RE: [gpc-informatics] #91: i2b2 metadata for Diagnoses Modifiers for data attribution
This is worth a copy to all of gpc-dev... Bonus points to anybody who can take a quick look and send feedback by email before today's teleconference. -- Dan From: GPC Informatics [d...@madmode.com] Sent: Tuesday, December 02, 2014 9:42 AM To: Dan Connolly; Nathan Graham; nwil...@uwhealth.org; huhick...@nebraskamed.com; Russ Waitman; nate.apa...@cerner.com Cc: campb...@unmc.edu Subject: Re: [gpc-informatics] #91: i2b2 metadata for Diagnoses Modifiers for data attribution #91: i2b2 metadata for Diagnoses Modifiers for data attribution -+--- Reporter: dconnolly| Owner: ngraham Type: enhancement | Status: closed Priority: major| Milestone: initial-data-domains Component: data-stds| Resolution: fixed Keywords: | Blocked By: 37, 90 Blocking: | -+--- Comment (by nateapathy): For our discussion today, I've attached the updated metadata per Phillip Reeder's suggestion for dx modifiers. The attachment has four tabs. gpc_diagnosis_modifiers is the original metadata from Nathan Wilson that is on Babel now. Reeder Dx Modifiers is Phillip's suggestions in their original form. NateA_CMH - i2b2 Metadata v1 is my interpretation of Phillip's suggestions into metadata for loading into Babel. NateA_CMH - i2b2 Metadata v2 is my suggestion for how to redesign the first 11 rows of the third tab. Rows 2-19 on the fourth tab are my changes to the modifier hierarchy, largely based on the assumption that researchers care far more about primary vs. non-primary than they do about the source of that data, and therefore will most heavily use the two terms in rows 2 and 11 of that sheet. I also include a source of Claims data, since Laurel pointed out two weeks ago that Marshfield has that as a separate source from Billing or EMR-derived diagnoses. The best next step is probably to load both into Babel (provided the additional fields for applied_path, etc. are correctly formatted) and compare. -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/91#comment:24 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
RE: gpc-dev agenda 2 Dec
oops... google doc for gpc-dev 2 Dechttps://docs.google.com/document/d/1MJZ2GMP1EF-Zf9op2bO-XreWGlk9HCywMvAIC400_vc/edit#, really this time. From: Dan Connolly Sent: Monday, December 01, 2014 12:05 PM To: gpc-dev@listserv.kumc.edu Subject: gpc-dev agenda 2 Dec Note to the scribe: I already made the google doc for gpc-dev 2 Dechttps://informatics.gpcnetwork.org/trac/Project/report/11?sort=datemax=100asc=1page=1. 1. Convene, take roll, review records and plan next meeting * Meeting ID and access code: 686-845-717https://global.gotomeeting.com/meeting/join/686845717; call +1 (267) 507-0008 * meeting notes (#12https://informatics.gpcnetwork.org/trac/Project/ticket/12): Nov 18 notes OK? today's scribe: ?? * roll: all 10 DevTeamshttps://informatics.gpcnetwork.org/trac/Project/wiki/DevTeams represented? comments on the agenda? * Today’s agenda is organized by site, around the work-by-site reporthttps://informatics.gpcnetwork.org/trac/Project/report/11?sort=datemax=100asc=1page=1. * KUMC, CMH, UIOWA, WISC, MCW, MCRF, UMN, UNMC, UTHSCSA, UTSW * regrets: Tom Mish @ WISC * next meeting: Dec 9. scribe volunteer? alternate chair? * Note new GotoMeeting coordinates in-coming 2. Thu-Fri 22-23 Jan 2015 in San Antonio HackathonTwohttps://informatics.gpcnetwork.org/trac/Project/wiki/HackathonTwo * remote participation * reminder: fill out the attendance surveyhttps://redcap.uthscsa.edu/REDCap/surveys/?s=qcLVmeAfzt%22%3EHackathonTwo 3. Roadmap: over-driving our headlights 4. CMH * #90 (Diagnoses Modifiers for data attribution) reopenedhttps://informatics.gpcnetwork.org/trac/Project/ticket/90#comment:6 * Nate @ CMH will take a shot at integrating feedback so far and supplying metadata in i2b2 format. 5. KUMC * Ticket #197 (REDCap data dictionary for ALS survey) createdhttps://informatics.gpcnetwork.org/trac/Project/ticket/197 * #160 GPC, CDM refresh * #145 transform i2b2 to CDM * #109 CDM as i2b2 metadata * #192 GPC REDCap for governance workflow * #159 GPC REDCap for data sharing * #175 federated login * #124 tool to copy query between i2b2 sites * #185 Tumor Registry Ontology * #172 UMN cancer tumor registry counts to babel * #178 last visit - blocked by #155 Encounter types 6. MCRF * due date for PopMedNed nodes? (#161 etc.) milestone for DRN Query goalhttps://informatics.gpcnetwork.org/trac/Project/wiki/KeyGoalTracking#drn-cdm-query? 7. MCW * #87 data builder - milestone:bc-survey-cohort-def due Dec 16 8. UIOWA * #193 quality measures for Obesity Cohort * notes from Prakashhttps://informatics.gpcnetwork.org/trac/Project/ticket/193#comment:9 * #168 tumor registry? * #162 PopMedNet (see MCRF) 9. UMN * #186 query by numerical constraints - on milestone:data-domains2, due Nov 30. Better guestimate? * #158 usable view of LOINC lab terms * #119 Federated breast cancer query with manual term alignment * fwd ref #87 under MCW * #139 Insurance status 10. UNMC * #67 demographics * #186 (Querying age by numerical constraints)https://informatics.gpcnetwork.org/trac/Project/ticket/186#comment:1 * PR: can we have a GPC Demographics folder on babel like the others? * HH: yes, I will move to creation of GPC demographics Justin will verify * Justin: age unit conversion days/years/etc.: performance impact? * HH: we haven’t seen any performance penalty due to unit conversion. facts are stored in days. Conversion seems to happen before the SQL is generated. * HH to send generated SQL * HH will point to documentation and will experimentally flip the server side conversion flag to measure any performance difference * #193 quality measures for Obesity Cohort * notes from Prakashhttps://informatics.gpcnetwork.org/trac/Project/ticket/193#comment:9 * #155 Encounter types, #120 encounter attributes * #186 age * #182 LOINC in CDM 11. UTHSCSA * #173 REDCap for ALS * GPC Terminology V1 (medication modifiers)http://listserv.kumc.edu/pipermail/gpc-dev/2014q4/000732.html #199 * Alex to follow up by email w.r.t. requirements for medication modifiers. * #33 obesity cohort characterization (tracked by MethodsCore) 12. UTSW * #165 PopMedNed node 13. WISC * 1st quarterly QA results: #180https://informatics.gpcnetwork.org/trac/Project/ticket/180, #188 closedhttps://informatics.gpcnetwork.org/trac/Project/ticket/188#comment:2 * #196 (Should the active patient be based on visits or encounters?) created by
Re: [gpc-informatics] #158: usable view of LOINC lab terms
#158: usable view of LOINC lab terms -+ Reporter: rwaitman | Owner: budh0007 Type: enhancement | Status: assigned Priority: major| Milestone: data-domains3 Component: data-stds| Resolution: Keywords: | Blocked By: Blocking: 68 | -+ Comment (by jmcclay): Comments from Scott Campbell at UNMC I have created a hierarchical view of the Lab LOINC items for approximately 2000 of the 2500 terms used at UNMC. This also includes orderable codes (i.e. batteries) and performable codes (tests/results). The hierarchy is based on LOINC class and refined by UNMC departments and logical groupings. Note: we have generalized the UNMC departments into categories that should make sense to most medical centers. Jim Campbell is reviewing my categories to ensure that they are in-line with a clinician’s perspective. Based on Jim’s feedback, I will refine and issue a testable code set to Hubert. -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/158#comment:13 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
Re: [gpc-informatics] #87: Deploy, document R Data Builder demo service
#87: Deploy, document R Data Builder demo service --+--- Reporter: dconnolly | Owner: gkowalski Type: task | Status: assigned Priority: major | Milestone: bc-survey-cohort-def Component: data-sharing | Resolution: Keywords:| Blocked By: 134, 179 Blocking: 119 | --+--- Comment (by dconnolly): George, the chrome fix is ec3328396f9f Thu Nov 06. It's been on elephant for some time. -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/87#comment:69 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
how to preserve saved queries on i2b2 refresh?
I didn't notice this question in today's meeting notes: * Question: on re-deploy to i2b2, how to preserve saved queries? Do patient IDs, etc change. Does i2b2 re-run saved queries or use stored patient sets with old ids? Here's hoping for time to answer... or maybe Nathan will beat me to it. grumble. We have extensive internal documentation on this issue; I wish I could just point you to it. -- Dan ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #90: Diagnoses Modifiers for data attribution
#90: Diagnoses Modifiers for data attribution --+ Reporter: campbell | Owner: lv Type: design-issue | Status: assigned Priority: major | Milestone: data-domains2 Component: data-stds | Resolution: Keywords:| Blocked By: Blocking: 70, 91, 120 | --+ Changes (by dconnolly): * owner: nateapathy = lv Comment: from today's teleconference (#12): Laurel: OK, I can look at the diagnosis modifiers Nate put together within the spreadsheet and give some feedback. DC: Hubert, Nathan flip coins to load into Babel -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/90#comment:19 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
RxNorm metadata
I am working on the RxNorm metadata using the KU epic_med_mapping.sql script. In there is the creation of a table rxnorm.clarity_name_to_rxcui_medex and then a second table is created off of that. I don't see where the rxnorm.clarity_name_to_rxcui_medex gets populated from. There is a link a medex tool in the script. What am I missing? Michael Munns Database Analyst 402-559-3821 The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender. ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
RE: RxNorm metadata
Michael, I think you're looking at obsolete code (well, obsolete with respect to the current KUMC ETL code anyway). The medication mapping code was recently rewrittenhttp://listserv.kumc.edu/pipermail/gpc-dev/2014q4/000655.html and the part you asked about was removed. The main design change implemented during the rewrite was the paths/full names are comprised of the RxNorm AUIs/local medication IDs (for example, \i2b2\Medications\RXAUI:3257490\RXAUI:3257495\MEDICATION_ID:129272\). As far as I know we plan to use the AUI-based paths as the GPC standard for medications (see also gpc-dev conference call notes for 2014.10.28http://listserv.kumc.edu/pipermail/gpc-dev/attachments/20141028/554bffae/attachment-0001.pdf). Before the rewrite the paths were a concatenation of the medication/NDF-RT names which got really long and messy. I think you'll also find that the new code is much easier to read and better documented (hopefully). For the newer code see epic_med_mapping.sqlhttps://informatics.kumc.edu/work/browser/heron_load/epic_med_mapping.sql on the KUMC Informatics wiki. Or, update to a newer version of the KUMC ETL code from the GPC shared repository (see MultiSiteDevhttps://informatics.gpcnetwork.org/trac/Project/wiki/MultiSiteDev). The GPC tickets relevant to the medication mapping rewrite include #78https://informatics.gpcnetwork.org/trac/Project/ticket/78, #181https://informatics.gpcnetwork.org/trac/Project/ticket/181, and #152https://informatics.gpcnetwork.org/trac/Project/ticket/152. Regards, Nathan From: gpc-dev-boun...@listserv.kumc.edu [mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Munns, Michael B Sent: Tuesday, December 02, 2014 3:59 PM To: gpc-dev@listserv.kumc.edu Subject: RxNorm metadata I am working on the RxNorm metadata using the KU epic_med_mapping.sql script. In there is the creation of a table rxnorm.clarity_name_to_rxcui_medex and then a second table is created off of that. I don't see where the rxnorm.clarity_name_to_rxcui_medex gets populated from. There is a link a medex tool in the script. What am I missing? Michael Munns Database Analyst 402-559-3821 The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender. ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
