RE: GPC 2nd quarter QA design looks nice!
Let us know how it goes, I have had to rewrite a couple of queries, one that took 17 min to update 3 rows, one due to our differences. I am now having another that will not return. Has anyone else had issues on an Oracle DB? Michael Munns Database Analyst 402-559-3821 From: gpc-dev-boun...@listserv.kumc.edu [mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Nathan Graham Sent: Thursday, July 23, 2015 10:47 AM To: GPC-DEV@LISTSERV.KUMC.EDU; Thomas Mish; James Van Schyndle (jvanschyn...@wisc.edu) Subject: GPC 2nd quarter QA design looks nice! Tom/James, I've just started working on running the GPC Q2 quality queries here at KUMC and wanted to say that the design looks pretty slick! I really like having the concept paths, codes, etc. split out into their own xlsx/csv file that loads nicely into REDCap to begin with. I think that'll make it a lot easier to port to various sites. Now, on to actually gathering results... Refs: * WISC BitBucket: gpc-2015-q2-qa-fileshttps://bitbucket.org/jvanschyndle/gpc-2015-q2-qa-files * My fork on BitBucket: gpc-2015-q2-qa-fileshttps://bitbucket.org/njgraham/gpc-2015-q2-qa-files Regards, Nathan 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: GPC-Dev Agenda 4-21
UNMC 6.4.4 Michael Munns Database Analyst 402-559-3821 From: gpc-dev-boun...@listserv.kumc.edu [mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Bos, Angela Sent: Monday, April 20, 2015 5:44 PM To: Dan Connolly; Apathy, Nate; gpc-dev@listserv.kumc.edu Subject: RE: GPC-Dev Agenda 4-21 Sorry for the late request, but could we add the following topic for the obesity survey: What version of Redcap are you running? How soon could your site potentially achieve 6.1.x? We would like to use Redcap “access code” functionality introduced in 6.1.0. Used in conjunction with participant lists, it allows a user to enter a general survey URL, then requires them to enter a non-case-sensitive 9-character access code to go to their unique survey link. -Angela | UTHSCSA From: gpc-dev-boun...@listserv.kumc.edumailto:gpc-dev-boun...@listserv.kumc.edu [mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Dan Connolly Sent: Monday, April 20, 2015 3:30 PM To: Apathy,Nate; gpc-dev@listserv.kumc.edumailto:gpc-dev@listserv.kumc.edu Subject: RE: GPC-Dev Agenda 4-21 Thanks for getting the ball rolling, Nate. I went over our business and made some adjustments. Note in particular that I dropped items where I couldn't find an update shared with the group. Reminder: if anyone wants something on the agenda, please send mail or update a ticket before 10am Monday. You can, of course, ask to have something added when we review the agenda at the beginning of the call, but things work better if materials are available in advance. 1.Convene, take roll, review records and plan next meeting. a.Meeting ID and access code: 817-393-381https://global.gotomeeting.com/meeting/join/817393381; call +1 (571) 317-3131 b.roll: all 10 DevTeamshttps://informatics.gpcnetwork.org/trac/Project/wiki/DevTeams represented? i.KUMC, CMH, UIOWA, WISC, MCW, MCRF, UMN, UNMC, UTHSCSA, UTSW, (MU), (IU) ii.Reminder - put institution after your name on the GoToMeeting (preferences) c.meeting notes (#12https://informatics.gpcnetwork.org/trac/Project/ticket/12): previous notes OK? today's scribe: Nate A (Cerner/CMH) comments on the agenda? chair dropped items where no update was available as of ~T-24hrs i.recent tickets opened/closed FYI: 1.#165:https://informatics.gpcnetwork.org/trac/Project/ticket/165 PopMedNet @ UTSW - closed 2.#270http://informatics.gpcnetwork.org/trac/Project/ticket/270 - Port Q1 QA query to Oracle opened 3.note also recent ticket comments reporthttps://informatics.gpcnetwork.org/trac/Project/report/13 d.Next Meeting April 28th: scribe? 2.#78 Shared GPC RxNORM/NDFRT medications ontologyhttps://informatics.gpcnetwork.org/trac/Project/ticket/78 re-opened; also #236https://informatics.gpcnetwork.org/trac/Project/ticket/236 a.Nate sent list of non-SCDF codeshttp://listserv.kumc.edu/pipermail/gpc-dev/2015q2/001525.html to group 1.#158 Usable LOINC Labs - March 27 commenthttps://informatics.gpcnetwork.org/trac/Project/ticket/158#comment:28 proposes that Jan 19 detailshttps://informatics.gpcnetwork.org/trac/Project/ticket/158#comment:20 suffice a.KUMC’s experience is positive so far, though we haven’t released b.is what’s on babel consistent with Jan 19 details? 1. milestone:data-quality3https://informatics.gpcnetwork.org/trac/Project/milestone/data-quality3 a.#270 (Port Q1 QA query to Oracle) closedhttps://informatics.gpcnetwork.org/trac/Project/ticket/270#comment:2 1.milestone:bc-survey-cohort-def (depgraphhttps://informatics.gpcnetwork.org/trac/Project/depgraph/ticket/227): a.#271https://informatics.gpcnetwork.org/trac/Project/ticket/271 IRB-wait b.#264https://informatics.gpcnetwork.org/trac/Project/ticket/264 confirm governance and workflow: ~7 sites responded 1.Milestone: obesity-survey-defhttps://informatics.gpcnetwork.org/trac/Project/milestone/obesity-survey-def a.#252 test results from wischttps://informatics.gpcnetwork.org/trac/Project/ticket/252#comment:5 1. milestone:cohort-char1https://informatics.gpcnetwork.org/trac/Project/milestone/cohort-char1 a.#258https://informatics.gpcnetwork.org/trac/Project/ticket/258 volunteer to take a whack at breast cancer treatment from NAACCR? 1.#242https://informatics.gpcnetwork.org/trac/Project/ticket/242 - Nate A. asks Apr 16 “where can we find the necessary attachments and code to attempt this? ...” 1. milestone:data-domains3 currently has no due date; is that OK? are there any customers waiting? -- Dan From: gpc-dev-boun...@listserv.kumc.edumailto:gpc-dev-boun...@listserv.kumc.edu [gpc-dev-boun...@listserv.kumc.edu] on behalf of Apathy,Nate [nate.apa...@cerner.com] Sent: Monday, April 20, 2015 9:50 AM To:
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
RE: RxNorm metadata
I am getting closer, the KU and the UTSW metadata on Bable both have modifiers, the GPC does not. I what do I need to do to end up with KUMC style modifiers? Michael Munns Database Analyst 402-559-3821 From: Nathan Graham [mailto:ngra...@kumc.edu] Sent: Monday, December 08, 2014 10:45 AM To: Munns, Michael B; gpc-dev@listserv.kumc.edu Subject: RE: RxNorm metadata We used the exclude modifiers table to remove the modifiers from things that didn't really need them like NO HOME MEDICATIONS, EMPTY CONTAINER, PLASTIC BAG, MISCELLANEOUS MEDICAL SUPPLY MISC, etc. These are things we put directly under the top level Medications folder as we didn't know where else to put them. Maybe it could be argued that some of these don't have much research value - I don't know. But, many of these concepts had lots of patient/fact counts so we didn't want to just exclude them. At least the NO HOME MEDICATIONS item was specifically discussed and deemed worth addinghttps://informatics.kumc.edu/work/ticket/1775. Our (KUMC) general approach is bring in everything - that way, we can all can see what we have available. If/when we find that things can be improved (based on user feedback, etc) we can do that later. From: gpc-dev-boun...@listserv.kumc.edumailto:gpc-dev-boun...@listserv.kumc.edu [mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Munns, Michael B Sent: Monday, December 08, 2014 10:30 AM To: gpc-dev@listserv.kumc.edumailto:gpc-dev@listserv.kumc.edu Subject: FW: RxNorm metadata We can put them on the mailing list. We did end up creating an empty table for the manual curation, also a empty table for the exclude modifiers. Michael Munns Database Analyst 402-559-3821 From: Nathan Graham [mailto:ngra...@kumc.edu] Sent: Monday, December 08, 2014 10:18 AM To: Munns, Michael B Subject: RE: RxNorm metadata Michael, I'd really like to keep these conversations on the gpc-devhttp://listserv.kumc.edu/pipermail/gpc-dev/ mailing list (sign up from herehttp://listserv.kumc.edu/mailman/listinfo/gpc-dev). If you have questions I think others will too. And, I think we all benefit from as much collaboration as we can have. Could we move future questions there? I think what you want is an empty table right now. The manual curation table is what it says - a place for you to manually specify parents for medications that we didn't link from Epic to RxNorm. The documentation could probably be better - from the comment at the top of the file: Notes about manual curation: med_map_manual_curation is a table that maps a clarity medication ID to a parent concept. It is designed to be used for medications that we couldn't map to RxNORM directly from information in Clarity (via GCN, NDC, etc). This parent could be a VA class or an SCDF/SBDF. The table has the following columns: CLARITY_MEDICATION_ID - the id of the med without direct linkage to RxNORM CLARITY_NAME (not used for mapping - just for eyeballing) FACTS (not used for mapping - just for eyeballing) PATIENTS (not used for mapping - just for eyeballing) VA_NAME (not used for mapping - just for eyeballing) VA_RXAUI - If we didn't map to an SDF AUI (below), the fall back on this one for VA class. SDF_RXAUI - Map here if not null, otherwise fall back on the VA_RXAUI (above) SDF_NAME (not used for mapping - just for eyeballing) I know I've probably made KU-specific assumptions in the code that make porting difficult. So, if you have improvements, suggestions, etc I'd be very happy to look at patches. Or, if you start using the Elephant repository (see MultiSiteDevhttps://informatics.gpcnetwork.org/trac/Project/wiki/MultiSiteDev) you could commit directly to a branch and we could work together to merge your changes into default as appropriate. Thanks. Regards, Nathan From: Munns, Michael B [mailto:mike.mu...@unmc.edu] Sent: Thursday, December 04, 2014 4:18 PM To: Nathan Graham Subject: RE: RxNorm metadata Importance: High I have more questions about this rxnorm_terms table. On line 274 there is a create the I am running as an insert, that contains a union for the manual curation. If I am following all of this correct, and I am not sure that I am, some of this may be that it's the first time we've ran and the rxnorm_terms is empty. To start though there is a view mapped_meds , that uses rxnorm_terms. Then the view unmapped_meds is built off of mapped_meds. The unmapped_meds view is used in a query to create the med_map_manual_curation.csv which is used to Populate the med_map_manual_curation table. The union in the create @274 calls the med_map_manual_curation table , which does not exist. The join is where its med id is not null. So I could remove that section of the code or put an empty table out there. Any downside to an empty table or skipping that union you are aware of? Am I missing something? Michael Munns Database Analyst 402-559-3821 From: Munns, Michael B Sent: Thursday, December 04, 2014 1:41 PM To: 'Nathan
FW: RxNorm metadata
We can put them on the mailing list. We did end up creating an empty table for the manual curation, also a empty table for the exclude modifiers. Michael Munns Database Analyst 402-559-3821 From: Nathan Graham [mailto:ngra...@kumc.edu] Sent: Monday, December 08, 2014 10:18 AM To: Munns, Michael B Subject: RE: RxNorm metadata Michael, I'd really like to keep these conversations on the gpc-devhttp://listserv.kumc.edu/pipermail/gpc-dev/ mailing list (sign up from herehttp://listserv.kumc.edu/mailman/listinfo/gpc-dev). If you have questions I think others will too. And, I think we all benefit from as much collaboration as we can have. Could we move future questions there? I think what you want is an empty table right now. The manual curation table is what it says - a place for you to manually specify parents for medications that we didn't link from Epic to RxNorm. The documentation could probably be better - from the comment at the top of the file: Notes about manual curation: med_map_manual_curation is a table that maps a clarity medication ID to a parent concept. It is designed to be used for medications that we couldn't map to RxNORM directly from information in Clarity (via GCN, NDC, etc). This parent could be a VA class or an SCDF/SBDF. The table has the following columns: CLARITY_MEDICATION_ID - the id of the med without direct linkage to RxNORM CLARITY_NAME (not used for mapping - just for eyeballing) FACTS (not used for mapping - just for eyeballing) PATIENTS (not used for mapping - just for eyeballing) VA_NAME (not used for mapping - just for eyeballing) VA_RXAUI - If we didn't map to an SDF AUI (below), the fall back on this one for VA class. SDF_RXAUI - Map here if not null, otherwise fall back on the VA_RXAUI (above) SDF_NAME (not used for mapping - just for eyeballing) I know I've probably made KU-specific assumptions in the code that make porting difficult. So, if you have improvements, suggestions, etc I'd be very happy to look at patches. Or, if you start using the Elephant repository (see MultiSiteDevhttps://informatics.gpcnetwork.org/trac/Project/wiki/MultiSiteDev) you could commit directly to a branch and we could work together to merge your changes into default as appropriate. Thanks. Regards, Nathan From: Munns, Michael B [mailto:mike.mu...@unmc.edu] Sent: Thursday, December 04, 2014 4:18 PM To: Nathan Graham Subject: RE: RxNorm metadata Importance: High I have more questions about this rxnorm_terms table. On line 274 there is a create the I am running as an insert, that contains a union for the manual curation. If I am following all of this correct, and I am not sure that I am, some of this may be that it's the first time we've ran and the rxnorm_terms is empty. To start though there is a view mapped_meds , that uses rxnorm_terms. Then the view unmapped_meds is built off of mapped_meds. The unmapped_meds view is used in a query to create the med_map_manual_curation.csv which is used to Populate the med_map_manual_curation table. The union in the create @274 calls the med_map_manual_curation table , which does not exist. The join is where its med id is not null. So I could remove that section of the code or put an empty table out there. Any downside to an empty table or skipping that union you are aware of? Am I missing something? Michael Munns Database Analyst 402-559-3821 From: Munns, Michael B Sent: Thursday, December 04, 2014 1:41 PM To: 'Nathan Graham' Subject: RE: RxNorm metadata Nathan, I found it there and created the view. There may be more questions coming though. Michael Munns Database Analyst 402-559-3821 From: Nathan Graham [mailto:ngra...@kumc.edu] Sent: Thursday, December 04, 2014 11:04 AM To: Munns, Michael B Subject: RE: RxNorm metadata Michael, Normal_concept is created in metadata_init.sqlhttps://informatics.kumc.edu/work/browser/heron_load/metadata_init.sql. I think it's just a shortcut since nearly all of our concepts have exactly the same values for those fields. -- Nathan From: Munns, Michael B [mailto:mike.mu...@unmc.edu] Sent: Wednesday, December 03, 2014 3:16 PM To: Nathan Graham Subject: RE: RxNorm metadata Importance: High Thanks Nathan. Do you know where the creation for BlueHeronMetadata.normal_concept@deidmailto:BlueHeronMetadata.normal_concept@deid code is? We have deid and blueheronmetadata but not the normal_concept table Michael Munns Database Analyst 402-559-3821 From: Nathan Graham [mailto:ngra...@kumc.edu] Sent: Tuesday, December 02, 2014 6:39 PM To: Munns, Michael B; gpc-dev@listserv.kumc.edumailto:gpc-dev@listserv.kumc.edu Subject: 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
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
