SNOMED CT mapping to ICD-9, ICD-10, LOINC

Hi, Does anyone know if there is a mapping from SNOMED CT to any or all of the three terminologies? ICD-9 ICD-10 LOINC Thanks! --- Keith Wanta | Data Management Developer | UW Health - Enterprise Analytics | 608-492-1099 ___ Gpc-dev mailing list Gp

de-identified vs LDS

Hi, Does anyone in this group have documentation outlining the differences between a de-identified data set versus limited data set? I used to have a PDF from years ago, but cannot find it. Thank you. --- Keith Wanta | Data Management Developer | UW Health - Enterprise Analytics | 608-492-10

RE: i2b2 shibboleth or SAML authentication

Hi Sri, That error typically indicates the PM cell isn't configured properly, but because you didn't authenticate, you won't be able to authorize into the PM cell at all. It could be one of a dozen things that went wrong. So you need to turn on error logging in PHP, Java, and all frameworks t

RE: UMN SNOW Shrine Maintenance

Hi Jim, Bill and I will get in touch with Jay and Mike to make this happen. Merry Christmas. --- Keith M. Wanta Data Management Developer Enterprise Analytics UW Health 608-492-1099 From: McClay, James C [mailto:jmcc...@unmc.edu] Sent: Tuesday, December 12, 2017 3:50 PM To: Wanta Keith M

RE: UMN SNOW Shrine Maintenance

Andrew, Is it okay if I pull you off the downstream nodes list for now, so it doesn’t disrupt other sites? I can add you back on tomorrow if you email or call. --- Keith M. Wanta Data Management Developer Enterprise Analytics UW Health 608-492-1099 From: Gpc-dev [mailto:gpc-dev-boun...@listser

RE: GPC SNOW SHRINE status at LEC - 2 Weeks: gold: UTSW, KUMC; silver: MCRF; bronze: WISC, UNMC

I would guess that the i2b2 server does not need to initate requests to the SHRINE server. To confirm this, try setting up an iptables rule on the SHRINE server to block the incoming TCP traffic on port 6443. If things are working, then the SHRINE server is only considered the client (sends re

RE: i2b2 shibboleth or SAML authentication

On our UW Madison i2b2 server, we are running Shibboleth. Even though i2b2 itself is running on Apache, the Shibboleth code is deployed on Tomcat. Feel free to ask questions. I fixed a bunch of issues dealing with browser compatibility so the 1.7 i2b2 source code is different from the origina

RE: [gpc-informatics] #605: UMN update spoke with prod hub cert

Sorry, I didn't look at Andrew's last name. Two Andrews. --- Keith M. Wanta Data Management Developer Enterprise Analytics UW Health 608-492-1099 -Original Message- From: Gpc-dev [mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Wanta Keith M Sent: Thursday, June 08,

RE: [gpc-informatics] #605: UMN update spoke with prod hub cert

Reassigned to Tim Meyer. --- Keith M. Wanta Data Management Developer Enterprise Analytics UW Health 608-492-1099 -Original Message- From: GPC Informatics [mailto:d...@madmode.com] Sent: Thursday, June 08, 2017 11:21 AM To: Wanta Keith M ; mcneele...@health.missouri.edu Cc: hangs

RE: Reminder to complete SNOW SHRINE 1.20.1 verification step!

u send it. If you don't, check with your organization's email server team or KUMC's email server team. --- Keith M. Wanta UW Health From: Gpc-dev [mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Wanta Keith M Sent: Tuesday, April 04, 2017 5:33 PM To: GPC-DEV@LISTSERV.KUMC.

Reminder to complete SNOW SHRINE 1.20.1 verification step!

SNOW SHRINE Administrators, We're still working on the SNOW on-boarding phase. (Close to half way there) To complete your SNOW SHRINE install for this on-boarding phase, please schedule time with me at your earliest convenience for SHRINE 1.20.1 verification to ensure your SHRINE configuratio

RE: SNOW SHRINE query with SCILHS PCORNet ontology (#525)

conno...@kumc.edu] Sent: Monday, April 03, 2017 1:51 PM To: Phillip Reeder; Wanta Keith M Cc: Subject: SNOW SHRINE query with SCILHS PCORNet ontology (#525) Keith, how is the transition from the i2b2 demo ontology to the SCILHS ontology going? Any news from anybody else along these lines?

RE: SCILHS ontology for demographics

All, To elaborate on Debbie's question here, let me expand a bit. RACE_CD is a standard column in PATIENT_DIMENSION. Ethnicity does not have a standard column in PATIENT_DIMENSION, but many of us in GPC added to a custom PATIENT_DIMENSION table in order to support a CDM requirement. Ideally,

RE: SNOW SHRINE update?

Dan, Eric LaRose and I have both agreed to demo a few things with SHRINE in tomorrow's GPC call with MCRF's spoke, before the upgrade. I'd also be happy to run a "working" query as well. Please set aside a few minutes during the call. --- Keith M. Wanta UW Health From: Gpc-dev [mailto:gpc-d

RE: Prawn (SHRINE ontology mapping tool)

conno...@kumc.edu] Sent: Thursday, January 19, 2017 2:14 PM To: Wanta Keith M Cc: Subject: Prawn (SHRINE ontology mapping tool) Keith, We talked about a demo of this tool. I always like to get the discussion started in writing before our calls. Can you point us at the code or anything for this tool? Or pr

SNOW SHRINE ticket for KUMC

Hi Dan, Can you please create a SNOW SHRINE ticket for GPC and assign it to Lav? We should link it to ticket #459. I will assist Lav using that ticket if he runs into anything during his spoke server implementation. In the ticket, can you please mention the OS details (distribution and versio

new firewall requirements for SHRINE build

Please be aware of the new requirements for firewall rules updates on the SNOW spoke build on the page below. https://wiki.ctri.mcw.edu/pages/editpage.action?pageId=44991750 Because multiple sites will need to concurrently verify against a hub for both SHRINE version 1.19.2 and SHRINE version 1

RE: SNOW authentication, client set-up?

I can put together a better explanation as part of my SHRINE presentation in Kansas City. How does that sound Dan? --- Keith M. Wanta UW Health From: Dan Connolly [mailto:dconno...@kumc.edu] Sent: Tuesday, January 03, 2017 10:29 AM To: Wanta Keith M Cc: ; Lav Patel Subject: RE: SNOW

RE: SNOW authentication, client set-up?

HRINE default port of 6443 should not allow any of those requests to leave your firewall. --- Keith M. Wanta UW Health From: Gpc-dev [mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Wanta Keith M Sent: Tuesday, January 03, 2017 10:09 AM To: 'Dan Connolly' Cc: Lav Patel; Su

RE: SNOW authentication, client set-up?

Wanta UW Health From: Dan Connolly [mailto:dconno...@kumc.edu] Sent: Tuesday, January 03, 2017 9:36 AM To: Wanta Keith M Cc: ; Lav Patel Subject: SNOW authentication, client set-up? Keith, We were going over the SNOW docs with the folks at KUMC that handle the firewalls, and I couldn't te

RE: days supply from EMR: help?!

Remove the "S" in DAYS_SUPPLY. You can find the data there. --- Keith M. Wanta WISC From: gpc-dev-boun...@listserv.kumc.edu [mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Phillip Reeder Sent: Wednesday, November 02, 2016 12:11 PM To: Dan Connolly; Pedersen, Jay G Cc: Subject: Re: days

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

ework conflicts. [cid:image001.png@01D23442.067E1DA0] WISC is currently using i2b2 version 1.7.05 for the SHRINE version 1.18. --- Keith M. Wanta WISC From: Phillip Reeder [mailto:phillip.ree...@utsouthwestern.edu] Sent: Tuesday, November 01, 2016 12:37 PM To: Russ Waitman; Wanta Keith M; GPC-DEV@LISTS

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

GPC - Does anyone have the specific SHRINE version of the SCILHS network? The SHRINE documentation gets as high as 1.19 for the SVN revision. But something tells me I heard 1.20 from someone in our group. I'm putting together our UW Health project proposal for the SHRINE upgrade for GPC, and

reversing SAS CPORT file back into SAS datasets

GPC - Thought this code would be helpful to the group. If you are wanting to pull out SAS data sets from a CPORT file (*.cpt) you submitted in PopMedNet, modify the the "in" and "out" variables appropriately. Then open up the appropriate data set from the "output" folder in SAS, by going to F

RE: DataBuilder installation instructions

University of Wisconsin will participate. From: gpc-dev-boun...@listserv.kumc.edu [mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of French, Tony Sent: Thursday, July 07, 2016 3:16 PM To: Campbell, James R; Dan Connolly Cc: GPC-DEV@LISTSERV.KUMC.EDU Subject: RE: DataBuilder installation inst

RE: CDM v3 Appendix B fixes - pencils down?

th Wanta (WISC) From: Dan Connolly [mailto:dconno...@kumc.edu] Sent: Monday, June 06, 2016 3:41 PM To: Wanta Keith M; GPC-DEV@LISTSERV.KUMC.EDU Subject: RE: CDM v3 Appendix B fixes - pencils down? If you're asking whether you should track your i2p-transform and shilhs-ontology changes using g

CDM v3 Appendix B fixes - pencils down?

GPC - Have we make a decision on whether we should be making our CDM v3 Appendix B fixes based on some past revision of the i2p-transform and scilhs-ontology repositories, or Should we be applying code changes overtime from GitHub for CDM v3 Appendix B fixes? (putting aside ontology mappi

PCORnet data characterization calls

GPC dev team - If anyone is interested, Duke sent me these meeting times for PCORnet DCQ calls. I'd suggest attending if you have questions about CDM, as a post mortem. We all go through these queries, but in case you have questions, feel free to join. Subtract an hour for CDT on your calend

source code enhancement to Duke University SAS script

Michael, James, et. al., When the SAS views are built using the script "data_step_view_prep.sas", the connection (or libname) to the RDBMS database in which the SAS views depend on, shows up in the SAS Server List tree panel (in the bottom left panel of SAS EG client) Servers > SASApp > Librar

PMNENCOUNTER.FACILITY_LOCATION - CDM v3

GPC - Are there any sites that populated FACILITY_LOCATION in PMNENCOUNTER? Based on the code in i2p-transform, my understanding is that this field is based on OBSERVATION_FACT.LOCATION_CD in i2b2. Here is the PCORI definition of this field for the CDM v3 specification: FACILITY_LOCATION R

RE: SAS views for CDM v3 data characterization query

: Wednesday, April 13, 2016 12:45 PM To: French, Tony Cc: Michael Prittie; Wanta Keith M; GPC-DEV@LISTSERV.KUMC.EDU; Hood, Daniel Robert; Ring, Nate Subject: Re: SAS views for CDM v3 data characterization query Hi Tony, Here at UMN we had the same problem and fixed it using the data step views you

RE: CDM ETL direct from Epic Clarity #464

Dan – WISC didn’t use that approach because our data is sourced from our data warehouse for i2b2. Our data warehouse data sources from Clarity, but not all of it. We used the SCILHS approach with a twist. Keith From: gpc-dev-boun...@listserv.kumc.edu [mailto:gpc-dev-boun...@listserv.kumc.ed

SAS views for CDM v3 data characterization query

GPC - Is there anyone in GPC that has built the SAS views for the data characterization query? I couldn't find any files that contain the SAS Views source code for the date and time conversions for the data characterization query for CDM v3. It appears that we have a choice of using them or n

RE: SNOW and SHRINE update?

That's correct. SNOW is an acronym for SHRINE Network of Wisconsin. MCW, MCRF and UW stood up three skos:ConceptScheme instances inside the SHRINE web client (hosted on each spoke) and got all three spokes to pull obfuscated patient counts. We have one Windows spoke, and two Linux spokes, as w

RE: NAACCR python code

ation) was the source of truth. For the most part it is, but not always. Just another topic for data quality I guess. Keith From: Dan Connolly [mailto:dconno...@kumc.edu] Sent: Tuesday, November 17, 2015 4:16 PM To: Wanta Keith M; Nathan Graham Cc: GPC-DEV@LISTSERV.KUMC.EDU Subject: RE: N

RE: NAACCR python code

.@kumc.edu] Sent: Tuesday, November 17, 2015 12:51 PM To: Wanta Keith M; Nathan Graham Cc: GPC-DEV@LISTSERV.KUMC.EDU Subject: RE: NAACCR python code The public version of heron_load/naaccr*.sql is out of date. Things are moving more quickly than our monthly publishing rhythm, so MultiSite dev a

RE: NAACCR python code

: Tuesday, November 17, 2015 9:25 AM To: Wanta Keith M; Dan Connolly Subject: RE: NAACCR python code Keith, Can we promote this thread to the gpc-dev mailing list? Others may have input/benefit from the conversation. Are you looking for the code that loads up the MORPH*/T_* tables? If so, ma

RE: ICD9 and CPT Procedures for GPC

Philip, We have an ICD-9 procedure terminology loaded in our instance of i2b2 at UW Madison. It's a start if you want to begin mapping your data to it. Once you get SCHILS, you might have to add a few hundred codes. https://drive.google.com/file/d/0B2_GBqEXJfhOaFJENXNxQktnNW8/view?usp=sharing

RE: GPC and ACT synergy

ation environment. We just change our input. Let me know if you would like more info. Keith From: Meeks-Johnson, Jim [mailto:jimme...@regenstrief.org] Sent: Monday, September 28, 2015 8:32 AM To: Campbell, James R; Wanta Keith M; 'Dan Connolly'; gpc-dev@listserv.kumc.edu Cc: McClay, Ja

RE: GPC and ACT synergy

Jim, If you prefer to keep isolated i2b2 systems, you could implement database swaps as a solution. We've recently installed SHRINE with other sites in Wisconsin and the systems are a bit different, so we use database swaps now at UW Health (as of a month ago). We chose this strategy not beca

RE: Jira ticket/workaround for backgrounded i2b2 queries that never return

UNMC and WISC rather.. too many acronyms. ☺ From: Susan Morrison [mailto:susan.morri...@utsouthwestern.edu] Sent: Tuesday, July 21, 2015 9:22 AM To: Wanta Keith M; Nathan Graham; GPC-DEV@LISTSERV.KUMC.EDU Cc: Jennifer Cai Subject: Re: Jira ticket/workaround for backgrounded i2b2 queries that

RE: Jira ticket/workaround for backgrounded i2b2 queries that never return

2:30) or tomorrow afternoon, if you and Jennifer can coordinate a time. We’ll need to monitor that server log for troubleshooting. Keith 608-492-1099 From: Susan Morrison [mailto:susan.morri...@utsouthwestern.edu] Sent: Tuesday, July 21, 2015 7:46 AM To: Nathan Graham; Wanta Keith M; GPC-DEV

RE: Jira ticket/workaround for backgrounded i2b2 queries that never return

Nathan, on the GPC call yesterday, do you recall which organization had this issue? I can suggest the fix to Partners, but it seems like a slightly different issue. I am just following up to confirm. ~Keith From: gpc-dev-boun...@listserv.kumc.edu [mailto:gpc-dev-boun...@listserv.kumc.edu] On

GPC Data Builder instructions w/ fixed VM i2b2 image (GPC ticket #202)

All, Please see the following PDF for Data Builder instructions in Windows. Dan Connolly had accurate instructions that he ran on his Apple machine, but there are some slight differences for Windows users. I've provided instructions to move the zip file from Windows to the Linux VM using a Sa

RE: how to preserve saved queries on i2b2 refresh?

Very good question Dan! UW Madison currently disables old queries on each i2b2 refresh if our concepts change. So we just do it for each release for now to be safe. We are not handling patient ids (or any ids) correctly yet after a refresh. This is an ice breaker for a great honest broker an

RE: [gpc-informatics] #90: Diagnoses Modifiers for data attribution

An order diagnosis originates from a clinical system and eventually makes its way into one of the two billing systems (Hospital or Professional). Typically the physician needs to sign for an order, so you shouldn't trust a diagnosis on an order unless it was signed. In the revenue cycle for pr

RE: [gpc-informatics] #178: determine whether last.visit is the last fulfilled visit or the last scheduled visit

ing provider to ask patient about something --150 --150-Abstract ) AND VISIT_PROV_ID IS NOT NULL -Original Message----- From: gpc-dev-boun...@listserv.kumc.edu [mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Wanta

RE: [gpc-informatics] #178: determine whether last.visit is the last fulfilled visit or the last scheduled visit

if the patient is deceased. I'd like to build a query, but I'd like to weed out what is needed by PCORI first. -Original Message- From: Dan Connolly [mailto:dconno...@kumc.edu] Sent: Tuesday, October 28, 2014 5:13 PM To: Wanta Keith M; gpc-dev@listserv.kumc.edu; Mish Thomas

RE: [gpc-informatics] #178: determine whether last.visit is the last fulfilled visit or the last scheduled visit

All, This afternoon I got up to speed on visit types. I have several dozen questions that may be relevant for this discussion. I could probably spend some time throwing a query together, but I'd prefer to ask the questions before helping with a query since it would get complicated quickly. T

RE: PCORnet DRN - Site Contacts C4

You have my contact info correct Laurel. WISC (UW Madison / UW Health) analyst for PopMedNet: Keith Wanta kwa...@uwhealth.org From: gpc-dev-boun...@listserv.kumc.edu [mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Bos, Angela Sent: Wednesday, September 17, 20

RE: [gpc-informatics] #139: insurance status

...@listserv.kumc.edu] on behalf of Wanta Keith M [kwa...@uwhealth.org] Sent: Thursday, July 03, 2014 3:38 PM To: Dan Connolly; Ahuja, Monika; gpc-dev@listserv.kumc.edu Subject: RE: [gpc-informatics] #139: insurance status Hi Dan, I'm going to touch base with Nathan Wilson (our analyst/ontologist) and h

RE: [gpc-informatics] #139: insurance status

y, July 03, 2014 1:30 PM To: Ahuja, Monika; Wanta Keith M; gpc-dev@listserv.kumc.edu Subject: RE: [gpc-informatics] #139: insurance status Thanks, everybody. I don't think I completely understand what's going on, but I found insurance company names and such in there. The query below ga

RE: [gpc-informatics] #139: insurance status

And if you wanted to JOIN on the actual encounter fact, take a look at charge slip number. From: gpc-dev-boun...@listserv.kumc.edu [gpc-dev-boun...@listserv.kumc.edu] on behalf of Wanta Keith M [kwa...@uwhealth.org] Sent: Thursday, July 03, 2014 12:30 PM

RE: [gpc-informatics] #139: insurance status

This would be accurate from an HB perspective, for clinical charges that get routed via the Charge Router. If we're referring to Epic. I can't speak for Cerner or Cattails. For PB charges, the CLARITY_TDL (view) is what is generally used. This view contains records from tables CLARITY_TDL_TR

RE: [gpc-informatics] #139: insurance status

This depends on whether we are talking about Professional Billing or Hospital Billing. Generally charges are grouped together by admission for HB, so you would check the coverage status for the admission. DNB means do not bill. And there can be multiple coverages depending on the admission, o

Re: [Gpc-dev] GPC De-Identification Plan - i2b2 re-identification process

Phillip, at your organization, is identified data built based on real time data (data mart built at the time of the identified data request)? Or is the identified data loaded synchronously with the de-identified data each time the ETL process occurs for each i2b2 load? It would seem that in ma

Re: optional columns in i2b2 dimension tables RE: Minutes of GPV-DEV call 20140128

tware Development [mailto:GPC-DEV@LISTSERV.KUMC.EDU] On Behalf Of Wanta Keith M Sent: Tuesday, February 04, 2014 1:42 PM To: GPC-DEV@LISTSERV.KUMC.EDU<mailto:GPC-DEV@LISTSERV.KUMC.EDU> Subject: Re: optional columns in i2b2 dimension tables RE: Minutes of GPV-DEV call 20140128 Jim, that is co

Re: optional columns in i2b2 dimension tables RE: Minutes of GPV-DEV call 20140128

Jim, that is correct about building multiple paths per concept, because of the multiple inheritance/multiple generalization. In a sense, you end up with multiple concepts (based on the number of parents) in the CONCEPT_DIMENSION. UW is also on 1.6. -Keith From: Greater Plains Collaborative S