[gpc-informatics] #296: breast cancer stage, receptor status, treatment from EMR
#296: breast cancer stage, receptor status, treatment from EMR --+-- Reporter: dconnolly| Owner: dconnolly Type: enhancement | Status: new Priority: major| Milestone: cohort-char1 Component: data-stds| Keywords: Blocked By: | Blocking: 295 --+-- In our June 18 meeting (ticket:265#comment:7), we discussed a few variables beyond breast cancer diagnosis for comparison between the EMR and tumor registry: - stage - receptor status - treatment - chemo - surgery - radiation - endocrine or hormonal therapy We already have a breast cancer diagnosis in a [wiki:DataRepositoryManagement#gpc-ont GPC standard ontology], but it's not clear that we do for these others. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/296> 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] #296: breast cancer stage, receptor status, treatment from EMR
#296: breast cancer stage, receptor status, treatment from EMR -+--- Reporter: dconnolly| Owner: preeder Type: enhancement | Status: assigned Priority: major| Milestone: cohort-char1 Component: data-stds| Resolution: Keywords: | Blocked By: Blocking: 295 | -+--- Changes (by dconnolly): * owner: dconnolly => preeder * status: new => assigned Comment: Phillip, Where would you expect to find stage and receptor status? I see **UTSW - Cancer Staging \Breast** on babel (with various modifiers) under UTSW Beacon. I'm not sure KUMC uses Beacon, and if we do, whether it's feasible to get the data in i2b2 in a relevant timeframe. I don't see "receptor" under Beacon. I get >500 hits under UNMC SNOMEDCT. For chemo treatment, I gather HCPCS J9000-J999 is the thing to look for. KUMC HERON doesn't include HCPCS yet. Integrating the UTHSCSA HCPCS code is on our todo list, though it's not going very quickly. I suppose there are CPT codes for breast cancer surgery... I don't know about radiation, endocrine or hormonal therapy. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/296#comment:1> 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] #293: Report SAS and RDBMS version and packages to DSSNI
#293: Report SAS and RDBMS version and packages to DSSNI ---+-- Reporter: lv | Owner: badagarla Type: task | Status: assigned Priority: major | Milestone: data-quality-q2 Component: data-stds | Resolution: Keywords: | Blocked By: Blocking: | ---+-- Changes (by dconnolly): * milestone: cohort-char1 => data-quality-q2 -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/293#comment:6> 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] #80: assessment of GPC vs. data privacy and security standards
#80: assessment of GPC vs. data privacy and security standards --+- Reporter: dconnolly | Owner: nateapathy Type: task | Status: assigned Priority: major | Milestone: data-sec-check Component: data-sharing | Resolution: Keywords: security | Blocked By: 79 Blocking:| --+- Changes (by dconnolly): * owner: gkowalski => nateapathy Comment: Nate, We have at least an initial response from everybody but CMH. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/80#comment:22> 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] #284: Deploy GPC ALS Survey at GPC sites
#284: Deploy GPC ALS Survey at GPC sites ---+ Reporter: badagarla | Owner: budh0007 Type: task | Status: assigned Priority: major | Milestone: survey-redcap-als Component: data-stds | Resolution: Keywords: | Blocked By: 208 Blocking: | ---+ Changes (by dconnolly): * owner: badagarla => budh0007 * status: new => assigned Comment: pending as of 23 June: - Mark / MCW - Supreet / UMN - UNMC Confirmation from UIOWA would be ideal, though we understand they're all set. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/284#comment:4> 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] #80: assessment of GPC vs. data privacy and security standards
#80: assessment of GPC vs. data privacy and security standards --+- Reporter: dconnolly | Owner: nateapathy Type: task | Status: assigned Priority: major | Milestone: data-sec-check Component: data-sharing | Resolution: Keywords: security | Blocked By: 79 Blocking:| --+- Comment (by nateapathy): Warren Teachout and Dr. Fitzmaurice have been working on this for CMH. Most of these questions are for individuals familiar with the specific policies and protocols of the site, rather than questions Cerner can answer. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/80#comment:23> 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] #80: assessment of GPC vs. data privacy and security standards
#80: assessment of GPC vs. data privacy and security standards --+- Reporter: dconnolly | Owner: nateapathy Type: task | Status: assigned Priority: major | Milestone: data-sec-check Component: data-sharing | Resolution: Keywords: security | Blocked By: 79 Blocking:| --+- Comment (by nateapathy): I checked with Dr. Fitzmaurice and she noted that CMH is not available in the drop-down list on the survey. CMH's responses were submitted as KUMC with a note at the bottom of the survey clarifying that they are for CMH. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/80#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-informatics] #293: Report SAS and RDBMS version and packages to DSSNI
#293: Report SAS and RDBMS version and packages to DSSNI ---+-- Reporter: lv | Owner: lv Type: task | Status: assigned Priority: major | Milestone: data-quality-q2 Component: data-stds | Resolution: Keywords: | Blocked By: Blocking: | ---+-- Changes (by badagarla): * owner: badagarla => lv Comment: Re-assigning after the GPC-DEV call on 06/30/2015. LV to pull versions from existing files. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/293#comment:7> 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] #205: interim builder for breast cancer cohort summary
#205: interim builder for breast cancer cohort summary --+--- Reporter: dconnolly | Owner: prakashnadkarni Type: enhancement | Status: closed Priority: major | Milestone: bc-survey-cohort-def Component: data-sharing | Resolution: fixed Keywords: breast-cancer-cohort | Blocked By: 32, 204 Blocking:| --+--- Changes (by dconnolly): * cc: tmcmahon, bchrischilles, bradley-mcdowell@… (removed) Comment: See also UTHSCSA scripts: ticket:217#comment:18 -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/205#comment:16> 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] #191: represent PCORI CDM 2.x terminology as i2b2 metadata
#191: represent PCORI CDM 2.x terminology as i2b2 metadata --+ Reporter: dconnolly | Owner: dconnolly Type: design-issue | Status: new Priority: major | Milestone: data-domains3 Component: data-stds | Resolution: Keywords:| Blocked By: 109 Blocking:| --+ Changes (by dconnolly): * priority: minor => major * milestone: bariatric-study-data => data-domains3 Comment: Replying to [ticket:279#comment:11 nateapathy]: > Does the SCILHS CDRN CDM ontology and CDM transformation code effectively replace the comparable subject areas that are on the GPC_TERMS table? Since we have been pretty well aligned with SCILHS on goals and high level design, I expect the changes to be fairly small, but yes, this may involve updates to our design for demographics (#67), vitals (#23), and diagnoses (#63) and perhaps enrollment (#229). It should address our outstanding issues on procedures (#243). As SCILHS addresses CDM v2 and v3, it may impact our design for meds (#78) and address labs (#158). > We are starting this effort and don't want to pursue the GPC_TERMS work if we will be adopting the [https://community.i2b2.org/wiki/display/SCILHS/SCILHS+i2b2+PCORnet+Common+Data+Model+Ontology+Home ontologies from SCILHS] instead. Feel free to skip to the SCILHS ontology and let us know how it goes, but please don't let this stall your work. As I say, I expect the changes are small, and if you start work with the current `GPC_TERMS`, migrating should be a manageable effort. The major benefit to offset the cost of this disruption is filling in gaps in our CDM ETL (ticket:240#comment:6), as well as shared development costs with SCILHS going forward. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/191#comment:3> 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] #291: Gather 2015 2nd quarterly QA results
#291: Gather 2015 2nd quarterly QA results --+- Reporter: mish | Owner: dconnolly Type: problem | Status: assigned Priority: major | Milestone: data-quality-q2 Component: data-quality | Resolution: Keywords:| Blocked By: 259, 281, 285, 290 Blocking:| --+- Changes (by dconnolly): * cc: jvanschyndle@… (added) * owner: mish => dconnolly * status: new => assigned Comment: We've got some code: [https://bitbucket.org/jvanschyndle/gpc-2015-q2-qa- files/commits/4d7def85af3604448c0aac7dff5bbdeecfcc1948 4d7def8] Who wants to try it out? -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/291#comment:6> 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] #296: breast cancer stage, receptor status, treatment from EMR
#296: breast cancer stage, receptor status, treatment from EMR -+--- Reporter: dconnolly| Owner: tmcmahon Type: enhancement | Status: assigned Priority: major| Milestone: cohort-char1 Component: data-stds| Resolution: Keywords: | Blocked By: Blocking: 295 | -+--- Changes (by dconnolly): * owner: preeder => tmcmahon Comment: Tamara, Russ, Betsy, Some of these seem to be available as ICD9 or CPT or HCPCS procedure codes, which all sites more or less have in i2b2. The rest of the info (e.g. stage) seems to be just in text notes, which isn't feasible to collect in the coming few months. Following our 30 June discussion (notes excerpted below), Prakash made an i2b2 query for breast reconstruction surgeries on babel: - Augmentation ma at 12:12:51 [6-30-2015] [prakash-nadkarni at uiowa.edu] Notes from 30 June meeting (ticket:12#comment:69) #296 Dan: there was discussion about how to use breast cancer data; characterizing various sources, like tumor and EHR, will require additional data elements Russ and Betsy would like to compare stage, receptor status and treatment Dan: Does anyone know of a reliable place to get Stage from the EHR Justin: the Epic module Beacon has this information Other sites with Beacon: Iowa, UNMC, WISC Dan: does anyone have this in i2b2? Dan: Sounds like it may be a stretch to get this. Alex: What’s the prefix for Beacon? STG... (Supreet), STG_INFO (from Glenn via chat), also a view: V_CANCER_STAGING Dan: Does anyone have Receptor Status? Prakash: there’s no field for this; tumor registrars abstract it from notes Treatment Dan: there are HCPCs/jcodes for some of the treatments (chemo) Prakash: would need to look for ICD9 procedure codes; single category of code for breast reconstruction surgery; Prakash will check on code ranges; will build a query on babel with as much as he can find. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/296#comment:2> 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] #293: Report SAS and RDBMS version and packages to DSSNI
#293: Report SAS and RDBMS version and packages to DSSNI ---+-- Reporter: lv | Owner: gkowalski Type: task | Status: assigned Priority: major | Milestone: data-quality-q2 Component: data-stds | Resolution: Keywords: | Blocked By: Blocking: | ---+-- Changes (by lv): * owner: lv => gkowalski Comment: MCW Annotated Data Dictionary (completed by Glenn Bushee) does not provide the required information. ||(6) what database system is used to hoset and extract the PCORnet data at your site||Oracle|| ||(7) What SAS version and modules are available at your site?||Campus SAS license|| Please complete ASAP. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/293#comment:8> 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] #293: Report SAS and RDBMS version and packages to DSSNI
#293: Report SAS and RDBMS version and packages to DSSNI ---+-- Reporter: lv | Owner: gkowalski Type: task | Status: assigned Priority: major | Milestone: data-quality-q2 Component: data-stds | Resolution: Keywords: | Blocked By: Blocking: | ---+-- Comment (by lv): Prakash: same issue with UIowa. DSSNI is looking for the RDBMS version (e.g. SQL Server V10.50.1600.1) for each datamart; the UIowa Annotated Data Dictionary is not specific enough to provide this. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/293#comment:9> 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] #227: Data QA for Breast Cancer Finder File
#227: Data QA for Breast Cancer Finder File -+- Reporter: tmcmahon | Owner: jmcclay Type: task | Status: assigned Priority: major| Milestone: bc-survey-cohort-def Component: data-sharing | Resolution: Keywords: data-quality breast- | Blocked By: 217, 222, 223, 224, cancer-cohort | 230, 231, 234, 235, 244 Blocking: | -+- Comment (by bzschoche): As updated on the 7.1.15 Breast Cancer Survey webinar, UNMC and UTSW are also approved for mailing. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/227#comment:37> 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
[gpc-informatics] Batch modify: #295, #296, #297, #298, #214, #265
Batch modification to #295, #296, #297, #298, #214, #265 by dconnolly: milestone to cohort-char-bc-db Comment: Russ, Vince and Dan met to discuss cohort characterization. RW: let's do the next BC data pull from all sites (#297) in August so we can include the results (#298) in our phase 1 cohort characterization. re #296, Russ put together EMR_BC_Criteria [7-2-2015] [rwait...@kumc.edu] -- Tickets URL: <http://informatics.gpcnetwork.org/trac/Project/query?id=295%2C296%2C297%2C298%2C214%2C265> 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] #296: breast cancer treatment from EMR (was: breast cancer stage, receptor status, treatment from EMR)
#296: breast cancer treatment from EMR --+ Reporter: dconnolly | Owner: tmcmahon Type: design-issue | Status: closed Priority: major | Milestone: cohort-char-bc-db Component: data-stds | Resolution: fixed Keywords:| Blocked By: Blocking: 295 | --+ Changes (by dconnolly): * status: assigned => closed * type: enhancement => design-issue * resolution: => fixed Comment: Russ concurred that getting stage, receptor status from the EMR isn't feasible in our timeframe. Otherwise, I think I have what I need to build a query (#295) including treatment. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/296#comment:4> 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] #227: Data QA for Breast Cancer Finder File
#227: Data QA for Breast Cancer Finder File -+- Reporter: tmcmahon | Owner: tmcmahon Type: task | Status: assigned Priority: major| Milestone: bc-survey-cohort-def Component: data-sharing | Resolution: Keywords: data-quality breast- | Blocked By: 217, 222, 223, 224, cancer-cohort | 230, 231, 234, 235, 244 Blocking: | -+- Changes (by mish): * owner: jmcclay => tmcmahon Comment: Per my phone call with Tamara, WISC has completed all of the IRB hurdles and are ready to receive the ID's to validate. Tamara will be sending them to us shortly. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/227#comment:38> 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] #80: assessment of GPC vs. data privacy and security standards
#80: assessment of GPC vs. data privacy and security standards --+- Reporter: dconnolly | Owner: mish Type: task | Status: assigned Priority: major | Milestone: data-sec-check Component: data-sharing | Resolution: Keywords: security | Blocked By: 79 Blocking:| --+- Changes (by dconnolly): * owner: nateapathy => mish Comment: Patrick agreed to ask Umberto to get in touch with Dan about writing this up. Patrick sent mail June 30. Also, Tom Mish called me to catch up on things and said he'd bring this to Umberto's attention. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/80#comment:25> 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] #284: Deploy GPC ALS Survey at GPC sites
#284: Deploy GPC ALS Survey at GPC sites ---+ Reporter: badagarla | Owner: jmcclay Type: task | Status: assigned Priority: major | Milestone: survey-redcap-als Component: data-stds | Resolution: Keywords: | Blocked By: 208 Blocking: | ---+ Changes (by dconnolly): * owner: budh0007 => jmcclay Comment: Jim, Bhargav, is UNMC all set? -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/284#comment:5> 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
[gpc-informatics] Batch modify: #154, #117, #166, #161, #162
Batch modification to #154, #117, #166, #161, #162 by dconnolly: milestone to data-quality-q2 Comment: moving popmednet tickets to milestone:data-quality-q2 phasing out milestone:data-agg1 -- Tickets URL: <http://informatics.gpcnetwork.org/trac/Project/query?id=154%2C117%2C166%2C161%2C162> 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] #280: Medication ontology orgainzed by ingredient
#280: Medication ontology orgainzed by ingredient -+--- Reporter: preeder | Owner: rwaitman Type: enhancement | Status: assigned Priority: minor| Milestone: morning-star Component: data-stds| Resolution: Keywords: | Blocked By: Blocking: | -+--- Changes (by dconnolly): * priority: major => minor -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/280#comment:4> 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] #293: Report SAS and RDBMS version and packages to DSSNI
#293: Report SAS and RDBMS version and packages to DSSNI ---+-- Reporter: lv | Owner: gkowalski Type: task | Status: assigned Priority: major | Milestone: data-quality-q2 Component: data-stds | Resolution: Keywords: | Blocked By: Blocking: | ---+-- Comment (by lv): Confirmation from Casie with Harvard Pilgrim; still waiting on update from MCW and UIowa. -- From: Horgan,Casie Sent: Wednesday, July 01, 2015 3:12 PM To: Verhagen, Laurel A Cc: Sturtevant,Jessica; Greenlee, Robert T PHD Subject: RE: SAS and RDBMS version and packages Thank you for sending along, Laurel! It is much appreciated. I’ll go ahead and input this information into our technical tracking document and we will look forward to hearing from you when you hear back from your final two sites. Thanks again! -Casie Horgan -- From: Verhagen, Laurel A Sent: Wednesday, July 01, 2015 4:09 PM To: Horgan,Casie Cc: Sturtevant,Jessica; Greenlee, Robert T PHD Subject: RE: SAS and RDBMS version and packages Hi Casie, Here’s what we’ve compiled to date. We are waiting on information from two sites (Medical College of Wisconsin and University of Iowa). [table] -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/293#comment:10> 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] #293: Report SAS and RDBMS version and packages to DSSNI
#293: Report SAS and RDBMS version and packages to DSSNI ---+-- Reporter: lv | Owner: gkowalski Type: task | Status: assigned Priority: major | Milestone: data-quality-q2 Component: data-stds | Resolution: Keywords: | Blocked By: Blocking: | ---+-- Comment (by btaylor): MCW information added to the google doc -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/293#comment:11> 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] #293: Report SAS and RDBMS version and packages to DSSNI
#293: Report SAS and RDBMS version and packages to DSSNI ---+- Reporter: lv | Owner: Prakash-Nadkarni@… Type: task | Status: assigned Priority: major | Milestone: data-quality-q2 Component: data-stds | Resolution: Keywords: | Blocked By: Blocking: | ---+- Changes (by btaylor): * owner: gkowalski => Prakash-Nadkarni@… -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/293#comment:12> 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] #293: Report SAS and RDBMS version and packages to DSSNI
#293: Report SAS and RDBMS version and packages to DSSNI ---+-- Reporter: lv | Owner: prakashnadkarni Type: task | Status: assigned Priority: major | Milestone: data-quality-q2 Component: data-stds | Resolution: Keywords: | Blocked By: Blocking: | ---+-- Changes (by dconnolly): * owner: Prakash-Nadkarni@… => prakashnadkarni Comment: trac isn't smart enough to deal with email addresses in the owner field. :-/ -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/293#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] #293: Report SAS and RDBMS version and packages to DSSNI
#293: Report SAS and RDBMS version and packages to DSSNI ---+-- Reporter: lv | Owner: lv Type: task | Status: assigned Priority: major | Milestone: data-quality-q2 Component: data-stds | Resolution: Keywords: | Blocked By: Blocking: | ---+-- Changes (by dconnolly): * owner: prakashnadkarni => lv Comment: Laurel, Prakash added the info for UIOWA. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/293#comment:14> 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] #284: Deploy GPC ALS Survey at GPC sites
#284: Deploy GPC ALS Survey at GPC sites ---+ Reporter: badagarla | Owner: jmcclay Type: task | Status: assigned Priority: major | Milestone: survey-redcap-als Component: data-stds | Resolution: Keywords: | Blocked By: 208 Blocking: | ---+ Comment (by mikemunns): Replying to [comment:5 dconnolly]: > Jim, Bhargav, is UNMC all set? Yes, UNMC is set. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/284#comment:6> 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] #284: Deploy GPC ALS Survey at GPC sites
#284: Deploy GPC ALS Survey at GPC sites ---+ Reporter: badagarla | Owner: badagarla Type: task | Status: assigned Priority: major | Milestone: survey-redcap-als Component: data-stds | Resolution: Keywords: | Blocked By: 208 Blocking: | ---+ Changes (by dconnolly): * owner: jmcclay => badagarla Comment: Bhargav, which site is it that's not all set? Our records show all 9 participating DevTeams have it deployed... or is there something that happens after confirmation with screenshots? 1. KUMC - deployed May 20 ticket:208#comment:18 2. ''CMH - not participating'' 3. UIOWA - already set up as of 23 June call (#12) 4. WISC - confirmed with screenshots from Lisa as of 23 June call 5. MCW - 6+ responses as of 30 June call (#12) 6. MCRF - confirmed with screenshots from Laurel as of 23 June call 7. UMN - confirmed with screenshots as of 30 June 8. UNMC - Mike confirms in comment:6 9. UTHSCSA - confirmed with screenshots from Sergio as of 23 June call 10. UTSW - already collecting responses as of 23 June -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/284#comment:7> 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] #293: Report SAS and RDBMS version and packages to DSSNI
#293: Report SAS and RDBMS version and packages to DSSNI ---+-- Reporter: lv | Owner: lv Type: task | Status: closed Priority: major | Milestone: data-quality-q2 Component: data-stds | Resolution: fixed Keywords: | Blocked By: Blocking: | ---+-- Changes (by lv): * status: assigned => closed * resolution: => fixed Comment: Submitted to Casie Horgan, PCORnet Data Research Associate -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/293#comment:15> 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] #253: obesity survey REDCap tracker and tools
#253: obesity survey REDCap tracker and tools
--+-
Reporter: bokov | Owner: huhickman
Type: enhancement | Status: assigned
Priority: major | Milestone: obesity-survey-def
Component: data-sharing | Resolution:
Keywords:| Blocked By:
Blocking: 254 |
--+-
Comment (by huhickman):
I'm chugging along on this. I have limited our data time wise enough to
get down to appx 17000 patients and have two issues so far:
1. We do not have STATE_CD in patient_dimension (that is fixable).
2. '''However''', in looking at the SQL generated :
{{{
select pm.patient_ide, pd.patient_num, pd.pat_name
, substr(pd.zip_cd, 1, 5) pat_zip
--, upper(pd.state_cd) pat_state, '@' pat_state_c
, 'NE' pat_state
, pd.city pat_city
, pd.add_line_1 pat_addr_1, pd.add_line_2 pat_addr_2
, pd.home_phone pat_home_phone, pd.work_phone pat_work_phone
, pd.email_address pat_email
from "TMP_PATIENT_SET" tmp
join "NIGHTHERONDATA".patient_mapping pm on pm.patient_num =
tmp.patient_num
join "NIGHTHERONDATA".patient_dimension pd on pd.patient_num =
pm.patient_num
where pm.patient_ide_source = 'e...@nebraskamed.com'
and upper(pd.state_cd) = 'NEBRASKA'
}}}
It appears that the data will be limited to Nebraska based patients. We
are a stone's throw from Iowa, and we'll have patients from Iowa in the
set (there is nothing that said to limit to your home state based upon
what I see in the query instructions).
Is it the intention that this study be limited to a site's home state? Or
should it be constrained by geolocation data (50 miles from center or
similar?)
--
Ticket URL:
<http://informatics.gpcnetwork.org/trac/Project/ticket/253#comment:22>
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Re: [gpc-informatics] #253: obesity survey REDCap tracker and tools
#253: obesity survey REDCap tracker and tools --+- Reporter: bokov | Owner: huhickman Type: enhancement | Status: assigned Priority: major | Milestone: obesity-survey-def Component: data-sharing | Resolution: Keywords:| Blocked By: Blocking: 254 | --+- Comment (by bos): Replying to [comment:22 huhickman]: > Is it the intention that this study be limited to a site's home state? Or should it be constrained by geolocation data (50 miles from center or similar?) [[BR]] Excellent question, which I will forward to Dr. Hale. For our site, we intentionally limited the cohort to our home state (in which we are centrally located, so this doesn't filter out many people). As you mentioned, this probably does not translate to your institution. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/253#comment:23> 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] #253: obesity survey REDCap tracker and tools
#253: obesity survey REDCap tracker and tools
--+-
Reporter: bokov | Owner: huhickman
Type: enhancement | Status: assigned
Priority: major | Milestone: obesity-survey-def
Component: data-sharing | Resolution:
Keywords:| Blocked By:
Blocking: 254 |
--+-
Comment (by bos):
[[BR]]
OFFICIAL REPLY: no geographic limitation is intended for non-UTHSCSA
sites. Please remove/comment out the line of code (like below):
{{{#!python
def loadID(self, id_loader):
...
--and upper(pd.state_cd) = '&&state_long'
}}}
--
Ticket URL:
<http://informatics.gpcnetwork.org/trac/Project/ticket/253#comment:24>
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Re: [gpc-informatics] #240: Data Characterization queries for phase 1 CDM V1 compliance
#240: Data Characterization queries for phase 1 CDM V1 compliance -+- Reporter: campbell | Owner: lv Type: task | Status: assigned Priority: major| Milestone: data- Component: data-stds| quality-q2 Keywords: cdm-etl CDM Compliance data-quality | Resolution: Blocking: | Blocked By: -+- Comment (by susandm): Has this call been scheduled? -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/240#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] #80: assessment of GPC vs. data privacy and security standards
#80: assessment of GPC vs. data privacy and security standards --+- Reporter: dconnolly | Owner: mish Type: task | Status: assigned Priority: major | Milestone: data-sec-check Component: data-sharing | Resolution: Keywords: security | Blocked By: 79 Blocking:| --+- Comment (by mish): Umberto has acknowledged that this is on his list of tasks to accomplish. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/80#comment:26> 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] #240: Data Characterization queries for phase 1 CDM V1 compliance
#240: Data Characterization queries for phase 1 CDM V1 compliance -+- Reporter: campbell | Owner: lv Type: task | Status: assigned Priority: major| Milestone: data- Component: data-stds| quality-q2 Keywords: cdm-etl CDM Compliance data-quality | Resolution: Blocking: | Blocked By: -+- Comment (by dconnolly): The call was today at 1pm. It went well. Discussion was pretty much consistent with existing plans. My notes are on paper and I'm out next week, but we'll share the relevant info in due course. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/240#comment:14> 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] #240: Data Characterization queries for phase 1 CDM V1 compliance
#240: Data Characterization queries for phase 1 CDM V1 compliance -+- Reporter: campbell | Owner: lv Type: task | Status: assigned Priority: major| Milestone: data- Component: data-stds| quality-q2 Keywords: cdm-etl CDM Compliance data-quality | Resolution: Blocking: | Blocked By: -+- Comment (by susandm): Thanks! I wondered and wanted to attend but could not find the call in info. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/240#comment:15> 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] #240: Data Characterization queries for phase 1 CDM V1 compliance
#240: Data Characterization queries for phase 1 CDM V1 compliance -+- Reporter: campbell | Owner: lv Type: task | Status: assigned Priority: major| Milestone: data- Component: data-stds| quality-q2 Keywords: cdm-etl CDM Compliance data-quality | Resolution: Blocking: | Blocked By: -+- Comment (by huhickman): I'll update the status with my notes... I attended the DSSNI call on 7/10 substituting for Jim Campbell. === Data Characterization Queries === * The current set of queries will operate against CDM V1 tables. Hence, we do not need CDM V2/3 at this immediate juncture. * The Data Characterization Wiki is [https://pcornet.centraldesktop.com /workgroups-taskforces/doc/40435087/ here]. The ETL annotated data dictionary and the queries are available for download from this location. * Oracle V2.0 queries are available. The ETA for SQL Server/Postgres versions is 2 weeks (7/24/2015). * UNMC is up to bat first to produce the queries. They will distribute the queries to UNMC via PopMedNet on 7/15. The queries that they will distribute are precisely those available for download. * UNMC will have two weeks to produce results, which will be CSV files to be submitted via PopMedNet. * The ADD will need to completed at the same time. * Some high level analysis will be run and feedback given UNMC. Additionally, there will be a much more fine grained analysis of the data done and reported to UNMC. * There will be phone conversations regarding any data issues noted. * Other GPC sites can download and run the queries as well. === Transitions to CDMV2/3 === Several future studies will target CDM V3. None at present target V2. There was discussion about skipping V2 and concentrating on V3, but I do not recall that there was a clear resolution here. === Date shifting === There was discussion about the GPC date shifting policy, and we are OK in the way we date shift things. There was discussion and acknowledgement that our random date shifting may cause issues in some cases (seasonal disease research etc). === Other issues === Ultimately, the SQL code sets for the queries will be replaced with SAS code (and hence the push to get our SAS versions/capability in order for GPC). Other folks who attended will hopefully add to what I transcribed. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/240#comment:16> 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] #291: Gather 2015 2nd quarterly QA results
#291: Gather 2015 2nd quarterly QA results --+-- Reporter: mish | Owner: dconnolly Type: problem | Status: assigned Priority: major | Milestone: data-quality-q2 Component: data-quality | Resolution: Keywords:| Blocked By: 259, 281, 285, 290, 306 Blocking:| --+-- Comment (by lv): MCRF ran the scripts in < 4 hours (run incrementally, so may be less total time) on SQL server. What's the process to submit results: REDCap, Email to Tom, something else? After validating, the zero/null results seem appropriate. In some cases we have raw data that we might be able to use to fill calculated values. Example: \i2b2\LP29694-4\LP29696-9\LP146111-2\72165-4\72165-4: Pediatric systolic blood pressure percentile per age, gender and height [0 facts; 0 patients] *SUGGESTION: \i2b2\LP29694-4\LP32525-5\LP96828-6\72225-6\29545-1\8480-6\(8480-6: Systolic blood pressure [12308605 facts; 749329 patients]) *COULD THE PERCENTILE BE CALCULATED OFF OF THE VALUES PROVIDED BY THIS??? One other note: in some cases we have a term that's used in the query, but we're not using it in our data. Could likely swap these if 1559-6 is approximately the same as 1557-8? \i2b2\LP29693-6\LP7784-4\1557-8\1557-8: Fasting glucose [0 facts; 0 patients] *SUGGESTION: \i2b2\LP29693-6\LP7784-4\1558-6\ (1558-6: Fasting glucose [398797 facts; 150656 patients]) -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/291#comment:8> 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
[gpc-informatics] #308: LEA Feasibility Query
#308: LEA Feasibility Query +-- Reporter: tmcmahon | Owner: tmcmahon Type: task | Status: new Priority: major | Milestone: Component: data-stds | Keywords: Blocked By: | Blocking: +-- WI, MCW, UTSW, UTHSC-SA to run 8 feasibility queries for the [http://www.gpcnetwork.org/?q=Amputation Lower Extremity Amputation project] and to record the time spent on constructing and executing these queries. This will help determine future fee structures for feasibility requests. Please update this ticket when your institution has completed the queries and sent the numbers with estimated time to Tamara. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/308> 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] #308: LEA Feasibility Query
#308: LEA Feasibility Query ---+--- Reporter: tmcmahon | Owner: tmcmahon Type: task | Status: accepted Priority: major | Milestone: Component: data-stds | Resolution: Keywords: | Blocked By: Blocking: | ---+--- Changes (by tmcmahon): * cc: meiliu (added) * status: new => accepted -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/308#comment:1> 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] #253: obesity survey REDCap tracker and tools
#253: obesity survey REDCap tracker and tools --+- Reporter: bokov | Owner: huhickman Type: enhancement | Status: assigned Priority: major | Milestone: obesity-survey-def Component: data-sharing | Resolution: Keywords:| Blocked By: Blocking: 254 | --+- Comment (by lv): Couple quetsions from MCRF: 1.) We don't have Emergency Contact Addresses; however, we do capture addresses for Step-Mother and Step-Father. We'd like to use these as part of our matching, if possible. (Does Epic capture Step-Parent information? Was this intentionally excluded?) If Emergency Contact addresses are used for matching/de-dup'ing, could we just fill with Step-Parent addresses? 2.) For sites that will distribute the survey by email, how are you pulling parent email? Does Epic capture parent email in the patient email field? We currently plan to add email columns to the end of our input file to allow for analysis later. Just wondering if there's a standard method to handle this. Thanks! Laurel -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/253#comment:25> 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] #253: obesity survey REDCap tracker and tools
#253: obesity survey REDCap tracker and tools --+- Reporter: bokov | Owner: huhickman Type: enhancement | Status: assigned Priority: major | Milestone: obesity-survey-def Component: data-sharing | Resolution: Keywords:| Blocked By: Blocking: 254 | --+- Comment (by bos): Replying to [comment:25 lv]: 1) There are several groups of contact info fields, and the survey tracker will use the first valid one in this order of precedence: BILLING, MOTHER, FATHER, GUARDIAN, EMERG1, EMERG2. I think it is OK to use step mother/father info, but I am not sure which order of precedence they should have, which probably depends on the other contact info fields you have available. We expected that some sites would pre-filter their possible contact info down to one per patient by means that make sense locally. If that is the case for you, then you can populate the info into the GUARDIAN_* input file fields and use the -f option to load the contact info from a file instead of Clarity. 2) In UTHSCSA/Epic the only email field we have is in the patient table, which does not contain parental emails. This field is sparsely populated for those under age 20 and skews toward the upper ages, indicating independent young adults. Other sites may store parent emails in this field, but due to the ambiguity, survey tracker will only pull this email field from Clarity for adult-only survey sites. Sites doing pediatric surveys by email invitation will have to use the -f option and load a contact info file as input to the survey tracker. This email includes an example: http://www.mail-archive.com/gpc- d...@listserv.kumc.edu/msg01992.html. Because UTHSCSA is not using email for the obesity survey, '''I'd appreciate it if another site could respond''' about how they pull parental email data. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/253#comment:26> 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] #291: Gather 2015 2nd quarterly QA results
#291: Gather 2015 2nd quarterly QA results --+-- Reporter: mish | Owner: dconnolly Type: problem | Status: assigned Priority: major | Milestone: data-quality-q2 Component: data-quality | Resolution: Keywords:| Blocked By: 259, 281, 285, 290, 306 Blocking:| --+-- Comment (by mish): UPLOAD process... You can either hop onto to the [https://redcap.gpcnetwork.org/|gpcnetwork redcap server] and try to upload the results for yourself, or send the results to Tom and he can upload them for you. Big bonus points for uploading them yourself. A couple of notes: * Not everyone has registered their InCommons accounts yet. * On import, don't forget to set the upload paramter: * ''Record format: The file to be uploaded has its records stored as separate **Columns**'' -TM -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/291#comment:9> 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] #291: Gather 2015 2nd quarterly QA results
#291: Gather 2015 2nd quarterly QA results --+-- Reporter: mish | Owner: dconnolly Type: problem | Status: assigned Priority: major | Milestone: data-quality-q2 Component: data-quality | Resolution: Keywords:| Blocked By: 259, 281, 285, 290, 306 Blocking:| --+-- Comment (by jdale): We have the file ready with the records stored as separate columns but I can't find where in the REDCap project to upload/import the file? Can you advise? Thanks. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/291#comment:10> 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] #291: Gather 2015 2nd quarterly QA results
#291: Gather 2015 2nd quarterly QA results --+-- Reporter: mish | Owner: dconnolly Type: problem | Status: assigned Priority: major | Milestone: data-quality-q2 Component: data-quality | Resolution: Keywords:| Blocked By: 259, 281, 285, 290, 306 Blocking:| --+-- Comment (by mish): It appears as if I have permissions to fix this oversight. You should be able to access the Data Import Tool now. As a side note: ensure that Record ID is set to all upper case. I noticed that after running the script, mine was "Wisc" instead of "WISC". A simple edit corrected that. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/291#comment:11> 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] #291: Gather 2015 2nd quarterly QA results
#291: Gather 2015 2nd quarterly QA results --+-- Reporter: mish | Owner: dconnolly Type: problem | Status: assigned Priority: major | Milestone: data-quality-q2 Component: data-quality | Resolution: Keywords:| Blocked By: 259, 281, 285, 290, 306 Blocking:| --+-- Comment (by bos): The age breakdowns in this QA query differ from our GPC terms, e.g. `age_10_19` instead of `age_10_17`. Are we supposed to change this to the age range concepts used at our site? -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/291#comment:12> 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] #291: Gather 2015 2nd quarterly QA results
#291: Gather 2015 2nd quarterly QA results --+-- Reporter: mish | Owner: bos Type: problem | Status: assigned Priority: major | Milestone: data-quality-q2 Component: data-quality | Resolution: Keywords:| Blocked By: 259, 281, 285, 290, 306 Blocking:| --+-- Changes (by dconnolly): * owner: dconnolly => bos Comment: I don't think I understand the question. Why would you change the age ranges, Angela? -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/291#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] #253: obesity survey REDCap tracker and tools
#253: obesity survey REDCap tracker and tools --+- Reporter: bokov | Owner: huhickman Type: enhancement | Status: closed Priority: major | Milestone: obesity-survey-def Component: data-sharing | Resolution: fixed Keywords:| Blocked By: Blocking: 254 | --+- Changes (by dconnolly): * status: assigned => closed * resolution: => fixed Old description: > Send out: Python script for generating REDCap survey tracker (and a > separate table in the same format for suspected address duplicates), a > blank survey tracker form for sites that cannot or prefer not to use the > Python script, a data-dictionary form for creating the online survey, > possibly Microsoft Office templates for doing mail-merge and mailers with > certain fields auto-filled, instructions for using script and survey > tracker and MS Office files. (A > > see also [http://listserv.kumc.edu/pipermail/gpc-dev/2015q1/001245.html > survey management plan for Obesity] of Feb 17 > > ''Dan, reporting based on discussion with Alex'' New description: Development of [https://bitbucket.org/bos_uthscsa/survey_tracker survey_tracker]. original design sketch: Python script for generating REDCap survey tracker (and a separate table in the same format for suspected address duplicates), a blank survey tracker form for sites that cannot or prefer not to use the Python script, a data-dictionary form for creating the online survey, possibly Microsoft Office templates for doing mail-merge and mailers with certain fields auto-filled, instructions for using script and survey tracker and MS Office files. (A see also [http://listserv.kumc.edu/pipermail/gpc-dev/2015q1/001245.html survey management plan for Obesity] of Feb 17 ''Dan, reporting based on discussion with Alex and Angela'' -- Comment: Based on discussion with Angela Bos, the tracker seems stable as of b85e0b6 Jul 15. We can re-open this if evaluation by Hubert or anyone else turns up critical issues. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/253#comment:27> 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
[gpc-informatics] Batch modify: #240, #154, #117, #166, #161, #162
Batch modification to #240, #154, #117, #166, #161, #162 by dconnolly: milestone to drn-query-1 Comment: DRN query stuff (#240 etc.) has a distinct customer base and timeline from Q2 query results -- Tickets URL: <http://informatics.gpcnetwork.org/trac/Project/query?id=240%2C154%2C117%2C166%2C161%2C162> 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] #291: Gather 2015 2nd quarterly QA results
#291: Gather 2015 2nd quarterly QA results --+-- Reporter: mish | Owner: bos Type: problem | Status: assigned Priority: major | Milestone: data-quality-q2 Component: data-quality | Resolution: Keywords:| Blocked By: 259, 281, 285, 290, 306 Blocking:| --+-- Comment (by lv): Few issues with importing our data: 1. Some Dates were incorrectly formatted. Fixed. - obesity_max_admit_date - obesity_max_birth_date - obesity_min_admit_date - obesity_min_birth_date 2. obesity_per_pat_proc_cpt_99381_87 didn't like our output of 2.76; Deleted this to get the file to load. 3. NULL = "The value you provided could not be validated because it does not follow the expected format. Please try again." Fixed. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/291#comment:14> 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] #291: Gather 2015 2nd quarterly QA results
#291: Gather 2015 2nd quarterly QA results --+-- Reporter: mish | Owner: bos Type: problem | Status: assigned Priority: major | Milestone: data-quality-q2 Component: data-quality | Resolution: Keywords:| Blocked By: 259, 281, 285, 290, 306 Blocking:| --+-- Comment (by mish): For comment 2 above, REDCap was incorrectly expecting an integer, not a number. It worked fine for us (i.e. 0), so I missed it. Sorry, that's been fixed. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/291#comment:15> 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] #291: Gather 2015 2nd quarterly QA results
#291: Gather 2015 2nd quarterly QA results --+-- Reporter: mish | Owner: bos Type: problem | Status: assigned Priority: major | Milestone: data-quality-q2 Component: data-quality | Resolution: Keywords:| Blocked By: 259, 281, 285, 290, 306 Blocking:| --+-- Comment (by lv): One other note: our Age Bucket counts were very low initially. We identified a grouping issue where Netezza was joining results and SQL was selecting the first result it found. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/291#comment:16> 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] #240: Data Characterization queries for phase 1 CDM V1 compliance
#240: Data Characterization queries for phase 1 CDM V1 compliance -+- Reporter: campbell | Owner: lv Type: task | Status: assigned Priority: major| Milestone: drn- Component: data-stds| query-1 Keywords: cdm-etl CDM Compliance data-quality | Resolution: Blocking: | Blocked By: -+- Comment (by huhickman): I've had a couple of fits and starts but have their shell script running the queries now. My spot checks of the SQL yielded some concerns about efficiency but not SQL syntax problems. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/240#comment:18> 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] #284: Deploy GPC ALS Survey at GPC sites
#284: Deploy GPC ALS Survey at GPC sites ---+ Reporter: badagarla | Owner: badagarla Type: task | Status: assigned Priority: major | Milestone: survey-redcap-als Component: data-stds | Resolution: Keywords: | Blocked By: 208 Blocking: | ---+ Comment (by dconnolly): poll: 1. KUMC - deployed May 20 ticket:208#comment:18 2. CMH - not participating 3. UIOWA - handed off to clinicians; soon 4. WISC - regulatory stand-by 5. MCW - 6+ responses as of 30 June call (#12) 6. MCRF - in the hands of the study team 7. UMN - patient list construction ETA today; then "survey coming" letter, then survey 8. UNMC - Mike to find out 9. UTHSCSA - working on university REDCap look-n-feel; ETA any day now 10. UTSW - already collecting responses as of 23 June -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/284#comment:8> 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] #253: obesity survey REDCap tracker and tools
#253: obesity survey REDCap tracker and tools --+- Reporter: bokov | Owner: huhickman Type: enhancement | Status: closed Priority: major | Milestone: obesity-survey-def Component: data-sharing | Resolution: fixed Keywords:| Blocked By: Blocking: 254 | --+- Comment (by huhickman): It works for me - however I do have the following comments/questions * I did modify one line of code - where the data is pulled from `patient_dimension` changed to pull directly from clarity data instead (our clarity refresh runs regularly, and ahead of our warehouse load). Our patient dimension table does not have email address and the like. * We plan on doing an email only survey ; so I may have to loosen the date codes again to get enough patients with email addresses. We have 4300+ out of 17000+ patients with email addresses -- what is our target number of patients for the study? * Could that be a config option - use only patients with email addresses? Also seems to suggest that adding a "Patient has email address Y/N" to our demographics load would be a handy thing. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/253#comment:28> 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] #253: obesity survey REDCap tracker and tools
#253: obesity survey REDCap tracker and tools --+- Reporter: bokov | Owner: huhickman Type: enhancement | Status: closed Priority: major | Milestone: obesity-survey-def Component: data-sharing | Resolution: fixed Keywords:| Blocked By: Blocking: 254 | --+- Comment (by dconnolly): Replying to [comment:28 huhickman]: > Also seems to suggest that adding a "Patient has email address Y/N" to our demographics load would be a handy thing. FWIW, that's in the MultiSiteDev HERON source as of May 19 (email_2896 branch merged in cc978529086f, with some tweaks after that.) ''oops... elephant was 261 changesets behind... fixed now; tip is 174857924059'' -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/253#comment:29> 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] #291: Gather 2015 2nd quarterly QA results
#291: Gather 2015 2nd quarterly QA results --+--- Reporter: mish | Owner: bos Type: problem | Status: assigned Priority: major | Milestone: data-quality-q2 Component: data-quality | Resolution: Keywords:| Blocked By: 259, 281, 285, 290, 306, 309 Blocking:| --+--- Comment (by bos): In [https://bitbucket.org/jvanschyndle/gpc-2015-q2-qa- files/src/1b9cf89ef8bdec77c474e2ed8adfe1b6e0ac910a/Q2_2015_GPC_QA.sql?at=default Q2_2015_GPC_QA.sql], `/* Encounters with No ICD 9 Code */` uses the result of `'num_valid_icd9'` which hasn't yet been populated. Am I missing something? -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/291#comment:18> 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] #263: Adaptable cohort query design and administration
#263: Adaptable cohort query design and administration --+ Reporter: nateapathy| Owner: rwaitman Type: design-issue | Status: new Priority: minor | Milestone: adaptable-accrual Component: data-stds | Resolution: Keywords:| Blocked By: 276 Blocking:| --+ Comment (by bzschoche): On an ADAPTABLE IRB call on 7.23.15, we learned that Duke is now tentatively scheduling for the first ADAPTABLE patients to be enrolled in '''December 2015'''. Work on governance continues. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/263#comment:10> 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] #285: HbA1c and other laboratory data: data quality check, CDM ETL
#285: HbA1c and other laboratory data: data quality check, CDM ETL --+--- Reporter: dconnolly | Owner: mish Type: enhancement | Status: assigned Priority: major | Milestone: bariatric-study-data Component: data-stds | Resolution: Keywords: data-quality cdm-etl | Blocked By: 158 Blocking: 291 | --+--- Comment (by dconnolly): I'm trying to add a report on this to our [https://redcap.gpcnetwork.org/redcap_v6.2.2/index.php?pid=19 qa redcap project] about labs such as A1c, but I can't find the relevant variable. Help? Or have plans changed since early June? (ticket:291#comment:4) Should I wait 'till next quarter for this feature? I wonder what LOINC code people are using. The top google hit is: [http://r.details.loinc.org/LOINC/4548-4.html?sections=Comprehensive 4548-4 Hemoglobin A1c/Hemoglobin.total in Blood]. I haven't checked babel. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/285#comment:3> 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] #227: Data QA for Breast Cancer Finder File
#227: Data QA for Breast Cancer Finder File -+- Reporter: tmcmahon | Owner: tmcmahon Type: task | Status: assigned Priority: major| Milestone: bc-survey-cohort-def Component: data-sharing | Resolution: Keywords: data-quality breast- | Blocked By: 217, 222, 223, 224, cancer-cohort | 230, 231, 234, 235, 244 Blocking: | -+- Comment (by dconnolly): update from Brian Gryzlak in 24 June GPC PM meeting: > - 7 of 8 sites have sent out surveys > - 2 or 3 sites have sent remailing to non-responders > - Response rate differs across sites > - Iowa 57% > - A few others ~40% > - A couple others are just starting to come in > - Next steps at Iowa: > - Process and submit data to study database Hmm... KeyGoalTracking shows 3 of 9 sites have finished with their finder file; I'd appreciate it if somebody would update it to clarify which are the 7 (vs 3) and which of the 9 are the 8. Tamara, Brittany, I don't see anything related to breast cancer surveys that merits discussion in SoftwareDev this week (tomorrow). Let us know if you prefer otherwise. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/227#comment:39> 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] #227: Data QA for Breast Cancer Finder File
#227: Data QA for Breast Cancer Finder File -+- Reporter: tmcmahon | Owner: tmcmahon Type: task | Status: closed Priority: major| Milestone: bc-survey-cohort-def Component: data-sharing | Resolution: fixed Keywords: data-quality breast- | Blocked By: 217, 222, 223, 224, cancer-cohort | 230, 231, 234, 235, 244 Blocking: | -+- Changes (by dconnolly): * status: assigned => closed * resolution: => fixed Comment: 7 sites is pretty clearly critical mass. Let's track the remaining sites in: - #312 WISC - #311 UTHSCSA -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/227#comment:40> 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] #240: Data Characterization queries for phase 1 CDM V1 compliance
#240: Data Characterization queries for phase 1 CDM V1 compliance -+- Reporter: campbell | Owner: huhickman Type: task | Status: assigned Priority: major| Milestone: drn- Component: data-stds| query-1 Keywords: cdm-etl CDM Compliance data-quality | Resolution: Blocking: | Blocked By: -+- Changes (by dconnolly): * owner: lv => huhickman Comment: I'm curious how it's going, Hubert. On track for getting query results sent back in the two week timeframe? It's coming up: July 29. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/240#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
Re: [gpc-informatics] #291: Gather 2015 2nd quarterly QA results
#291: Gather 2015 2nd quarterly QA results --+--- Reporter: mish | Owner: bos Type: problem | Status: assigned Priority: major | Milestone: data-quality-q2 Component: data-quality | Resolution: Keywords:| Blocked By: 259, 281, 285, 290, 306, 309 Blocking:| --+--- Comment (by mish): I believe it was intended as Diagnosis w/ valid icd9's. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/291#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
Re: [gpc-informatics] #291: Gather 2015 2nd quarterly QA results
#291: Gather 2015 2nd quarterly QA results --+--- Reporter: mish | Owner: bos Type: problem | Status: assigned Priority: major | Milestone: data-quality-q2 Component: data-quality | Resolution: Keywords:| Blocked By: 259, 281, 285, 290, 306, 309 Blocking:| --+--- Comment (by mish): Here are the results so far: || ||=Qa Base Results =||=Qa Base Percentages =||=Qa Base Results=||= Qa Base Percentages =||=Qa Bc Results =||=Qa Ob Results =||=Qa Base Results=||= Qa Base Percentages=||= Qa Bc Results=||= Qa Ob Results=||= Qa Term Matching=||=Qa Pcori Report+|| || ||=2014 Q4 =||=2014 Q4=||= 2015 Q1 =||=2015 Q1=||= 2015 Q1=||= 2015 Q1=||= 2015 Q2=||= 2015 Q2=||= 2015 Q2 =||=2015 Q2 =||=2015 Q2 =||=2015 Q2|| ||CMH||X||X||X||X|| ||X|| || || || || || || ||KUMC||X||X||X||X||X||X|| || || || || || || ||MCRF||X||X||X||X||X||X||X||X||X||X||X||X|| ||MCW||X||X|| || || || || || || || || || || ||UIOWA||X||X|| || || || || || || || || || || ||UMN||X||X||X||X||X||X||X||X||X||X||X||X|| ||UNMC||X||X||X||X||X||X|| || || || || || || ||UTHSCSA||X||X||X||X||X||X|| || || || || || || ||UTSW||X||X||X||X||X||X|| || || || || || || ||WISC||X||X||X||X||X||X||X||X||X||X||X||X|| I have heard from KUMC (Nathan) and they hope to have results in yet this week. I need to start the write up soon. Are there any other sites I should wait for before starting (UTHSCSA perhaps??) This Friday is the absolute latest for getting your data in before I start trying to draw some conclusions. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/291#comment:20> 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] #291: Gather 2015 2nd quarterly QA results
#291: Gather 2015 2nd quarterly QA results --+--- Reporter: mish | Owner: bos Type: problem | Status: assigned Priority: major | Milestone: data-quality-q2 Component: data-quality | Resolution: Keywords:| Blocked By: 259, 281, 285, 290, 306, 309 Blocking:| --+--- Comment (by bos): Replying to [comment:13 dconnolly]: > I don't think I understand the question. Why would you change the age ranges, Angela? Sorry, please allow me to retract the question. It was based on a faulty assumption after looking at the input file but before looking at the SQL code. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/291#comment:21> 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] #291: Gather 2015 2nd quarterly QA results
#291: Gather 2015 2nd quarterly QA results --+--- Reporter: mish | Owner: bos Type: problem | Status: assigned Priority: major | Milestone: data-quality-q2 Component: data-quality | Resolution: Keywords:| Blocked By: 259, 281, 285, 290, 306, 309 Blocking:| --+--- Comment (by bos): Replying to [comment:20 mish]: > (UTHSCSA perhaps??) Yes, we should have results posted by Wednesday. Sorry, results have delayed by my attendance at the PMN conference. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/291#comment:22> 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] #240: Data Characterization queries for phase 1 CDM V1 compliance
#240: Data Characterization queries for phase 1 CDM V1 compliance
-+-
Reporter: campbell | Owner: huhickman
Type: task | Status: assigned
Priority: major| Milestone: drn-
Component: data-stds| query-1
Keywords: cdm-etl CDM Compliance data-quality | Resolution:
Blocking: | Blocked By:
-+-
Comment (by huhickman):
We've ran through all of the 70 queries except for two; these two as
written will never complete - I've let them run for days just to see what
will happen. These two are
The SQL is generally quite inefficient - with exclusive use of subqueries
for correlation of data (no WITH clause to factor out common query
clauses).
1. Repeatedly converting the ISO-8601 character string dates (per
CDM spec) into native date datatypes on the fly.
2. No use of with clause to factor out subqueries (so that they get
evaluated only once).
3. No recommended indexes in CDM V1,2, or 3.
One of the samples that never completes :
{{{
#!sql
set echo off
set feedback off
SET HEAD OFF
SET PAGES 0
SET VERIFY OFF
SET FEED OFF
SET SHOW OFF
SET TERMOUT OFF
ALTER SESSION SET PLSQL_WARNINGS='DISABLE:ALL';
--
TotalValidHt Function - variable
create or replace function fnTotalValidHt return int is
TotalValidHt number;
begin
SELECT COUNT(ht) INTO TotalValidHt FROM Vital WHERE ht IS NOT NULL;
return TotalValidHt;
end;
/
--vit_l3_ht_dist
SET TERMOUT ON
SELECT vit_l3_ht_dist FROM
(SELECT 0 AS position, '"Statistic","HT"' AS vit_l3_ht_dist FROM dual
UNION
SELECT 1 AS position, '"' || Statistic || '",' || CAST(ht AS
VARCHAR(15)) FROM
(SELECT 'MIN' AS Statistic, MIN(ht) AS ht FROM Vital WHERE ht IS
NOT NULL
UNION
SELECT 'MAX' AS Statistic, MAX(ht) AS ht FROM
Vital WHERE ht IS NOT NULL
UNION
SELECT 'MEAN' AS Statistic, SUM(ht)/COUNT(ht) AS
ht FROM Vital WHERE ht IS NOT NULL
UNION
-- Median is calculated by sorting all
records by ht AND getting the ht value of the midpoint of all records
SELECT 'MEDIAN' AS Statistic, d.ht AS ht FROM
(SELECT ROW_NUMBER() OVER (ORDER BY ht desc) AS
rowno, ht FROM Vital WHERE ht IS NOT NULL
) d
WHERE d.rowno = CAST(fnTotalValidHt / 2 AS INT)
AND ht IS NOT NULL
UNION
-- Records with missing patid are counted here for completeness.
SELECT 'NULL or missing' AS Statistic, COUNT(*) AS
ht FROM Vital WHERE ht IS NULL
UNION
SELECT 'record_n' AS Statistic, COUNT(*) AS ht
FROM Vital WHERE ht IS NOT NULL
)csv
ORDER BY position,vit_l3_ht_dist
)m;
exit
}}}
The other one that does not complete is the same query except for weight.
In the above example using Oracle's MEDIAN function will help cure some of
the ills along with factoring out some of the subselects. I will rewrite
and send feedback for these two in particular.
--
Ticket URL:
<http://informatics.gpcnetwork.org/trac/Project/ticket/240#comment:20>
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Re: [gpc-informatics] #285: HbA1c and other laboratory data: data quality check, CDM ETL
#285: HbA1c and other laboratory data: data quality check, CDM ETL --+--- Reporter: dconnolly | Owner: mish Type: enhancement | Status: assigned Priority: major | Milestone: bariatric-study-data Component: data-stds | Resolution: Keywords: data-quality cdm-etl | Blocked By: 158 Blocking:| --+--- Changes (by dconnolly): * blocking: 291 => Comment: Tom says next time. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/285#comment:4> 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] #240: Data Characterization queries for phase 1 CDM V1 compliance
#240: Data Characterization queries for phase 1 CDM V1 compliance
-+-
Reporter: campbell | Owner: huhickman
Type: task | Status: assigned
Priority: major| Milestone: drn-
Component: data-stds| query-1
Keywords: cdm-etl CDM Compliance data-quality | Resolution:
Blocking: | Blocked By:
-+-
Comment (by huhickman):
I've rewritten the wt query (exactly same structure as above). It now
returns in 7 seconds instead of NEVER.
Removed the function and used a couple of with clauses.
Now to see what they say about the revised queries.
{{{
#!sql
with
valid_weights as
(select count(*) as TotalValidWt from Vital where wt is not null),
weights_with_rows as
(
SELECT ROW_NUMBER() OVER (ORDER BY wt desc) AS rowno, wt FROM Vital WHERE
wt IS NOT NULL
)
SELECT vit_l3_wt_dist FROM
(SELECT 0 AS position, '"Statistic","WT"' AS vit_l3_wt_dist FROM dual
UNION
SELECT 1 AS position, '"' || Statistic || '",' || CAST(WT AS
VARCHAR(15)) FROM
(SELECT 'MIN' AS Statistic, MIN(wt) AS WT FROM Vital WHERE wt IS
NOT NULL
UNION
SELECT 'MAX' AS Statistic, MAX(wt) AS WT FROM
Vital WHERE wt IS NOT NULL
UNION
SELECT 'MEAN' AS Statistic, SUM(wt)/COUNT(wt) AS
WT FROM Vital WHERE wt IS NOT NULL
UNION
-- Median is calculated by sorting all
records by wt AND getting the wt value of the midpoint of all records
select 'MEDIAN' As Statistic, wwr.wt as wt from
weights_with_rows wwr cross join valid_weights vw
where wwr.rowno = CAST(vw.TotalValidWt/2 as int) and WT is not null
UNION
SELECT 'NULL or missing' AS Statistic, COUNT(*) AS
wt FROM Vital WHERE wt IS NULL
UNION
SELECT 'record_n' AS Statistic, COUNT(*) AS wt
FROM Vital WHERE wt IS NOT NULL
)csv
ORDER BY position,vit_l3_wt_dist
)m;
--
Ticket URL:
<http://informatics.gpcnetwork.org/trac/Project/ticket/240#comment:21>
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Re: [gpc-informatics] #308: LEA Feasibility Query
#308: LEA Feasibility Query ---+--- Reporter: tmcmahon | Owner: tmcmahon Type: task | Status: accepted Priority: major | Milestone: Component: data-stds | Resolution: Keywords: | Blocked By: Blocking: | ---+--- Comment (by tmcmahon): Patient counts received from UTSW. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/308#comment:2> 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] #240: Data Characterization queries for phase 1 CDM V1 compliance
#240: Data Characterization queries for phase 1 CDM V1 compliance -+- Reporter: campbell | Owner: huhickman Type: task | Status: assigned Priority: major| Milestone: drn- Component: data-stds| query-1 Keywords: cdm-etl CDM Compliance data-quality | Resolution: Blocking: | Blocked By: -+- Comment (by dconnolly): Hubert / UNMC submitted results; Jessica and company are to send (a) high level metrics and (b) a characterization report (c) an invitation to meet and discuss the report. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/240#comment:22> 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] #291: Gather 2015 2nd quarterly QA results
#291: Gather 2015 2nd quarterly QA results --+- Reporter: mish | Owner: bos Type: problem | Status: assigned Priority: major | Milestone: data-quality-q2 Component: data-quality | Resolution: Keywords:| Blocked By: 259, 281, 306, 309 Blocking:| --+- Comment (by mish): I've started the [https://docs.google.com/document/d/1lECK43_tp- PblFtGIbFLvaJGq14Q9Miugcspe5A8Hr0/edit write up] and hope to be finished this week. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/291#comment:25> 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] #80: assessment of GPC vs. data privacy and security standards
#80: assessment of GPC vs. data privacy and security standards --+- Reporter: dconnolly | Owner: mish Type: task | Status: assigned Priority: major | Milestone: data-sec-check Component: data-sharing | Resolution: Keywords: security | Blocked By: 79 Blocking:| --+- Comment (by bzschoche): Umberto told Russ he would get the draft back to KUMC by end of next week, ~Aug5. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/80#comment:27> 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] #253: obesity survey REDCap tracker and tools
#253: obesity survey REDCap tracker and tools --+- Reporter: bokov | Owner: huhickman Type: enhancement | Status: closed Priority: major | Milestone: obesity-survey-def Component: data-sharing | Resolution: fixed Keywords:| Blocked By: Blocking: 254 | --+- Comment (by dconnolly): The `tracker_load.py` script worked for me, after a couple tweaks: 84. Test DB connections before doing any work \\[a9cef5738229] Angela Bos 85. add config option to access clarity tables over a database link \\[35fe2794a4f0] Dan Connolly https://bitbucket.org/DanC/survey_tracker/overview -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/253#comment:30> 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] #253: obesity survey REDCap tracker and tools
#253: obesity survey REDCap tracker and tools --+- Reporter: bokov | Owner: huhickman Type: enhancement | Status: closed Priority: major | Milestone: obesity-survey-def Component: data-sharing | Resolution: fixed Keywords:| Blocked By: Blocking: 254 | --+- Comment (by bos): Replying to [comment:30 dconnolly]: Awesome! Your pull request for `35fe2794a4f0` has been merged into our [https://bitbucket.org/bos_uthscsa/survey_tracker/overview default repo]. You can get some overview stats by running this: `$ python tracker_load.py stats` -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/253#comment:31> 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] #80: assessment of GPC vs. data privacy and security standards
#80: assessment of GPC vs. data privacy and security standards --+- Reporter: dconnolly | Owner: mish Type: task | Status: assigned Priority: major | Milestone: data-sec-check Component: data-sharing | Resolution: Keywords: security | Blocked By: 79 Blocking:| --+- Comment (by dconnolly): Umberto, I see a message of Monday, August 03, 2015 9:21 AM with a link to a draft, but neither Brittany nor I can get at it. How about you send it to gpc-dev@listserv.kumc.edu? -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/80#comment:28> 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] #291: Gather 2015 2nd quarterly QA results
#291: Gather 2015 2nd quarterly QA results --+-- Reporter: mish | Owner: bos Type: problem | Status: assigned Priority: major | Milestone: data-quality-q2 Component: data-quality | Resolution: Keywords:| Blocked By: 259, 281, 306 Blocking:| --+-- Changes (by mish): * blockedby: 259, 281, 306, 309 => 259, 281, 306 -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/291#comment:26> 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
[gpc-informatics] #327: Gather 2015 3rd quarterly QA results
#327: Gather 2015 3rd quarterly QA results ---+-- Reporter: mish | Owner: mish Type: problem | Status: new Priority: major | Milestone: Component: data-quality | Keywords: Blocked By: 309 | Blocking: ---+-- This represents the effort for the creation of the 2015 Q3 quarterly QA query and tabulation of the results. Issues to be addressed in this quarter's QA review include: * #309 - Better support for QA results on MS SQL Server * ''#tbd'' - Better support for QA results on Oracle Server -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/327> 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] #291: Gather 2015 2nd quarterly QA results
#291: Gather 2015 2nd quarterly QA results --+-- Reporter: mish | Owner: bos Type: problem | Status: assigned Priority: major | Milestone: data-quality-q2 Component: data-quality | Resolution: Keywords:| Blocked By: 259, 281, 306 Blocking:| --+-- Comment (by mish): Results from UNMC and UTSCSA have3 been incorporated in the REDCap database. Partial results from CMH have also been integrated. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/291#comment:27> 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] #327: Gather 2015 3rd quarterly QA results
#327: Gather 2015 3rd quarterly QA results --+--- Reporter: mish | Owner: mish Type: problem | Status: new Priority: major | Milestone: Component: data-quality | Resolution: Keywords:| Blocked By: 309 Blocking:| --+--- Description changed by mish: Old description: > This represents the effort for the creation of the 2015 Q3 quarterly QA > query and tabulation of the results. > > Issues to be addressed in this quarter's QA review include: > * #309 - Better support for QA results on MS SQL Server > * ''#tbd'' - Better support for QA results on Oracle Server New description: This represents the effort for the creation of the 2015 Q3 quarterly QA query and tabulation of the results. Issues to be addressed in this quarter's QA review include: * #309 - Better support for QA results on MS SQL Server * ''#tbd'' - Better support for QA results on Oracle Server * #326 - Add "volume" to med terms. * Back to the basics, we need to ensure that we have full ethnicity and race questions tackled. -- -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/327#comment:1> 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] #308: LEA Feasibility Query
#308: LEA Feasibility Query ---+--- Reporter: tmcmahon | Owner: tmcmahon Type: task | Status: accepted Priority: major | Milestone: Component: data-stds | Resolution: Keywords: | Blocked By: Blocking: | ---+--- Comment (by mish): Counts and time spent sent to Tamara from WISC. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/308#comment:3> 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] #191: represent PCORI CDM 2.x terminology as i2b2 metadata
#191: represent PCORI CDM 2.x terminology as i2b2 metadata ---+ Reporter: dconnolly | Owner: dconnolly Type: problem| Status: new Priority: medium | Milestone: Component: data-stds | Resolution: Keywords: | Blocked By: 109 Blocking: 317| ---+ Changes (by dconnolly): * type: => problem Comment: I finally got the SCHILS ontology on babel. "PCORnet Demographics" shows up twice, as do the other top level folders because I inserted the TABLE_ACCESS rows twice. I hope that's not too much of a distraction. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/191#comment:6> 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] #295: breast cancer correspondence between EHR and tumor registry variables - i2b2 query
#295: breast cancer correspondence between EHR and tumor registry variables - i2b2 query --+ Reporter: dconnolly | Owner: dconnolly Type: enhancement | Status: new Priority: major | Milestone: cohort-char-bc-db Component: data-sharing | Resolution: Keywords: breast-cancer-cohort | Blocked By: 296 Blocking: 297, 302 | --+ Comment (by dconnolly): I made a query, in the shared "Breast Cancer cohort characterization" folder on babel: - BC DX treatment #295 [8-4-2015] [dconno...@kumc.edu] It's got treatment and diagnosis info from the EMR. Treatment consists of the procedures Prakash identified as well as the chemo, radiology, etc. that Russ identified. This should suffice for an initial investigation, but I suppose we need to mix in all the stuff from #204 before it's finished. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/295#comment:5> 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] #295: breast cancer correspondence between EHR and tumor registry variables - i2b2 query
#295: breast cancer correspondence between EHR and tumor registry variables - i2b2 query --+ Reporter: dconnolly | Owner: dconnolly Type: enhancement | Status: new Priority: major | Milestone: cohort-char-bc-db Component: data-sharing | Resolution: Keywords: breast-cancer-cohort | Blocked By: 296 Blocking: 297, 302 | --+ Comment (by dconnolly): looks like we grabbed the chemo meds from MCRF and the rest from KUMC. Is that an issue? We'll see. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/295#comment:6> 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] #240: Data Characterization queries for phase 1 CDM V1 compliance
#240: Data Characterization queries for phase 1 CDM V1 compliance
-+-
Reporter: campbell | Owner: huhickman
Type: task | Status: assigned
Priority: major| Milestone: drn-
Component: data-stds| query-1
Keywords: cdm-etl CDM Compliance data-quality | Resolution:
Blocking: | Blocked By:
-+-
Comment (by huhickman):
Had a phone conversation with Jessica Sturtevant today regarding feedback
on UNMC's submitted data. As it turns out there is an issue with the
shell script truncating a bit too much of the output.
The line in question is:
{{{
#!sh
sqlplus $USERNAME/$PASSWORD@$ORACLE_SID @$i | head -n -2 | tail -n +12 >
$MYFILE
}}}
The head and tail commands whack off the last 2 and first 11 lines of
output. The intent was to strip off Oracle sqlplus output and just leave
their CSV output. Our UNIX environment only has 1 extra line at the
bottom of a file and 9 at the top of the file, so submitted files were not
what they intended.
They are going to resubmit the queries to us via PopMedNet and we are to
re-run and resubmit by next Friday (8/14/12015).
I'll either adjust their script, remove the head/tail, or modify it in way
that may be less susceptible to the variability of a site's particular
Oracle environment.
I am to omit the two queries that don't complete for now - Jessica
appreciated our feedback and they are working on revised queries that they
will disseminate when they have revisions complete.
Take Deux, here we go !
--
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Re: [gpc-informatics] #308: LEA Feasibility Query
#308: LEA Feasibility Query ---+--- Reporter: tmcmahon | Owner: tmcmahon Type: task | Status: accepted Priority: major | Milestone: Component: data-stds | Resolution: Keywords: | Blocked By: Blocking: | ---+--- Comment (by gbushee): MCW counts and times sent to Tamara today. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/308#comment:4> 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] #161: PopMedNet node at CMH
#161: PopMedNet node at CMH --+-- Reporter: lv| Owner: nateapathy Type: enhancement | Status: accepted Priority: minor | Milestone: drn-query-1 Component: data-sharing | Resolution: Keywords:| Blocked By: 209 Blocking:| --+-- Old description: > Outcome of September 16th teleconference was that Aaron Meyer will be the > contact person for CMH with regard to PopMedNet. New description: Outcome of September 16th teleconference was that Aaron Meyer will be the contact person for CMH with regard to PopMedNet. Update August 7 - Rita Fothergill and Warren Teachout are CMH leads for Pop MedNet. -- Comment (by nateapathy): PopMedNet DataMart Client has been installed and configured at CMH and is in a production Citrix environment with access to the CDM tables. We have this query request available and are ready to execute the queries at this time. Rita Fothergill and Warren Teachout will be the point people, instead of Aaron Meyer. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/161#comment:14> 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] #291: Gather 2015 2nd quarterly QA results
#291: Gather 2015 2nd quarterly QA results --+-- Reporter: mish | Owner: bos Type: problem | Status: closed Priority: major | Milestone: data-quality-q2 Component: data-quality | Resolution: fixed Keywords:| Blocked By: 259, 281, 306 Blocking:| --+-- Changes (by dconnolly): * status: assigned => closed * resolution: => fixed Comment: Tom, feel free to polish the write-up more as you see fit, but this is done to my satisfaction. If you think it's worth more group attention, go ahead and re-open it. For follow-up work, see milestone:data-quality-q3 -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/291#comment:28> 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] #308: LEA Feasibility Query
#308: LEA Feasibility Query ---+--- Reporter: tmcmahon | Owner: tmcmahon Type: task | Status: closed Priority: major | Milestone: Component: data-stds | Resolution: fixed Keywords: | Blocked By: Blocking: | ---+--- Changes (by dconnolly): * status: accepted => closed * resolution: => fixed Comment: UTHSCSA reported completion in the 4 Aug teleconference (#12). So that's all 4 sites. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/308#comment:5> 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] #80: assessment of GPC vs. data privacy and security standards
#80: assessment of GPC vs. data privacy and security standards --+- Reporter: dconnolly | Owner: mish Type: task | Status: assigned Priority: major | Milestone: data-sec-check Component: data-sharing | Resolution: Keywords: security | Blocked By: 79 Blocking:| --+- Comment (by bzschoche): Russ will review the final draft on 8.10 in the KUMC PMO meeting. Brittany will submit once approved. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/80#comment:29> 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] #80: assessment of GPC vs. data privacy and security standards
#80: assessment of GPC vs. data privacy and security standards --+- Reporter: dconnolly | Owner: bzschoche Type: task | Status: assigned Priority: major | Milestone: data-sec-check Component: data-sharing | Resolution: Keywords: security | Blocked By: 79 Blocking:| --+- Changes (by dconnolly): * owner: mish => bzschoche -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/80#comment:30> 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] #240: Data Characterization queries for phase 1 CDM V1 compliance
#240: Data Characterization queries for phase 1 CDM V1 compliance
-+-
Reporter: campbell | Owner: huhickman
Type: task | Status: assigned
Priority: major| Milestone: drn-
Component: data-stds| query-1
Keywords: cdm-etl CDM Compliance data-quality | Resolution:
Blocking: | Blocked By:
-+-
Comment (by huhickman):
I've changed the script line above to be:
{{{
#!sh
sqlplus $USERNAME/$PASSWORD@$ORACLE_SID @$i | sed -e '/SQL\*Plus/d' -e
'/Copyright/d' -e '/Connected to:/d' -e '/Disconnected/d' -e '/Oracle/d'
-e '/^\s*$/d' > $MYFILE
}}}
The scripts are running once more. There may be more elegant solutions,
but `sed` works.
--
Ticket URL:
<http://informatics.gpcnetwork.org/trac/Project/ticket/240#comment:24>
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Re: [gpc-informatics] #166: PopMedNet node at WISC
#166: PopMedNet node at WISC --+-- Reporter: lv| Owner: kwanta Type: enhancement | Status: reopened Priority: minor | Milestone: drn-query-1 Component: data-sharing | Resolution: Keywords:| Blocked By: 209 Blocking:| --+-- Comment (by kwanta): This performance issue with PopMedNet was discovered when UW Health installed version 4. UW Health has since installed version 5, and have had no major issues. Closing ticket. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/166#comment:11> 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] #166: PopMedNet node at WISC
#166: PopMedNet node at WISC --+-- Reporter: lv| Owner: kwanta Type: enhancement | Status: closed Priority: minor | Milestone: drn-query-1 Component: data-sharing | Resolution: fixed Keywords:| Blocked By: 209 Blocking:| --+-- Changes (by kwanta): * status: reopened => closed * resolution: => fixed -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/166#comment:12> 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] #327: Gather 2015 3rd quarterly QA results
#327: Gather 2015 3rd quarterly QA results --+ Reporter: mish | Owner: gkowalski Type: problem | Status: assigned Priority: major | Milestone: Component: data-quality | Resolution: Keywords:| Blocked By: 309 Blocking:| --+ Changes (by dconnolly): * owner: mish => gkowalski * status: new => assigned Comment: Thanks for taking the ball on this, George. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/327#comment:2> 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] #327: Gather 2015 3rd quarterly QA results
#327: Gather 2015 3rd quarterly QA results --+--- Reporter: mish | Owner: mish Type: problem | Status: assigned Priority: major | Milestone: Component: data-quality | Resolution: Keywords:| Blocked By: 309 Blocking:| --+--- Changes (by dconnolly): * owner: gkowalski => mish Comment: oops... I assigned this to George thinking it was an Oracle specific ticket. Sorry for the email noise. Tom, I trust you'll create a ticket for George. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/327#comment:3> 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] #191: represent PCORI CDM 2.x terminology as i2b2 metadata
#191: represent PCORI CDM 2.x terminology as i2b2 metadata
---+
Reporter: dconnolly | Owner: dconnolly
Type: problem| Status: new
Priority: medium | Milestone:
Component: data-stds | Resolution:
Keywords: | Blocked By: 109
Blocking: 317|
---+
Comment (by nateapathy):
Following up on the discussion from 8.11.15 GPC Dev call:
{{{
c) how cost effective to switch to SCHILS terms from GPC?
i) Dan : feedback from Cerner folks? (not here today). I’ll try to
catch up with
them
ii) PR/UTSW: vote to not switch, prefer to maybe map between the two,
but our
GPC terms cover more granular and we’d lose that if we switch
iii) DC/KUMS: maybe adopt SCHILS terms for things we haven’t settled
for GPC
yet, e.g. use SCHILS for procedures but not diagnoses
iv) RW/KUMC: obesity & adaptable trials drive timeline (for Sept.) to
implement new
CDM terms
}}}
The most significant improvement that the SCILHS ontology provides is that
it aligns with best practices for i2b2 design and comes with CDM creation
scripts using the "PCORNET_CD" field. The most obvious design improvements
are how demographics are stored in the database and how modifiers are
structured. The transition from the Cerner standard i2b2 ontology to the
SCILHS ontology was relatively straightforward, largely thanks to the use
of best-practice designs for i2b2. For example, storing patient
demographic data as observations in the OBSERVATION_FACT table is not a
standard design practice, and the SCILHS ontology resolves this.
As for granularity, it can always be added back in later versions, and I
would like to see us pursue that with SCILHS as a partner rather than
creating a hybrid which will undoubtedly be more convoluted for the end
user.
It also gives us significant ability to leverage other groups' work, and
decreases the distance between "proprietary" i2b2 design and something
moderately resembling a standard, at least across i2b2-using PCORnet
CDRNs. It would behoove us to tack as closely as possible to any
repeatable standards emerging from other groups, as it only increases our
economies of scale. My understanding from comment3 on this ticket is that
we would be adopting the SCILHS ontology as a group - I did not think the
decision was still up for debate.
I also recognize that other groups are focusing on the Obesity terms and
ADAPTABLE terms. As CMH will not be participating in ADAPTABLE, we've had
cycles to focus on the SCILHS effort that other teams won't have for some
time.
--
Ticket URL:
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Re: [gpc-informatics] #191: represent PCORI CDM 2.x terminology as i2b2 metadata
#191: represent PCORI CDM 2.x terminology as i2b2 metadata ---+ Reporter: dconnolly | Owner: dconnolly Type: problem| Status: new Priority: medium | Milestone: Component: data-stds | Resolution: Keywords: | Blocked By: 109 Blocking: 317| ---+ Comment (by dconnolly): Thanks for the experience report. On process... Replying to [comment:7 nateapathy]: > ... My understanding from comment:3 on this ticket is that we would be adopting the SCILHS ontology as a group - I did not think the decision was still up for debate. Well, your experience report aligns with my expectation that adopting SCILHS would be cost-effective overall, but where it overlaps with designs we have already adopted, for example demographics (#67), [wiki:DataRepositoryManagement#design-process due process] involves re- opening such tickets and then closing them again. I probably should have started to do that by now but I have been reluctant on behalf of dev groups (such as KUMC!) that have investment in the existing design. (see also [https://informatics.kumc.edu/work/wiki/SemanticWeb#TerminologyEvolution terminology evolution].) This whole SCHILS business really shouldn't be hiding under this CDM 2.x ticket at all. I just haven't managed to re-organize tickets properly. Here's hoping for time to do so. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/191#comment:8> 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] #80: assessment of GPC vs. data privacy and security standards
#80: assessment of GPC vs. data privacy and security standards --+- Reporter: dconnolly | Owner: bzschoche Type: task | Status: assigned Priority: major | Milestone: data-sec-check Component: data-sharing | Resolution: Keywords: security | Blocked By: 79 Blocking:| --+- Comment (by bzschoche): Tom is checking to see if the draft applies to Milestones 3.10 and 3.11 as well before I submit to PCORI. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/80#comment:31> 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
