unmc.edu> wrote:

Hi,


The Medication ontology exists in BABEL, at folder UNMC: SCILHS, in the 
Medications subfolder.


I tried it moments ago, and it still opened VERY slow.  So ... I include links 
to a couple

of pictures taken from BABEL that shows the metadata -- from the VA class level 
through

the RxNorm code level for ingredients and orderable drugs down to the NDC code 
level

for packaged drugs.


The 'VA class' hierarchy is the first subfolder of Medications, and we also have

a second which has the ingredients in alphabetical order.  We have a folder for

letters A through Z.  Taking any of these folders lists the ingredients which 
start

with that letter, and underneath of ingredients lie the orderable drugs and the

drug packages.


Links to BABEL pictures of SCILHS Medications Ontology (NOTE: there are quite a 
rows for modifiers (blue dot rows), that repeat at each level,

and can be hidden by modifying their C_VISUALATTRIBUTES if they don't apply at 
any particular site):


https://dl.dropboxusercontent.com/u/5167630/UNMC_SCILHS_MEDS_p1.png

[https://dl.dropboxusercontent.com/u/5167630/UNMC_SCILHS_MEDS_p1.png]


https://dl.dropboxusercontent.com/u/5167630/UNMC_SCILHS_MEDS_p2.png

[https://dl.dropboxusercontent.com/u/5167630/UNMC_SCILHS_MEDS_p2.png]

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.harvard.edu>
Sent: Monday, April 24, 2017 11:15:23 AM
To: gpc-dev@listserv.kumc.edu; Pedersen, Jay G; Campbell, James R; 
huhick...@nebraskamed.com; dconno...@kumc.edu; rwait...@kumc.edu
Cc: mprit...@kumc.edu
Subject: 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" <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:  all-sites|  Blocked By:  568, 592
 Blocking:   |
-+

Comment (by dconnolly):

 Campbell writes Wednesday, April 12, 2017 6:27 PM
 > Jay is pushing a copy along with documentation up to your GITHUB site
 for you and the SCILHS community to comment.

 Jay, point us to the results of that push? URL? commit hash?

--
Ticket URL: 
<http://informatics.gpcnetwork.org/trac/Project/ticket/280#comment:25>
gpc-informatics <http://informatics.gpcnetwork.org/>
Greater Plains Network - Informatics




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

2017-04-24 Thread Pedersen, Jay G

Hi,


The Medication ontology exists in BABEL, at folder UNMC: SCILHS, in the 
Medications subfolder.


I tried it moments ago, and it still opened VERY slow.  So ... I include links 
to a couple

of pictures taken from BABEL that shows the metadata -- from the VA class level 
through

the RxNorm code level for ingredients and orderable drugs down to the NDC code 
level

for packaged drugs.


The 'VA class' hierarchy is the first subfolder of Medications, and we also have

a second which has the ingredients in alphabetical order.  We have a folder for

letters A through Z.  Taking any of these folders lists the ingredients which 
start

with that letter, and underneath of ingredients lie the orderable drugs and the

drug packages.


Links to BABEL pictures of SCILHS Medications Ontology (NOTE: there are quite a 
rows for modifiers (blue dot rows), that repeat at each level,

and can be hidden by modifying their C_VISUALATTRIBUTES if they don't apply at 
any particular site):


https://dl.dropboxusercontent.com/u/5167630/UNMC_SCILHS_MEDS_p1.png

[https://dl.dropboxusercontent.com/u/5167630/UNMC_SCILHS_MEDS_p1.png]


https://dl.dropboxusercontent.com/u/5167630/UNMC_SCILHS_MEDS_p2.png

[https://dl.dropboxusercontent.com/u/5167630/UNMC_SCILHS_MEDS_p2.png]

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.harvard.edu>
Sent: Monday, April 24, 2017 11:15:23 AM
To: gpc-dev@listserv.kumc.edu; Pedersen, Jay G; Campbell, James R; 
huhick...@nebraskamed.com; dconno...@kumc.edu; rwait...@kumc.edu
Cc: mprit...@kumc.edu
Subject: 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" <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:  all-sites|  Blocked By:  568, 592
 Blocking:   |
-+

Comment (by dconnolly):

 Campbell writes Wednesday, April 12, 2017 6:27 PM
 > Jay is pushing a copy along with documentation up to your GITHUB site
 for you and the SCILHS community to comment.

 Jay, point us to the results of that push? URL? commit hash?

--
Ticket URL: 
<http://informatics.gpcnetwork.org/trac/Project/ticket/280#comment:25>
gpc-informatics <http://informatics.gpcnetwork.org/>
Greater Plains Network - Informatics




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The information in this e-mail may be privileged and confidential, intended 
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Re: [gpc-informatics] #280: Medication ontology orgainzed by ingredient

2017-04-24 Thread Klann, Jeffrey G.

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:  jay.pedersen
 Type:  enhancement  |  Status:  assigned
 Priority:  major|   Milestone:  snow-shrine-2
Component:  data-stds|  Resolution:
 Keywords:  all-sites|  Blocked By:  568, 592
 Blocking:   |
-+

Comment (by dconnolly):

 Campbell writes Wednesday, April 12, 2017 6:27 PM
 > Jay is pushing a copy along with documentation up to your GITHUB site
 for you and the SCILHS community to comment.

 Jay, point us to the results of that push? URL? commit hash?

--
Ticket URL: 

gpc-informatics 
Greater Plains Network - Informatics




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

2017-04-24 Thread GPC Informatics

#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:  all-sites|  Blocked By:  568, 592
 Blocking:   |
-+

Comment (by dconnolly):

 Campbell writes Wednesday, April 12, 2017 6:27 PM
 > Jay is pushing a copy along with documentation up to your GITHUB site
 for you and the SCILHS community to comment.

 Jay, point us to the results of that push? URL? commit hash?

--
Ticket URL: 

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

2017-04-18 Thread GPC Informatics

#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:  all-sites|  Blocked By:  568, 592
 Blocking:   |
-+
Changes (by dconnolly):

 * keywords:   => all-sites


Comment:

 This enhancement isn't available to users of the SNOW SHRINE network until
 essentially all GPC sites deploy it.

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

2017-04-18 Thread GPC Informatics

#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:  568, 592
 Blocking:   |
-+

Comment (by campbell):

 Keith
 If you check the notes from the ?third call you hosted, discussion on the
 PROCEDURES table concluded that medication administration events could be
 stored there…a surprise to me.  At any rate, GPC is simply trying to
 achieve consensus on where to store medication events.  For right now, and
 based upon your response, I am concluding:

 ORDERS(Inpatient, clinic and prescriptions) ==> CDMV31.PRESCRIBING
 DISPENSE EVENTS(Inpatient and community pharmacy) ==> CDMV31.DISPENSING
 ADMINISTRATION EVENTS(Inpatient, clinic) ==> CDMV31.PROCEDURES

 You further caution us to record events indexed to the most specific level
 of clinical detail: NDC codes for dispense and administration events and
 RXNORM SBD and SCD (or I assume BPCK or GPCK) for orders.
 Have I interpreted you correctly?

 At Nebraska and for SCILHS, we have our metadata organized so that we can
 aggregate by ingredient for searches, but do not store events at that
 level.
 Jim
 >>>
 Jim,
 You can end up looking at this from a couple of different angles.  If you
 are an investigator, and want to research on chemotherapy treatments, you
 can look at the available tables that may contain medications and decide
 which to investigate.  For chemotherapy, that’d probably be PROCEDURES and
 PRESCRIBING.  It’s likely that an institution would have data in one of
 those tables, or both, depending on their source system.

 If you’re approaching the problem as an ETL programmer (which is what I
 think you’re asking), then it’s a different question.  Given chemotherapy
 data, where do I put it in the CDM?  Assuming that the chemotherapy
 treatments look something like medication administration data, I think
 we’d want the orders to be put into the PRESCRIBING table.  Right now, we
 don’t really have a place to store the administration event itself, but
 that’s something we hope to address in the next version of the CDM.

 In the antibiotic study, the main challenge was getting network partners
 to map their data to the right level of RxNorm.  The preference is to use
 a more inclusive term level, like Semantic Branded Drug (SBD) or Semantic
 Clinical Drug (SCD).  I understand that storing by ingredient can make the
 ontology more straightforward, but it greatly complicates any downstream
 analysis.  So my recommendation would be to store the SBD or SCD RxCUI as
 part of the observation (perhaps as a modifier) even if you use ingredient
 as a concept code.  That way there isn’t any loss of analytic utility when
 it comes time to populate the CDM.

 I’m copying Laura in case she’d like to add anything.

 Keith
 >>>On Apr 4, 2017, at 1:08 PM, Campbell, James R 
 wrote:

 Keith
 From the Data characterization calls with DRNOC a couple weeks back, I
 took away to a confusing discussion within GPC about how we are deploying
 medications in CDMV3+.  In particular, you noted that medication
 administration events were to be expected in PROCEDURES in NDC codes but
 orders are in PRESCRIBING (at least ambulatory) in RXNORM and dispense
 events in DISPENSING with NDC.  Discussing this with our Cancer workgroup,
 they have a requirement for tracking chemotherapy treatments and are
 asking for advice on standardization of deployment.

 We are organizing our i2b2 medication metadata from NLM by ingredient
 (RXNORM) and subsuming all clinical formulations (RXNORM) and packaging
 (NDC) in a tree structure with top level organization by VA drug classes.

 I understand you are involved in a national antibiotic study and ask if
 you can provide some advice or direct me to guidance from PCORI/Sentinel
 about how we should be planning our i2b2 deployment of medication events.
 Jim

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

2017-04-17 Thread Nathan Graham

Jeff/All,

It looks like we were missing an index on the UNMC table - try now?  Initial 
manual testing shows that it's a lot faster (the UNMC hierarchy anyway).

See also https://informatics.gpcnetwork.org/trac/Project/ticket/568#comment:11.

--
Nathan

-Original Message-
From: Gpc-dev [mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Klann, 
Jeffrey G.
Sent: Wednesday, April 12, 2017 3:36 PM
To: Campbell, James R; gpc-dev@listserv.kumc.edu; Pedersen, Jay G; 
huhick...@nebraskamed.com; Dan Connolly; Russ Waitman
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> 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 
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you in error but does not contain patient information, please contact the 
sender and properly disp

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

2017-04-12 Thread Pedersen, Jay G

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 (office)
402-739-3496 (mobile)

From: Klann, Jeffrey G. <jeff.kl...@mgh.harvard.edu>
Sent: Wednesday, April 12, 2017 3:35:31 PM
To: Campbell, James R; gpc-dev@listserv.kumc.edu; Pedersen, Jay G; 
huhick...@nebraskamed.com; dconno...@kumc.edu; rwait...@kumc.edu
Cc: 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> 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 t

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

2017-04-12 Thread Klann, Jeffrey G.

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

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

2017-04-12 Thread Campbell, James R

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

2017-04-12 Thread Kowalski, George

Well just some testing after I cleaned out our data.

Logged back into babel and started clicking on ontologies. First one I tried 
“CMH: Diagnosis” thru a “Database Error” also. But  “CMH: Demographics” worked.

Weird but all our ontologies are still there at the top level and still throw 
“Database Error”  when I expand them.


G


From: Gpc-dev <gpc-dev-boun...@listserv.kumc.edu> on behalf of "Kowalski, 
George" <gkowal...@mcw.edu>
Date: Wednesday, April 12, 2017 at 8:04 AM
To: "gpc-dev@listserv.kumc.edu" <gpc-dev@listserv.kumc.edu>
Subject: Re: [gpc-informatics] #280: Medication ontology orgainzed by ingredient

I’ve emptied our terms table until such time as we can determine what’s going 
wrong with the import process.



From: Gpc-dev 
<gpc-dev-boun...@listserv.kumc.edu<mailto:gpc-dev-boun...@listserv.kumc.edu>> 
on behalf of "Kowalski, George" <gkowal...@mcw.edu<mailto:gkowal...@mcw.edu>>

Date: Wednesday, April 12, 2017 at 8:00 AM

To: "gpc-dev@listserv.kumc.edu<mailto:gpc-dev@listserv.kumc.edu>" 
<gpc-dev@listserv.kumc.edu<mailto:gpc-dev@listserv.kumc.edu>>

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



All,







I reloaded our ontology here at MCW on Monday , It seemed to go well via 
phpPgAdmin, but Now I can’t browse our ontology without a “database error”  
coming back .











From: Gpc-dev 
<gpc-dev-boun...@listserv.kumc.edu<mailto:gpc-dev-boun...@listserv.kumc.edu><mailto:gpc-dev-boun...@listserv.kumc.edu><mailto:gpc-dev-boun...@listserv.kumc.edu%3e>>
 on behalf of "Klann, Jeffrey G." 
<jeff.kl...@mgh.harvard.edu<mailto:jeff.kl...@mgh.harvard.edu><mailto:jeff.kl...@mgh.harvard.edu><mailto:jeff.kl...@mgh.harvard.edu%3e>>



Date: Tuesday, April 11, 2017 at 10:37 PM



To: 
"gpc-dev@listserv.kumc.edu<mailto:gpc-dev@listserv.kumc.edu><mailto:gpc-dev@listserv.kumc.edu><mailto:gpc-dev@listserv.kumc.edu%3e>"
 
<gpc-dev@listserv.kumc.edu<mailto:gpc-dev@listserv.kumc.edu><mailto:gpc-dev@listserv.kumc.edu><mailto:gpc-dev@listserv.kumc.edu%3e>>,
 
"jay.peder...@unmc.edu<mailto:jay.peder...@unmc.edu><mailto:jay.peder...@unmc.edu><mailto:jay.peder...@unmc.edu%3e>"
 
<jay.peder...@unmc.edu<mailto:jay.peder...@unmc.edu><mailto:jay.peder...@unmc.edu><mailto:jay.peder...@unmc.edu%3e>>,
 
"campb...@unmc.edu<mailto:campb...@unmc.edu><mailto:campb...@unmc.edu><mailto:campb...@unmc.edu%3e>"
 
<campb...@unmc.edu<mailto:campb...@unmc.edu><mailto:campb...@unmc.edu><mailto:campb...@unmc.edu%3e>>,
 
"huhick...@nebraskamed.com<mailto:huhick...@nebraskamed.com><mailto:huhick...@nebraskamed.com><mailto:huhick...@nebraskamed.com%3e>"
 
<huhick...@nebraskamed.com<mailto:huhick...@nebraskamed.com><mailto:huhick...@nebraskamed.com><mailto:huhick...@nebraskamed.com%3e>>,
 
"dconno...@kumc.edu<mailto:dconno...@kumc.edu><mailto:dconno...@kumc.edu><mailto:dconno...@kumc.edu%3e>"
 
<dconno...@kumc.edu<mailto:dconno...@kumc.edu><mailto:dconno...@kumc.edu><mailto:dconno...@kumc.edu%3e>>,
 
"rwait...@kumc.edu<mailto:rwait...@kumc.edu><mailto:rwait...@kumc.edu><mailto:rwait...@kumc.edu%3e>"
 
<rwait...@kumc.edu<mailto:rwait...@kumc.edu><mailto:rwait...@kumc.edu><mailto:rwait...@kumc.edu%3e>>



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><mailto:d...@madmode.com><mailto:d...@madmode.com><mailto:d...@madmode.com%3e><mailto:d...@madmode.com%3e%3cmailto:d...@madmode.com%3e%3cmailto:d...@madmode.com%3e%3e>>
 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:   |







-

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

2017-04-12 Thread Kowalski, George

I’ve emptied our terms table until such time as we can determine what’s going 
wrong with the import process.

From: Gpc-dev <gpc-dev-boun...@listserv.kumc.edu> on behalf of "Kowalski, 
George" <gkowal...@mcw.edu>
Date: Wednesday, April 12, 2017 at 8:00 AM
To: "gpc-dev@listserv.kumc.edu" <gpc-dev@listserv.kumc.edu>
Subject: Re: [gpc-informatics] #280: Medication ontology orgainzed by ingredient

All,



I reloaded our ontology here at MCW on Monday , It seemed to go well via 
phpPgAdmin, but Now I can’t browse our ontology without a “database error”  
coming back .





From: Gpc-dev 
<gpc-dev-boun...@listserv.kumc.edu<mailto:gpc-dev-boun...@listserv.kumc.edu>> 
on behalf of "Klann, Jeffrey G." 
<jeff.kl...@mgh.harvard.edu<mailto:jeff.kl...@mgh.harvard.edu>>

Date: Tuesday, April 11, 2017 at 10:37 PM

To: "gpc-dev@listserv.kumc.edu<mailto:gpc-dev@listserv.kumc.edu>" 
<gpc-dev@listserv.kumc.edu<mailto:gpc-dev@listserv.kumc.edu>>, 
"jay.peder...@unmc.edu<mailto:jay.peder...@unmc.edu>" 
<jay.peder...@unmc.edu<mailto:jay.peder...@unmc.edu>>, 
"campb...@unmc.edu<mailto:campb...@unmc.edu>" 
<campb...@unmc.edu<mailto:campb...@unmc.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>>

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><mailto:d...@madmode.com><mailto:d...@madmode.com%3e>>
 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: 
<https://urldefense.proofpoint.com/v2/url?u=http-3A__informatics.gpcnetwork.org_trac_Project_ticket_280-23comment-3A20=DwIGaQ=aFamLAsxMIDYjNglYHTMV0iqFn3z4pVFYPQkjgspw4Y=C_iDrPTjMjNVakiaVcSiVk-6jAlbEoLBTtmMo_3OTb0=OweRWiaUZzSbQdgaQuxsxHqDK80FJf9Laofx0ZRAuRw=Gamomccl8eONNAqA0xxXdwPZxPo_We-msfkKsS1zAc0=>



gpc-informatics 
<https://urldefense.proofpoint.com/v2/url?u=http-3A__informatics.gpcnetwork.org_=DwIGaQ=aFamLAsxMIDYjNglYHTMV0iqFn3z4pVFYPQkjgspw4Y=C_iDrPTjMjNVakiaVcSiVk-6jAlbEoLBTtmMo_3OTb0=OweRWiaUZzSbQdgaQuxsxHqDK80FJf9Laofx0ZRAuRw=lDqm9XxOCpZnAuPAyrKhcoBHWFiMMCtQ6GrEkXYmQgM=>



Greater Plains Network - Informatics















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

2017-04-11 Thread Klann, Jeffrey G.

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"  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: 

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

2017-04-10 Thread GPC Informatics

#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 campbell):

 SCILHS/Medication metadata issues addressed with load to BABEL toiday:
 •   SCILHS medication metadata subset only includes 40,617,709 of UNMC
 60,955,630  prescriptions and pharmacy dispense data
 •   Many historical RXNORM and NDC codes no longer in active use are
 not found in SCILHS even though we have valid observation facts in i2b2
 •   UMLS metathesaurus does not provide history mechanism for RXNORM
 or NDC
 •   NLM willing to expand RXCLASS API to include history mechanisms
 but not deployed yet; they provided work-around for this load until API
 available
 •   VA drug classes are SCILHS/SHRINE preferred top level ontology for
 browsing and querying clinical medication events but that is static scheme
 as of 12/31/2017
 •   VA drug classes deploy different ingredient-level subsets of codes
 based upon clinical indication
 •   (therefore) with VA drug classes as sole top-level ontology, not
 all clinical formulations or packages can be deployed
 •   Other top-level classifications for medications, like ATC, have
 similar limitations

--
Ticket URL: 

gpc-informatics 
Greater Plains Network - Informatics
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RE: [gpc-informatics] #280: Medication ontology orgainzed by ingredient

2017-03-23 Thread Campbell, James R

I understand now your concerns about the volume of facts, although I think that 
the issue is minor from the standpoint of volume of data.  I was asking for 
discussion whether within GPC we would be rolling out the additional datatypes 
in SNOW SHRINE that would be additions to Jeff's modifiers, not replacing them 
and I did not hear a consensus on whether we wanted to do so.  To be clear, 
below we have core SCILHS medication modifiers which I assume we are all 
commiting:

\PCORI_MOD\RX_BASIS\
\PCORI_MOD\RX_BASIS\DI\
\PCORI_MOD\RX_BASIS\PR\
\PCORI_MOD\RX_BASIS\01\
\PCORI_MOD\RX_BASIS\02\
\PCORI_MOD\RX_QUANTITY\
\PCORI_MOD\RX_REFILLS\
\PCORI_MOD\RX_FREQUENCY\...(12 MODIFIERS)
\PCORI_MOD\DAYS_SUPPLY\
\PCORI_MOD\

I propose supporting inpatient and outpatient dispensing events
\PCORI_MOD\RX_BASIS\DI\INPT\
\PCORI_MOD\RX_BASIS\DI\OUTPT\
But these are optional  if dispensing events are deployed as a modifier folder 
and a site can choose to ignore the distinction and we can still query for 
aggregate dispense events across SNOW SHRINE

I pointed out that CDMV3 supports med administration events in PROCEDURES and 
asked if we would agree on adding administration events but got no answer, so 
it appears right now that GPC has no commitment and I would consider these 
optional although UNMC will be supporting them:
\PCORI_MOD\RX_BASIS\AD\
\PCORI_MOD\RX_BASIS\AD\OUTPT\
\PCORI_MOD\RX_BASIS\AD\INPT\

Finally, I am not hearing interest from other GPC sites, and so UNMC will be 
rolling out facts on order detail as our optional extension to SCILHS for local 
consumption:
\PCORI_MOD\RX_STRENGTH\Ordered strength
\PCORI_MOD\RX_ROUTE\Ordered route
\PCORI_MOD\RX_DOSE\Ordered dose
\PCORI_MOD\RX_DETAIL\Ordered detail(SIG)

Jim Campbell

-Original Message-
From: Debbie Yoshihara [mailto:dlyos...@wisc.edu]
Sent: Monday, March 20, 2017 10:56 AM
To: Dan Connolly <dconno...@kumc.edu>; gpc-dev@listserv.kumc.edu; Thomas Mish 
<m...@wisc.edu>; Campbell, James R <campb...@unmc.edu>; 
huhick...@nebraskamed.com; Russ Waitman <rwait...@kumc.edu>
Cc: jeff.kl...@mgh.harvard.edu
Subject: RE: [gpc-informatics] #280: Medication ontology orgainzed by ingredient

Ok, here is how I count 11

1) RX_BASIS DI
2) RX_BASIS PR
3) RX_BASIS AD
4) RX_DAYS_SUPPLY
5) RX_FREQ
6) RX_QUANTITY
7) RX_REFILLS
8) RX_STRENGTH
9) RX_ROUTE
10) RX_DOSE
11) RX_DETAIL

I guess you're counting the RX_BASIS as 1 instead of 3.

--- Debbie Yoshihara

-Original Message-
From: Dan Connolly [mailto:dconno...@kumc.edu]
Sent: Monday, March 20, 2017 10:38 AM
To: Debbie Yoshihara; gpc-dev@listserv.kumc.edu; Thomas Mish; 
campb...@unmc.edu; huhick...@nebraskamed.com; Russ Waitman
Cc: jeff.kl...@mgh.harvard.edu
Subject: RE: [gpc-informatics] #280: Medication ontology orgainzed by ingredient

As to who is going to look at them: i2p-transform (i.e. software to build 
PCORNet CDM from i2b2) consumes these modifiers.

As to 11x: how many modifiers are you currently storing? You're already storing 
RX_BASIS, RX_FREQUENCY, RX_DAYS_SUPPLY, RX_QUANTITY, and RX_REFILLS somehow, 
yes?

UNMC was proposing adding RX_STRENGTH, RX_ROUSE, RX_DOSE, and RX_SIG, but in 
discussion it emerged that "justification for including route, dose and detail 
modifiers ... is weakest in terms of use cases"

I count 9 total modifiers in the proposal, 5 of which KUMC (and presumably the 
other 8 sites using the i2p-transform code) are already loading, and 3 of which 
could (from discussion so far) be removed without much objection. So to me, it 
looks like this is a proposal to go from 5 to 6 modifiers.

--
Dan


From: Debbie Yoshihara [dlyos...@wisc.edu]
Sent: Monday, March 20, 2017 10:09 AM
To: gpc-dev@listserv.kumc.edu; Thomas Mish; campb...@unmc.edu; 
huhick...@nebraskamed.com; Dan Connolly; Russ Waitman
Cc: jeff.kl...@mgh.harvard.edu
Subject: RE: [gpc-informatics] #280: Medication ontology orgainzed by ingredient

I have looked over these explosion of modifiers.
For the med modifiers if you populated all of them that would make the facts 
11x bigger for the med facts.
Who is going to look at all of these? Or even populate them if they have them?

The only other question I have is for the lab_mod, what is the difference 
between stat and expedite?

--- Debbie Yoshihara



-Original Message-
From: Gpc-dev [mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of GPC 
Informatics
Sent: Monday, March 20, 2017 8:46 AM
To: Thomas Mish; campb...@unmc.edu; huhick...@nebraskamed.com; 
dconno...@kumc.edu; rwait...@kumc.edu
Cc: gpc-dev@listserv.kumc.edu; jeff.kl...@mgh.harvard.edu
Subject: Re: [gpc-informatics] #280: Medication ontology orgainzed by ingredient

#280: Medication ontology orgainzed by ingredient
-+
 Reporter:  preeder  |   Owner:  mish
 Type:  enhancement  |  Status:  assigned
 Priority:  major|   Milestone:  snow-shrine-2
Comp

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

2017-03-20 Thread Debbie Yoshihara

Ok, here is how I count 11

1) RX_BASIS DI
2) RX_BASIS PR
3) RX_BASIS AD
4) RX_DAYS_SUPPLY
5) RX_FREQ
6) RX_QUANTITY
7) RX_REFILLS
8) RX_STRENGTH
9) RX_ROUTE
10) RX_DOSE
11) RX_DETAIL

I guess you're counting the RX_BASIS as 1 instead of 3.

--- Debbie Yoshihara

-Original Message-
From: Dan Connolly [mailto:dconno...@kumc.edu] 
Sent: Monday, March 20, 2017 10:38 AM
To: Debbie Yoshihara; gpc-dev@listserv.kumc.edu; Thomas Mish; 
campb...@unmc.edu; huhick...@nebraskamed.com; Russ Waitman
Cc: jeff.kl...@mgh.harvard.edu
Subject: RE: [gpc-informatics] #280: Medication ontology orgainzed by ingredient

As to who is going to look at them: i2p-transform (i.e. software to build 
PCORNet CDM from i2b2) consumes these modifiers.

As to 11x: how many modifiers are you currently storing? You're already storing 
RX_BASIS, RX_FREQUENCY, RX_DAYS_SUPPLY, RX_QUANTITY, and RX_REFILLS somehow, 
yes?

UNMC was proposing adding RX_STRENGTH, RX_ROUSE, RX_DOSE, and RX_SIG, but in 
discussion it emerged that "justification for including route, dose and detail 
modifiers ... is weakest in terms of use cases"

I count 9 total modifiers in the proposal, 5 of which KUMC (and presumably the 
other 8 sites using the i2p-transform code) are already loading, and 3 of which 
could (from discussion so far) be removed without much objection. So to me, it 
looks like this is a proposal to go from 5 to 6 modifiers.

-- 
Dan


From: Debbie Yoshihara [dlyos...@wisc.edu]
Sent: Monday, March 20, 2017 10:09 AM
To: gpc-dev@listserv.kumc.edu; Thomas Mish; campb...@unmc.edu; 
huhick...@nebraskamed.com; Dan Connolly; Russ Waitman
Cc: jeff.kl...@mgh.harvard.edu
Subject: RE: [gpc-informatics] #280: Medication ontology orgainzed by ingredient

I have looked over these explosion of modifiers.
For the med modifiers if you populated all of them that would make the facts 
11x bigger for the med facts.
Who is going to look at all of these? Or even populate them if they have them?

The only other question I have is for the lab_mod, what is the difference 
between stat and expedite?

--- Debbie Yoshihara



-Original Message-
From: Gpc-dev [mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of GPC 
Informatics
Sent: Monday, March 20, 2017 8:46 AM
To: Thomas Mish; campb...@unmc.edu; huhick...@nebraskamed.com; 
dconno...@kumc.edu; rwait...@kumc.edu
Cc: gpc-dev@listserv.kumc.edu; jeff.kl...@mgh.harvard.edu
Subject: Re: [gpc-informatics] #280: Medication ontology orgainzed by ingredient

#280: Medication ontology orgainzed by ingredient
-+
 Reporter:  preeder  |   Owner:  mish
 Type:  enhancement  |  Status:  assigned
 Priority:  major|   Milestone:  snow-shrine-2
Component:  data-stds|  Resolution:
 Keywords:   |  Blocked By:
 Blocking:   |
-+
Changes (by dconnolly):

 * owner:  jay.pedersen => mish


Comment:

 Tom,

 Is Debbie likely to complete her review this morning?

--
Ticket URL: 
<http://informatics.gpcnetwork.org/trac/Project/ticket/280#comment:17>
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Re: [gpc-informatics] #280: Medication ontology orgainzed by ingredient

2017-03-20 Thread Phillip Reeder

The explosion of the number of facts has been my biggest concern with the
med modifiers as well.  With 115 million medication rows, a 10x increase
would give us double our existing number of facts. At UTSW, I¹ve populated
the data for many of these modifiers into the observation_blob column in a
flat XML schema. This allows me to use them in my ETL for the PCORI CDM.
But it doesn¹t allow me to query on them in i2b2. It would be nice if i2b2
could be modified to allow me use that XML data in a query, but for now,
it¹s meeting my needs.  However with the SHRINE work we are doing, I might
be forced to populate them as modifiers.


Phillip

On 3/20/17, 10:37 AM, "Gpc-dev on behalf of Dan Connolly"
<gpc-dev-boun...@listserv.kumc.edu on behalf of dconno...@kumc.edu> wrote:

>As to who is going to look at them: i2p-transform (i.e. software to build
>PCORNet CDM from i2b2) consumes these modifiers.
>
>As to 11x: how many modifiers are you currently storing? You're already
>storing RX_BASIS, RX_FREQUENCY, RX_DAYS_SUPPLY, RX_QUANTITY, and
>RX_REFILLS somehow, yes?
>
>UNMC was proposing adding RX_STRENGTH, RX_ROUSE, RX_DOSE, and RX_SIG, but
>in discussion it emerged that "justification for including route, dose
>and detail modifiers ... is weakest in terms of use cases"
>
>I count 9 total modifiers in the proposal, 5 of which KUMC (and
>presumably the other 8 sites using the i2p-transform code) are already
>loading, and 3 of which could (from discussion so far) be removed without
>much objection. So to me, it looks like this is a proposal to go from 5
>to 6 modifiers.
>
>--
>Dan
>
>
>From: Debbie Yoshihara [dlyos...@wisc.edu]
>Sent: Monday, March 20, 2017 10:09 AM
>To: gpc-dev@listserv.kumc.edu; Thomas Mish; campb...@unmc.edu;
>huhick...@nebraskamed.com; Dan Connolly; Russ Waitman
>Cc: jeff.kl...@mgh.harvard.edu
>Subject: RE: [gpc-informatics] #280: Medication ontology orgainzed by
>ingredient
>
>I have looked over these explosion of modifiers.
>For the med modifiers if you populated all of them that would make the
>facts 11x bigger for the med facts.
>Who is going to look at all of these? Or even populate them if they have
>them?
>
>The only other question I have is for the lab_mod, what is the difference
>between stat and expedite?
>
>--- Debbie Yoshihara
>
>
>
>-Original Message-
>From: Gpc-dev [mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of GPC
>Informatics
>Sent: Monday, March 20, 2017 8:46 AM
>To: Thomas Mish; campb...@unmc.edu; huhick...@nebraskamed.com;
>dconno...@kumc.edu; rwait...@kumc.edu
>Cc: gpc-dev@listserv.kumc.edu; jeff.kl...@mgh.harvard.edu
>Subject: Re: [gpc-informatics] #280: Medication ontology orgainzed by
>ingredient
>
>#280: Medication ontology orgainzed by ingredient
>-+
> Reporter:  preeder  |   Owner:  mish
> Type:  enhancement  |  Status:  assigned
> Priority:  major|   Milestone:  snow-shrine-2
>Component:  data-stds|  Resolution:
> Keywords:   |  Blocked By:
> Blocking:   |
>-+
>Changes (by dconnolly):
>
> * owner:  jay.pedersen => mish
>
>
>Comment:
>
> Tom,
>
> Is Debbie likely to complete her review this morning?
>
>--
>Ticket URL:
><http://informatics.gpcnetwork.org/trac/Project/ticket/280#comment:17>
>gpc-informatics <http://informatics.gpcnetwork.org/>
>Greater Plains Network - Informatics
>___
>Gpc-dev mailing list
>Gpc-dev@listserv.kumc.edu
>http://listserv.kumc.edu/mailman/listinfo/gpc-dev
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>Gpc-dev@listserv.kumc.edu
>http://listserv.kumc.edu/mailman/listinfo/gpc-dev




UT Southwestern


Medical Center



The future of medicine, today.


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

2017-03-20 Thread Dan Connolly

As to who is going to look at them: i2p-transform (i.e. software to build 
PCORNet CDM from i2b2) consumes these modifiers.

As to 11x: how many modifiers are you currently storing? You're already storing 
RX_BASIS, RX_FREQUENCY, RX_DAYS_SUPPLY, RX_QUANTITY, and RX_REFILLS somehow, 
yes?

UNMC was proposing adding RX_STRENGTH, RX_ROUSE, RX_DOSE, and RX_SIG, but in 
discussion it emerged that "justification for including route, dose and detail 
modifiers ... is weakest in terms of use cases"

I count 9 total modifiers in the proposal, 5 of which KUMC (and presumably the 
other 8 sites using the i2p-transform code) are already loading, and 3 of which 
could (from discussion so far) be removed without much objection. So to me, it 
looks like this is a proposal to go from 5 to 6 modifiers.

-- 
Dan


From: Debbie Yoshihara [dlyos...@wisc.edu]
Sent: Monday, March 20, 2017 10:09 AM
To: gpc-dev@listserv.kumc.edu; Thomas Mish; campb...@unmc.edu; 
huhick...@nebraskamed.com; Dan Connolly; Russ Waitman
Cc: jeff.kl...@mgh.harvard.edu
Subject: RE: [gpc-informatics] #280: Medication ontology orgainzed by ingredient

I have looked over these explosion of modifiers.
For the med modifiers if you populated all of them that would make the facts 
11x bigger for the med facts.
Who is going to look at all of these? Or even populate them if they have them?

The only other question I have is for the lab_mod, what is the difference 
between stat and expedite?

--- Debbie Yoshihara



-Original Message-
From: Gpc-dev [mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of GPC 
Informatics
Sent: Monday, March 20, 2017 8:46 AM
To: Thomas Mish; campb...@unmc.edu; huhick...@nebraskamed.com; 
dconno...@kumc.edu; rwait...@kumc.edu
Cc: gpc-dev@listserv.kumc.edu; jeff.kl...@mgh.harvard.edu
Subject: Re: [gpc-informatics] #280: Medication ontology orgainzed by ingredient

#280: Medication ontology orgainzed by ingredient
-+
 Reporter:  preeder  |   Owner:  mish
 Type:  enhancement  |  Status:  assigned
 Priority:  major|   Milestone:  snow-shrine-2
Component:  data-stds|  Resolution:
 Keywords:   |  Blocked By:
 Blocking:   |
-+
Changes (by dconnolly):

 * owner:  jay.pedersen => mish


Comment:

 Tom,

 Is Debbie likely to complete her review this morning?

--
Ticket URL: 
<http://informatics.gpcnetwork.org/trac/Project/ticket/280#comment:17>
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RE: [gpc-informatics] #280: Medication ontology orgainzed by ingredient

2017-03-20 Thread Debbie Yoshihara

I have looked over these explosion of modifiers.
For the med modifiers if you populated all of them that would make the facts 
11x bigger for the med facts.
Who is going to look at all of these? Or even populate them if they have them?

The only other question I have is for the lab_mod, what is the difference 
between stat and expedite?

--- Debbie Yoshihara



-Original Message-
From: Gpc-dev [mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of GPC 
Informatics
Sent: Monday, March 20, 2017 8:46 AM
To: Thomas Mish; campb...@unmc.edu; huhick...@nebraskamed.com; 
dconno...@kumc.edu; rwait...@kumc.edu
Cc: gpc-dev@listserv.kumc.edu; jeff.kl...@mgh.harvard.edu
Subject: Re: [gpc-informatics] #280: Medication ontology orgainzed by ingredient

#280: Medication ontology orgainzed by ingredient
-+
 Reporter:  preeder  |   Owner:  mish
 Type:  enhancement  |  Status:  assigned
 Priority:  major|   Milestone:  snow-shrine-2
Component:  data-stds|  Resolution:
 Keywords:   |  Blocked By:
 Blocking:   |
-+
Changes (by dconnolly):

 * owner:  jay.pedersen => mish


Comment:

 Tom,

 Is Debbie likely to complete her review this morning?

--
Ticket URL: 
<http://informatics.gpcnetwork.org/trac/Project/ticket/280#comment:17>
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RE: [gpc-informatics] #280: Medication ontology orgainzed by ingredient

2017-03-20 Thread Thomas Mish

I don't think so. 

-TM

-Original Message-
From: GPC Informatics [mailto:d...@madmode.com] 
Sent: Monday, March 20, 2017 8:46 AM
To: Thomas Mish <m...@wisc.edu>; campb...@unmc.edu; huhick...@nebraskamed.com; 
dconno...@kumc.edu; rwait...@kumc.edu
Cc: gpc-dev@listserv.kumc.edu; mprit...@kumc.edu; jeff.kl...@mgh.harvard.edu
Subject: Re: [gpc-informatics] #280: Medication ontology orgainzed by ingredient

#280: Medication ontology orgainzed by ingredient
-+
 Reporter:  preeder  |   Owner:  mish
 Type:  enhancement  |  Status:  assigned
 Priority:  major|   Milestone:  snow-shrine-2
Component:  data-stds|  Resolution:
 Keywords:   |  Blocked By:
 Blocking:   |
-+
Changes (by dconnolly):

 * owner:  jay.pedersen => mish


Comment:

 Tom,

 Is Debbie likely to complete her review this morning?

--
Ticket URL: 
<http://informatics.gpcnetwork.org/trac/Project/ticket/280#comment:17>
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Re: [gpc-informatics] #280: Medication ontology orgainzed by ingredient

2017-03-20 Thread GPC Informatics

#280: Medication ontology orgainzed by ingredient
-+
 Reporter:  preeder  |   Owner:  mish
 Type:  enhancement  |  Status:  assigned
 Priority:  major|   Milestone:  snow-shrine-2
Component:  data-stds|  Resolution:
 Keywords:   |  Blocked By:
 Blocking:   |
-+
Changes (by dconnolly):

 * owner:  jay.pedersen => mish


Comment:

 Tom,

 Is Debbie likely to complete her review this morning?

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

2017-03-15 Thread GPC Informatics

#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 rwaitman):

 As discussed on gpc-dev yesterday,
 I agree on
 3   \PCORI_MOD\RX_BASIS\DI\OUTPT\   Community Pharmacy Dispensing
 Event N   RHE 0   RX_BASIS:DI\OUTPT\
 3   \PCORI_MOD\RX_BASIS\DI\INPT\Hospital Pharmacy Dispensing Event
 N   RHE 0   RX_BASIS:DI\INPT\

 2   \PCORI_MOD\RX_BASIS\AD\ Administration EventN   RHE 0
 RX_BASIS:AD

 But wouldn't do the distinction between in and outpatient administrations
 as that should be driven by the linked encounter.  I think if you try to
 do it at the modifier level we'll create inconsistencies  (so no to rows
 14 and 15 for my vote).

 For the last 4 modifiers, I'd like those recommended modifiers to be
 aligned with the work from the cancer CRG and antibiotic study in terms of
 which gaps we have in the CDM to support analysis.  Also appreciated the
 comment for either consistent use of "unit" in i2b2 or need perhaps for a
 modifier to support the cdm.

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

2017-03-06 Thread GPC Informatics

#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 campbell):

 For review and comment by Jeff Klann and GPC sites implementing SCILHS for
 SNOW SHRINE, we have uploaded a spreadsheet SCILHS_MODIFIERS.  The
 worksheet MED_MOD_UNMC has Jeff's modifier metadata in BLACK with proposed
 additions by UNMC in BLUE. The additions propose to add several types of
 medication events that Jeff has not included and several types of
 Observation_facts that we routinely include in our ETLs.  The core
 modifiers from Jeff are untouched.
 Please review and add thoughts as to additional GPC requirements.
 Jim

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

2017-03-06 Thread GPC Informatics

#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:   |
-+
Changes (by campbell):

 * cc: Jeff.Klann@… (added)


Comment:

 For comment by GPC sites implementing SCILHS and SNOW SHRINE, I enclose
 the SCILHS modifier metadata from Jeff Klann and have highlighted in BLUE
 our additions on the worksheet MED_MOD_UNMC.  This adds proposed modifiers
 for a number of medication events and observation_facts that Jeff did not
 include but that we extract at Nebraska.

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

2017-03-06 Thread GPC Informatics

#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:   |
-+
Changes (by dconnolly):

 * owner:  jpedersen => jay.pedersen


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

2017-01-30 Thread GPC Informatics

#280: Medication ontology orgainzed by ingredient
-+
 Reporter:  preeder  |   Owner:  dconnolly
 Type:  enhancement  |  Status:  accepted
 Priority:  major|   Milestone:  snow-shrine-1
Component:  data-stds|  Resolution:
 Keywords:   |  Blocked By:
 Blocking:   |
-+
Changes (by dconnolly):

 * owner:  ngraham => dconnolly
 * status:  assigned => accepted


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

2017-01-19 Thread GPC Informatics

#280: Medication ontology orgainzed by ingredient
-+
 Reporter:  preeder  |   Owner:  ngraham
 Type:  enhancement  |  Status:  assigned
 Priority:  major|   Milestone:  snow-shrine-1
Component:  data-stds|  Resolution:
 Keywords:   |  Blocked By:
 Blocking:   |
-+

Comment (by dconnolly):

 Nathan,

 So we did the "swap in, discuss with Russ" bit from comment:5 on Jan 3.
 Would you please do the "report to gpc-dev" within the next week or so? If
 you're not available, re-assign this.

 Nick from UIOWA asked me about this stuff and I told him about the messy
 stuff we found below ingredient in our Jan 3 meeting with Russ.

 I can't find any notes beyond one from Mike:

   - how to link va drug class to drug ingredient?

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

2016-12-27 Thread GPC Informatics

#280: Medication ontology orgainzed by ingredient
-+
 Reporter:  preeder  |   Owner:  ngraham
 Type:  enhancement  |  Status:  assigned
 Priority:  major|   Milestone:  snow-shrine-1
Component:  data-stds|  Resolution:
 Keywords:   |  Blocked By:
 Blocking:   |
-+
Changes (by dconnolly):

 * priority:  minor => major
 * milestone:  bariatric-study-data => snow-shrine-1


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

2016-06-14 Thread GPC Informatics

#280: Medication ontology orgainzed by ingredient
-+
 Reporter:  preeder  |   Owner:  ngraham
 Type:  enhancement  |  Status:  assigned
 Priority:  minor|   Milestone:  data-domains3
Component:  data-stds|  Resolution:
 Keywords:   |  Blocked By:
 Blocking:   |
-+
Changes (by dconnolly):

 * cc: mprittie (added)
 * owner:  rwaitman => ngraham
 * milestone:  morning-star => data-domains3


Comment:

 NG to swap in, discuss with Russ, and report to gpc-dev

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gpc-informatics 
Greater Plains Network - Informatics
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