RE: Medication Mapping Issue (organization by ingredient)
The change in hierarchy (adding ingredient) Phillip proposed would solve my problem where I can easily grab all tamoxifen or levofloxacin medications. Mei From: gpc-dev-boun...@listserv.kumc.edu [mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Dan Connolly Sent: Monday, April 06, 2015 2:48 PM To: Phillip Reeder; Apathy,Nate; Russ Waitman Cc: Tamara McMahon; gpc-dev@listserv.kumc.edu Subject: RE: Medication Mapping Issue (organization by ingredient) Phillip, Maybe it's obvious to people who deal with this stuff regularly, but I don't see how adding in the ingredient level makes for a more useful hierarchy. Would you please elaborate? What sort of thing would a researcher do that's easier if the terms are organized by ingredient? A researcher here at KUMC just asked: ... in HERON, for example, the drug levofloxacin can be found in different paths as Levofloxacin 500 mg PO TAB or Levofloxacin IN DJW. For this project, dosage or forms of administration is not important, for instance oral tablet or injection of the same drug should be considered together. So I need to an algorithm to automatically treat levofloxacin 500 mg PO TAB or Levofloxacin IN DJW as just Levofloxacin. Would organizing by ingredient let this researcher search for just Levofloxacin more easily? Is the UTSW med hierarchy on babel already organized this way? When I search the one with lots of counts, I get dozens of hits for Levofloxacin and they don't seem to have a common ancestor. Under NCATS they sort of have a common ancestor, but it seems to have two homes in the hierarchy: dimcode\NCATS\Medications\N010574\N029216\N029216\N029218\N029327\82122\/dimcode tooltip\NCATS\Medications\Ophthalmic agents\Ophthalmic agents\Anti-infective,topical ophthalmic\Antibacterials,topical ophthalmic\Levofloxacin/tooltip dimcode\NCATS\Medications\N010574\N029074\N183553\82122\/dimcode tooltip\NCATS\Medications\Antimicrobials\Antimicrobials\Quinolones\Levofloxacin/tooltip same code, 82122, in both cases. I guess it's both an Opthalmic and an Antimicrobial? Here's hoping I find time to ask this researcher if that NCATS hierarchy would be more natural to work with. -- Dan From: Phillip Reeder [phillip.ree...@utsouthwestern.edu] Sent: Thursday, April 02, 2015 2:47 PM To: Dan Connolly; Apathy,Nate; Russ Waitman Cc: gpc-dev@listserv.kumc.edumailto:gpc-dev@listserv.kumc.edu; Meyer,Aaron Subject: Re: Medication Mapping Issue (standardization measurement framework, milestone:data-quality3) If we really want to reconsider the design, I'd propose adding in the ingredient level to the hierarchy, making it for example: ANTINEOPLASTICS\ ANTINEOPLASTIC HORMONES\Tamoxifen\Tamoxifen Oral Solution ANTINEOPLASTICS\ ANTINEOPLASTIC HORMONES\Tamoxifen\Tamoxifen Oral Tablet Basically it groups the SCDFs by ingredient so that the user can easily grab all Tamoxifen medications. And for UTSW, with medications that are simply Tamoxifen Oral without the tablet/solution/dosage, I can map them to the ingredient level, instead of at the SCDF level. And it would be inline with how the NCATS/ACT project has their terminology created. This would probably be a more disruptive of a change in the terminology than simply adding the SCD level, but it does make for a more useful hierarchy. Phillip ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
April 7 gpc-dev agenda and meeting notes
gpc-dev April 7 noteshttps://docs.google.com/document/d/1ZljGo18My60RHmy1ZRZLRK8aNOWIw6wapCkCa1SfW6A/edit?usp=sharing include proposed agenda: 1. Convene, take roll, review records and plan next meeting. * Meeting ID and access code: 817-393-381https://global.gotomeeting.com/meeting/join/817393381; call +1 (571) 317-3131 * meeting notes (#12https://informatics.gpcnetwork.org/trac/Project/ticket/12): previous notes OK? today's scribe: Prakash / UIOWA * roll: all 10 DevTeamshttps://informatics.gpcnetwork.org/trac/Project/wiki/DevTeams represented? comments on the agenda? * KUMC, CMH, UIOWA, WISC, MCW, MCRF, UMN, UNMC, UTHSCSA, UTSW, (MU), (IU) * recent tickets opened/closed, FYI: * #263 (Adaptable cohort query design and administration) createdhttps://informatics.gpcnetwork.org/trac/Project/ticket/263 * #265 (QA ER/PR status and other Breast Cancer data elements) createdhttps://informatics.gpcnetwork.org/trac/Project/ticket/265 * #103 (subject of observation (e.g. maternal findings relevant to child)) closed https://informatics.gpcnetwork.org/trac/Project/ticket/103#comment:10 wontfix * #141 (differentiate well-child visits, sick visits, and chronic visits ...) closedhttps://informatics.gpcnetwork.org/trac/Project/ticket/141#comment:10 * #33 (data elements for obesity cohort characterization) closedhttps://informatics.gpcnetwork.org/trac/Project/ticket/33#comment:37 * Next meeting: 14 Apr. recruit Scribe, recruit chair 2. Q1 2015 Quality Queryhttp://listserv.kumc.edu/pipermail/gpc-dev/2015q1/001424.html * Angela: send a diff of changes at UTHSCSA. done: ticket:238#comment:11https://informatics.gpcnetwork.org/trac/Project/ticket/238#comment:11, f8f4a58https://bitbucket.org/njgraham/pcori-qa/commits/f8f4a5819a186c2f94907d37f04dcc0beed59207 * sites need to do their part in the next week so we can review and write up the results on time. expect ~1day work at each site * #174https://informatics.gpcnetwork.org/trac/Project/ticket/174 federated login for GPC data storehttps://informatics.gpcnetwork.org/trac/Project/ticket/174 3. Milestone: bc-survey-cohort-defhttps://informatics.gpcnetwork.org/trac/Project/milestone/bc-survey-cohort-def site governance, workflow #264https://informatics.gpcnetwork.org/trac/Project/ticket/264 4. ALS Survey: redcap usage plan in #208https://informatics.gpcnetwork.org/trac/Project/ticket/208#comment:5 * UTSW offers to test * Angela: to can share documentation. done: Redcap survey link managementhttp://listserv.kumc.edu/pipermail/gpc-dev/2015q1/001454.html 5. Milestone: obesity-survey-defhttps://informatics.gpcnetwork.org/trac/Project/milestone/obesity-survey-def * WISC (at least) to report experience on steps 1, 2 of Obesity query v0.2 (#252) * #210https://informatics.gpcnetwork.org/trac/Project/ticket/210 BMI percentile: WISC ready to run queries? CMH/MU? MCW? MCRF? 6. Med ontology (re-open #78https://informatics.gpcnetwork.org/trac/Project/ticket/78?) 7. #228https://informatics.gpcnetwork.org/trac/Project/ticket/228 DataBuilder output not directly analyzablehttps://informatics.gpcnetwork.org/trac/Project/ticket/228 * Note recent related work: April 1, 2015: Gutting Fish and Introduction to Programminghttps://informatics.gpcnetwork.org/trac/Project/wiki/HERONIndependentStudy#April12015:GuttingFishandIntroductiontoProgramming in HERONIndependentStudyhttps://informatics.gpcnetwork.org/trac/Project/wiki/HERONIndependentStudy class. 8. devtools updates: Babel DB web IDE (time permitting) * #261 (Babel SQL DB Account for metadata) closedhttps://informatics.gpcnetwork.org/trac/Project/ticket/261#comment:2 * #260 (Can't log in to babel rep_admin page) createdhttps://informatics.gpcnetwork.org/trac/Project/ticket/260 -- Dan ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
RE: Obesity query v0.2
Counts for Marshfield: 1a: 103,124 1b: 153,005 Thanks, Laurel From: gpc-dev-boun...@listserv.kumc.edu [mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Alex Bokov Sent: Tuesday, March 31, 2015 3:59 AM To: gpc-dev@listserv.kumc.edu Subject: Obesity query v0.2 Hello, colleagues. Here is the updated obesity query. The main document is the PDF. I'm including the HTML generated by Print Query in case it's helpful, but I recommend reading the PDF. In principle, every site should be able to run steps I and II of this document and report back their counts. Please let us know what roadblocks you run into if you find this is not the case. Steps III and IV of this document are still alpha. The counts for UTHSCSA are: 30,500 adults meeting selection criteria 5,222 children and young adults meeting selection criteria (estimating this to be about 4,400 unique households) Thanks. --Alex __ The contents of this message may contain private, protected and/or privileged information. If you received this message in error, you should destroy the e-mail message and any attachments or copies, and you are prohibited from retaining, distributing, disclosing or using any information contained within. Please contact the sender and advise of the erroneous delivery by return e-mail or telephone. Thank you for your cooperation. ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: Medication Mapping Issue (organization by ingredient)
At UMN we received the NDC drug code from Epic and mapped it to the RxNorm CUI at the most granular level possible using the NLM API. We also created a set of rules when the NCD was missing of how to map to RxNorm. We then used NDF-RT to categorize medications. So levofloxacin displays in i2b2 as follows AM000] ANTIMICROBIALS - 729065 [AM400] QUINOLONES - 171011 Levofloxacin Injectable Product - 16194 Levofloxacin Oral Liquid Product - 1173 Levofloxacin Oral Product - 63357 Under each of the Levofloxacin categories are more detailed drugs I've missed [image: Inline image 1] https://i2b2.ahc.umn.edu/webclient/# https://i2b2.ahc.umn.edu/webclient/# Bonnie L. Westra, PhD, RN, FAAN, FACMI Associate Professor, University of Minnesota, School of Nursing Institute for Health Informatics Director, Center for Nursing Informatics Location - WDH 6-155 P - 612-625-4470, Fax - 612-625-7091 email - westr...@umn.edu Mail - WDH 5-140, 308 Harvard St SE, Minneapolis, MN 55455 On Mon, Apr 6, 2015 at 2:47 PM, Dan Connolly dconno...@kumc.edu wrote: Phillip, Maybe it's obvious to people who deal with this stuff regularly, but I don't see how adding in the ingredient level makes for a more useful hierarchy. Would you please elaborate? What sort of thing would a researcher do that's easier if the terms are organized by ingredient? A researcher here at KUMC just asked: ... in HERON, for example, the drug levofloxacin can be found in different paths as Levofloxacin 500 mg PO TAB or Levofloxacin IN DJW. For this project, dosage or forms of administration is not important, for instance oral tablet or injection of the same drug should be considered together. So I need to an algorithm to automatically treat levofloxacin 500 mg PO TAB or Levofloxacin IN DJW as just Levofloxacin. Would organizing by ingredient let this researcher search for just Levofloxacin more easily? Is the UTSW med hierarchy on babel already organized this way? When I search the one with lots of counts, I get dozens of hits for Levofloxacin and they don't seem to have a common ancestor. Under NCATS they sort of have a common ancestor, but it seems to have two homes in the hierarchy: dimcode\NCATS\Medications\N010574\N029216\N029216\N029218\N029327\82122\/dimcode tooltip\NCATS\Medications\Ophthalmic agents\Ophthalmic agents\Anti-infective,topical ophthalmic\Antibacterials,topical ophthalmic\Levofloxacin/tooltip dimcode\NCATS\Medications\N010574\N029074\N183553\82122\/dimcode tooltip\NCATS\Medications\Antimicrobials\Antimicrobials\Quinolones\Levofloxacin/tooltip same code, 82122, in both cases. I guess it's both an Opthalmic and an Antimicrobial? Here's hoping I find time to ask this researcher if that NCATS hierarchy would be more natural to work with. -- Dan -- *From:* Phillip Reeder [phillip.ree...@utsouthwestern.edu] *Sent:* Thursday, April 02, 2015 2:47 PM *To:* Dan Connolly; Apathy,Nate; Russ Waitman *Cc:* gpc-dev@listserv.kumc.edu; Meyer,Aaron *Subject:* Re: Medication Mapping Issue (standardization measurement framework, milestone:data-quality3) If we really want to reconsider the design, I’d propose adding in the ingredient level to the hierarchy, making it for example: ANTINEOPLASTICS\ ANTINEOPLASTIC HORMONES\Tamoxifen\Tamoxifen Oral Solution ANTINEOPLASTICS\ ANTINEOPLASTIC HORMONES\Tamoxifen\Tamoxifen Oral Tablet Basically it groups the SCDFs by ingredient so that the user can easily grab all “Tamoxifen” medications. And for UTSW, with medications that are simply “Tamoxifen Oral” without the tablet/solution/dosage, I can map them to the ingredient level, instead of at the SCDF level. And it would be inline with how the NCATS/ACT project has their terminology created. This would probably be a more disruptive of a change in the terminology than simply adding the SCD level, but it does make for a more useful hierarchy. Phillip ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: Question about Cerner
Hi Rachel, I haven’t looked but ccing those on the gpc-dev group, Russ On Apr 6, 2015, at 9:46 PM, Rachel Hess rachel.h...@hsc.utah.edumailto:rachel.h...@hsc.utah.edu wrote: Hi Russ, Have you identified any way to get dispensing data out of cerner. We found the right tables in Epic but not cerner. Rachel Russ Waitman, PhD Director of Medical Informatics Assistant Vice Chancellor for Enterprise Analytics Associate Professor, Department of Internal Medicine University of Kansas Medical Center, Kansas City, Kansas 913-945-7087 (office) rwait...@kumc.edumailto:rwait...@kumc.edu http://www.kumc.edu/ea-mi/ http://informatics.kumc.eduhttp://informatics.kumc.edu/ http://informatics.gpcnetwork.org – a PCORNet collaborative ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
[gpc-informatics] #266: CDM V3 Development for Phase 2
#266: CDM V3 Development for Phase 2 ---+--- Reporter: campbell | Owner: campbell@… Type: design-issue | Status: new Priority: major | Milestone: data-domains3 Component: data-stds | Keywords: CDM V3 Blocked By:| Blocking: ---+--- DSSNI meeting today discussed development process for CDM V3 which was stated as required at beginning of phase2. Slide set enclosed. -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/266 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] #232: Q1 2015 QA exercise
Reminder: materials for the Tuesday teleconference agenda are due at T-24hrs, i.e. 11am Monday. Recall from last weekhttp://listserv.kumc.edu/pipermail/gpc-dev/2015q1/001450.html: * ... http://listserv.kumc.edu/pipermail/gpc-dev/2015q1/001424.html * Q1 2015 Quality Queryhttp://listserv.kumc.edu/pipermail/gpc-dev/2015q1/001424.html * ... * Tom: OK; please everybody share such diffs/experience; perhaps it merits changes to GPC ontologies. * Dan: mid-April milestone due date sound OK? So sites need to do their part in the next week so we can review and write up the results on time. Tom: I expect ~1day work at each site, so don’t delay! * Jim M: can’t be sure UNMC has bandwidth for that timeline; HH on holiday this week. I see an experience report from UTHSCSAhttps://informatics.gpcnetwork.org/trac/Project/ticket/238#comment:11 and a few questions from other sites. So we're at 1 for 10, Tom? Or did I miss some? Or did they report experience privately? If anyone has experience they haven't shared with the group, NOW is the time. Anything from we have our results complete and we went to upload them but failed to log in to REDCap to we tried to run the query but all we got was a pile of syntax errors is welcome (though only one site, UNMC, said they didn't have bandwidth to spend up to one day working through syntax errors). But please don't wait 'till the teleconference to share your status. -- Dan From: Munns, Michael B [mike.mu...@unmc.edu] Sent: Thursday, April 02, 2015 9:53 AM To: Tom Mish; gpc-dev@listserv.kumc.edu; Dan Connolly Cc: Bhargav Adagarla; John Steinmetz Subject: RE: [gpc-informatics] #232: Q1 2015 QA exercise In the create script for the obesity active patients (Q1_2015_GPC_OBESITY_ACTIVE_PATIENTS) the where condition for the BMI part it has ” concept_path = '\GPC\Vital Signs\LOINC:39156-5\' “ We do not have the GPC metadata installed. We do have BMI under PCORI that does have facts. Can that be used instead? Should we download and install GPC metadata? Michael Munns Database Analyst 402-559-3821 From: gpc-dev-boun...@listserv.kumc.edu [mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Tom Mish Sent: Thursday, April 02, 2015 8:15 AM To: gpc-dev@listserv.kumc.edu; dconno...@kumc.edu Cc: badaga...@kumc.edu; jsteinm...@kumc.edu Subject: Re: [gpc-informatics] #232: Q1 2015 QA exercise A new version of the query was updated. * Jim moved the comments/version history section to a separate document * The changes in this are to the output (variable names and ordering) produced to make it easier to import into redcap. -TM 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
