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 mish): * owner: bzschoche => mish -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/80#comment:32> 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): As I read it, * 3.9 lays out our security plan, * 3.10 is an assessment of our performance to the plan, * 3.11 is the risk assessment/mediation given our performance, and * 3.12 is the actual "we're complete" GPC has completed the plan, we still need to do a survey to ask each sites their compliance with: 3.3.1 Compliance with Laws 3.3.2 Security Risk Assessment and Policies 3.3.3 Breaches 3.3.4 Training For 3.10 - in the case of WISC, I can say that we comply with 3.3.1, 3.3.3, 3.3.4 in full. But 3.3.2 is lacking written documentation. For 3.11 - for WISC the mitigation plan would be to complete the documentation by Aug 31st. Once the mitigation plans are in place, we can claim that we have achieved 3.12 Note: we do not have to have all of the risks mitigated, we simply need to have mitigation plans in place to be complete. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/80#comment:33> 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): Tom, we did the survey; see comment:21. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/80#comment:34> 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): I sit corrected, the survey in 21 comes close (enough?). We just need to follow through with it (do actual risk planning with the information) and continue to do so on an annual basis. Two comments: * I think the question about "active participation" of "those responsible for interpretation of applicable laws and regulations" needs to change or we need an additional question that asks if each site is in actual compliance. Simply having key people in a conversation does not ensure that compliance is being met. * We should probably come right out and ask if everyone participating has had the appropriate training. While a description of the process is nice, it doesn't necessarily mean that the appropriate training has been had by all those involved. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/80#comment:35> 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): Tom, let's scope this ticket to 3.9 and 3.10, claim victory on that much (I made a new ticket for the rest: #334). Please revise the 3.9 draft to note that we have done one round of assessment. (I think this amounts to changing "will do..." to "have done..." in one or two places). And I guess put 3.10 on the cover page. (Or ask Umberto to do it or let me know you'd rather I do it.) For reference: - [http://listserv.kumc.edu/pipermail/gpc-dev/2015q3/001922.html 3.9 and beyond] \\ UMBERTO TACHINARDI Mon Aug 3 11:50:23 CDT 2015 - revised Thursday, August 06, 2015 5:42 PM -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/80#comment:36> 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: reopened Priority: minor | Milestone: drn-query-1 Component: data-sharing | Resolution: Keywords:| Blocked By: 209 Blocking:| --+-- Changes (by dconnolly): * status: closed => reopened * resolution: fixed => Comment: IBQ todo. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/166#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] #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:| --+-- Comment (by dconnolly): ETA: >= 2 weeks (18 Aug call. Warren, via Rita) -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/161#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] #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): 18 Aug dev call update: - UIOWA - ??? - WISC - no news - MCRF - study team still validating patient list - UMN - Justin: looks like it should have gone out; I'll try to confirm - UNMC - plan to meet with coordinator later this week -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/284#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] #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:| --+ Changes (by bzschoche): * cc: schandaka (added) Comment: From the ADAPTABLE protocol draft released Aug 12, 2015, pp. 20-21. (see attachment:"ADAPTABLE Protocol_081215.docx") Inclusion / Exclusion criteria: 1. Known atherosclerotic cardiovascular disease (ASCVD), defined by a history of prior myocardial infarction, prior coronary angiography showing ≥75% stenosis of at least one epicardial coronary vessel, or prior coronary revascularization procedures (either PCI or CABG) 2. Age ≥ 18 years 3. No known safety concerns or side effects considered to be related to aspirin, including - No history of significant allergy to aspirin such as anaphylaxis, urticaria, or significant gastrointestinal intolerances - No history of recent upper gastrointestinal events including a symptomatic gastric or duodenal ulcer or an upper gastrointestinal bleeding event within the past 12 months - Significant bleeding disorders that preclude the use of aspirin 4. Access to the Internet or agreement to collect follow-up information by the DCRI Call Center from patients without Internet access 5. Not currently treated with an oral anticoagulant – either warfarin or a novel anticoagulant (dabigatran, rivaroxaban, apixaban, edoxaban) – and not planned to be treated in the future with an oral anticoagulant for indications such as atrial fibrillation, deep venous thrombosis, or pulmonary embolism. 6. Female patients who are not pregnant or nursing an infant 7. Estimated risk of a major cardiovascular event (MACE) > 8% over next 3 years as defined by the presence of at least one or more of the following enrichment factors: - Age > 65 years - Known serum creatinine > 1.5 mg/dL - Diabetes mellitus - Known 3-vessel coronary artery disease - Known cerebrovascular disease and/or peripheral arterial disease - Known left ventricular ejection fraction (LVEF) < 50% - Current cigarette smoker. 8. Able and willing to provide informed consent and agreeing to be followed through the Internet and/or through calls by the DCRI Call Center for the duration of the trial (maximum expected follow-up of 30 months) There will be no exclusions for any upper age limit, comorbid conditions, or concomitant medications other than oral anticoagulants that are used at the time of randomization or are planned to be used during the study follow-up. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/263#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] #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 nateapathy): As an aside, I am probably not the right person to be the final approver for this. CMH is not participating in ADAPTABLE which makes me think that the "reporter" should change from me to someone with more of a stake in the ADAPTABLE study. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/263#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] #263: Adaptable cohort query design and administration
#263: Adaptable cohort query design and administration --+ Reporter: schandaka | Owner: rwaitman Type: design-issue | Status: new Priority: minor | Milestone: adaptable-accrual Component: data-stds | Resolution: Keywords:| Blocked By: 276 Blocking:| --+ Changes (by dconnolly): * reporter: nateapathy => schandaka Comment: Good point, Nate. I gather Sravani is doing informatics work on ADAPTABLE. Sravani, feel free to re-organize this ticket as you see fit; e.g. change the scope or split it into multiple tickets or whatever. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/263#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 | --+- Comment (by lv): Our study team contacted Sarah Schlachter about Survey 1 Email Letter, which includes the line, "3. If you do not wish to participate in this survey, please click [HERE]." The explanation provided by Dan Hale was that one site wanted this in order for a person to ACTIVELY decline to participate (as opposed to simply not proceeding). Has anyone developed a method for this? -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/253#comment:32> 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): Yes, we added a question to our survey: "By marking YES, you are agreeing to participate in this study. If you do not want to participate in this study, click NO, and the survey will close" I'm not sure how we got the survey to click close if they click NO. Bhargav? We also put a blurb in the invitation text: "3. If you do not wish to participate in this survey, please open the survey and select NO to the first question." -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/253#comment:33> 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 badagarla): Replying to [comment:33 dconnolly] and [comment:32 lv]: - Yes. We added a yes/no field at the very top of the survey. - Then we used "Set up Stop actions for this Survey question" actions on that field so the survey will end if the user says NO. - We also changed the third option in the letter as Dan pointed out. - But, before we made the changes Sarah contacted IRB folks and got a reply from Rhonda at UTHSCA who said the changes should be ok as "''this study has been approved for a Waiver of documentation of consent under 45CFR46.117(c)''". -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/253#comment:34> 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 bzschoche): ALS survey update from today's PM call: - Iowa: status not available; BZ will follow up with Brian Gryzlak next week - WISC: waiting on GPC reliance checklist; data query is done - MCRF: Next week, Bob Greenlee will work with the PI to validate the 89 individuals, after that the surveys will go out; combination email/snailmail - UMN: Survey alert letter went out 7/27 to 58 patients, packet followed on 8/6 to those 58 patients - UNMC: the coordinator has everything in-hand ready to go. Russ Buzalko said they're aiming for mailing within the next 1-2 weeks Both KUMC and MCW have surpassed the 50% participation threshold. Yay. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/284#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] #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:|
--+---
Comment (by bzschoche):
Tom: I need to use these results (specifically race and ethnicity) to
address Milestone 1.10 ("Diversity goals are reached"). Please add me to
any relevant REDCap surveys.
The original due date has been revised to September; let me know when I
can look for results.
--
Ticket URL:
<http://informatics.gpcnetwork.org/trac/Project/ticket/327#comment:4>
gpc-informatics <http://informatics.gpcnetwork.org/>
Greater Plains Network - Informatics
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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 Comment: Brittany has a handle on the edits needed for 3.9 and 3.10. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/80#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] #348: Data Profile over time: How fresh is it (e.g. cancer tumor registry)? how far back does the data go?
#348: Data Profile over time: How fresh is it (e.g. cancer tumor registry)? how far back does the data go? ---+--- Reporter: dconnolly | Owner: dconnolly Type: enhancement | Status: new Priority: major | Milestone: cohort-char-bc-db Component: data-sharing | Keywords: data-quality Blocked By:| Blocking: ---+--- During the recent MU site visit, a researcher asked how far back our data goes. Russ explained that it varies from site to site and from system to system within sites. Russ answered on behalf of KUMC by way of a recent HERON release contents summary: - [https://informatics.kumc.edu/work/blog/heron-calhoun- update#HERONCalhounContentsSummary HERON Calhoun Contents Summary] The code we use to generate the summary above is - [https://informatics.kumc.edu/work/browser/heron_load/report_stats.sql report_stats.sql] which draws from `concepts_stats`, which is built in - [https://informatics.kumc.edu/work/browser/heron_load/concept_stats.sql concept_stats.sql] Actually, the numbers from that code are only part of the story; we manually maintain info about when the various systems went live and when is our most recent snapshot. Let's integrate this sort of data profiling into our quarterly data quality review process. For bonus points, let's actually do breakdowns by year (or quarter or month). But perhaps that's a large goal that we should break down into parts. A smaller scoped task is something that I owe the breast cancer research team: info about how fresh tumor registry data is at each site. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/348> 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] #348: Data Profile over time: How fresh is it (e.g. cancer tumor registry)? how far back does the data go?
#348: Data Profile over time: How fresh is it (e.g. cancer tumor registry)? how far back does the data go? --+ Reporter: dconnolly | Owner: bzschoche Type: enhancement | Status: assigned Priority: major | Milestone: cohort-char-bc-db Component: data-sharing | Resolution: Keywords: data-quality | Blocked By: Blocking:| --+ Changes (by dconnolly): * cc: bzschoche (added) * owner: dconnolly => bzschoche * status: new => assigned Comment: I hope we can integrate this data into babel somehow, but meanwhile, let's try the everybody-edit-a-spreasheet approach: - [https://docs.google.com/spreadsheets/d/1JE9IGm2cA1xtybHF6AAljCOpKvjhOerIn985BfP1qPU/edit?usp=sharing GPC Data Freshness and Temporal Coverage] Each site please add a row for your tumor registry. Feel free to add others. Again, bonus points for breakdown by year or month or whatever. Brittany, I hope this just takes each site a few minutes and it doesn't merit coordination with the project managers, but just in case... when is the next time you meet with site project managers? Is it convenient to get ETAs from them? -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/348#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] #348: Data Profile over time: How fresh is it (e.g. cancer tumor registry)? how far back does the data go?
#348: Data Profile over time: How fresh is it (e.g. cancer tumor registry)? how far back does the data go? --+ Reporter: dconnolly | Owner: bzschoche Type: enhancement | Status: assigned Priority: major | Milestone: cohort-char-bc-db Component: data-sharing | Resolution: Keywords: data-quality | Blocked By: Blocking:| --+ Comment (by bzschoche): The next call is September 18th. I can request ETAs via email if needed. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/348#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] #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 lv): Is the idea that we'll need CDM v3 compliance earlier than the SCILHS timeline (end of the year for v2.1/3), which could provide an opportunity to contribute our work? Can either KUMC or NateA comment in a general way on the effort required to implement the SCILHS work? I agree with following one standard rather than creating our own hybrid. If the level of granularity is requied, maybe we should advocate for including it in their later release? -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/191#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] #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: vleonardo Type: enhancement | Status: assigned Priority: major | Milestone: cohort-char-bc-db Component: data-sharing | Resolution: Keywords: breast-cancer-cohort | Blocked By: 296, 328 Blocking: 297, 302 | --+ Changes (by dconnolly): * owner: dconnolly => vleonardo * status: new => assigned Comment: Looks like you're ahead of me on some details in this area; over you to move the ball for a while, Vince. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/295#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] #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): Our implementation effort estimation ended up being much more than the actual work effort, which was very reassuring. The SCILHS ontology, due to its limited granularity, is pretty straightforward to implement, and follows best practices for i2b2 design, which makes it easier to implement. In terms of mapping our hierarchies and terms to the SCILHS ontology hierarchies and terms, that effort which we thought would be monumental, was actually not nearly as cumbersome as we thought, largely because we were already fairly well aligned since (specifically for demographics) Cerner i2b2 uses the standard i2b2 demographic ontology, and the SCILHS ontology sticks fairly closely to that design. Granted, the ease of that transition was due in large part to our local standard following the i2b2 standard pretty tightly, so the degree to which on a site has deviated from the i2b2 standard ontologies will be a good proxy for work effort to align with SCILHS. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/191#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] #240: Data Characterization queries for phase 1 CDM V1 compliance
#240: Data Characterization queries for phase 1 CDM V1 compliance -+- Reporter: campbell | Owner: campbell 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: huhickman => campbell Comment: Jim C. writes Monday, August 24, 2015 2:22 PM: > ... I will be picking back up the data characterization activities he covered while I was on vacation -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/240#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] #254: prepare Weight and Health survey contact information at all sites
#254: prepare Weight and Health survey contact information at all sites +- Reporter: bokov | Owner: nateapathy Type: task| Status: assigned Priority: major | Milestone: obesity-survey-def Component: data-sharing| Resolution: Keywords: obesity-cohort | Blocked By: 249, 250, 252, 253 Blocking: | +- Changes (by dconnolly): * cc: gpc-dev@… (added) * owner: susandm => nateapathy Comment: Nate, can you give us an ETA on this? i.e. column G "Estimated date to upload data builder file into GPC REDCap" of the spreadsheet linked from comment:17. If it's not clear what's involved, let us know and re-assign this (e.g. to Alex or me). UMN folks, your ETA was Aug 20; how have plans changed? UTSW, WISC, any news on regulatory status? Alex, do you understand MCW's alternative approach? Does it look workable? If not, please open a separate ticket. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/254#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] #254: prepare Weight and Health survey contact information at all sites
#254: prepare Weight and Health survey contact information at all sites +- Reporter: bokov | Owner: nateapathy Type: task| Status: assigned Priority: major | Milestone: obesity-survey-def Component: data-sharing| Resolution: Keywords: obesity-cohort | Blocked By: 249, 250, 252, 253 Blocking: | +- Comment (by nateapathy): I can't give an update on the data builder file upload; Warren and Rita at CMH own that process. Warren has been trying to generate the file using the python scripts, as the data builder plugin is not ready in production yet. Warren might be interested in talking to the MCW folks about their alternative approach, if it's viable. The R Data Builder plugin install has been delayed due to a non-i2b2 issue here that required Aaron's attention. Since Aaron is our only 100% dedicated engineering resource for GPC, the setup of the R Data Builder has been on pause until that issue is resolved. We anticipate releasing the new hardware with the R Data Builder enabled in early October. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/254#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] #254: prepare Weight and Health survey contact information at all sites
#254: prepare Weight and Health survey contact information at all sites +- Reporter: bokov | Owner: bokov Type: task| Status: assigned Priority: major | Milestone: obesity-survey-def Component: data-sharing| Resolution: Keywords: obesity-cohort | Blocked By: 249, 250, 252, 253 Blocking: | +- Changes (by nateapathy): * owner: nateapathy => bokov -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/254#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: campbell 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): * cc: bzschoche (added) Comment: Jim, Laurel, what's a realistic and useful due date for this work? Our previous best guess at a completion date for this was today. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/240#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] #267: CDM V2 Vitals.Smoking History compliance
#267: CDM V2 Vitals.Smoking History compliance ---+-- Reporter: campbell | Owner: mish Type: task | Status: assigned Priority: major | Milestone: data-quality-q3 Component: data-stds | Resolution: Keywords: Smoking history DM V2 | Blocked By: Blocking: | ---+-- Changes (by dconnolly): * owner: campbell => mish * milestone: => data-quality-q3 Comment: Is it feasible to measure where we are in the Q3 timeframe? -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/267#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: data-quality-q3 Component: data-quality | Resolution: Keywords:| Blocked By: 309 Blocking:| --+-- Changes (by dconnolly): * milestone: => data-quality-q3 -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/327#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] #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: data-domains3 Component: data-stds | Resolution: Keywords: | Blocked By: 109 Blocking: 317| ---+ Changes (by dconnolly): * milestone: => data-domains3 Comment: oops... milestone got deleted in batch update (comment:4) -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/191#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
[gpc-informatics] Batch modify: #191, #287, #314, #316, #317, #318, #319, #336
Batch modification to #191, #287, #314, #316, #317, #318, #319, #336 by dconnolly: priority to major Comment: oops... "medium" priority should be "major" -- Tickets URL: <http://informatics.gpcnetwork.org/trac/Project/query?id=191%2C287%2C314%2C316%2C317%2C318%2C319%2C336> 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: reopened Priority: minor | Milestone: drn-query-1 Component: data-sharing | Resolution: Keywords:| Blocked By: 209 Blocking:| --+-- Comment (by kwanta): Been waiting on Lincoln Peak and Harvard Pilgrim since 8/24. Once their support contacts me, I will update this ticket. Did notice one new issue. When the tool is installed in Windows for multiple users, multiple people can open the tool, but when the person who installed the tool logs off that machine, the program is inaccessible, because the exe path is based on a hash. So for backup purposes, this will be an issue in the future. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/166#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] #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: major | Milestone: data-domains3 Component: data-stds | Resolution: Keywords: | Blocked By: 109 Blocking: 317| ---+ Comment (by lv): How did sites that implemented SCILHS handle Procedures? Has anyone requested the CPT ontology yet? -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/191#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] #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: major | Milestone: data-domains3 Component: data-stds | Resolution: Keywords: | Blocked By: 109 Blocking: 317| ---+ Comment (by nateapathy): We propogated the procedures ontology with ICD9 procedure codes as SCILHS indicated. We have a default Cerner i2b2 CPT ontology, but have not had any requests or a need to request, so it only exists insofar as the Babel ontologies and those on the PCORnet Central Desktop. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/191#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: campbell 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 campbell): ETL ADD for Nebraska submitted to Casie Horgan; appended to this ticket as information Jim -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/240#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] #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): I emailed drafts of 3.11 and 3.12 to Tom for review, prior to sending to KUMC colleagues for review before final submission. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/80#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: bzschoche Type: task | Status: closed Priority: major | Milestone: data-sec-check Component: data-sharing | Resolution: fixed Keywords: security | Blocked By: 79 Blocking: 334 | --+- Changes (by dconnolly): * status: assigned => closed * resolution: => fixed * blocking: => 334 Comment: Note comment:4 where (I thought) I closed this one and opened #334 to track 3.11 and 3.12. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/80#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
[gpc-informatics] #356: BC Datamart Protoype - aggregated and consolidated
#356: BC Datamart Protoype - aggregated and consolidated +--- Reporter: vleonardo | Owner: dconnolly Type: problem| Status: new Priority: major | Milestone: cohort-char-bc-db Component: data-stds | Keywords: Blocked By: | Blocking: 295 +--- Prototype the construction of a consolidated dataset using the inital BC REDCap db files, submitted last spring. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/356> 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] #356: BC Datamart Protoype - aggregated and consolidated
#356: BC Datamart Protoype - aggregated and consolidated ---+ Reporter: vleonardo | Owner: dconnolly Type: problem| Status: new Priority: major | Milestone: cohort-char-bc-db Component: data-stds | Resolution: Keywords: | Blocked By: Blocking: 295| ---+ Comment (by vleonardo): Walked-thru the list of proposed elements for the datamart, using the attached spreadsheet (which was based of the variables listed in the BC Codebook #328). A few changes were made: -- Reinstating 0170 Race Coding Sys--Current -- Reinstating 0180 Race Coding Sys--Original -- Reinstating 'SEER Site Summary Breast' Since the above variables are available and already submitted in the existing datasets, we will include them in the datamart. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/356#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] #356: BC Datamart Protoype - aggregated and consolidated
#356: BC Datamart Protoype - aggregated and consolidated ---+ Reporter: vleonardo | Owner: dconnolly Type: problem| Status: new Priority: major | Milestone: cohort-char-bc-db Component: data-stds | Resolution: Keywords: | Blocked By: Blocking: 295| ---+ Old description: > Prototype the construction of a consolidated dataset using the inital BC > REDCap db files, submitted last spring. New description: Prototype the construction of a consolidated dataset using the inital BC REDCap db files, submitted last spring. Initial review, shows that we have data from the sites for approximately 40 of the variables in the codebook. (See attached spreadsheet). These will be the variable we go after for constructing this prototype. -- Comment (by vleonardo): Discussed w/ Brad options for the overall scope Discussed w/ Brad the value of adding columns which document the 'tumor inclusion' criteria, as individual columns to be included in the datamart. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/356#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] #348: NAACCR Data Profile: How fresh is it? (was: Data Profile over time: How fresh is it (e.g. cancer tumor registry)? how far back does the data go?)
#348: NAACCR Data Profile: How fresh is it? ---+ Reporter: bchrischilles | Owner: bzschoche Type: design-issue | Status: closed Priority: major | Milestone: cohort-char-bc-db Component: data-sharing | Resolution: fixed Keywords: data-quality | Blocked By: Blocking: 297| ---+ Changes (by dconnolly): * status: assigned => closed * reporter: dconnolly => bchrischilles * type: enhancement => design-issue * resolution: => fixed * blocking: => 297 Old description: > During the recent MU site visit, a researcher asked how far back our data > goes. Russ explained that it varies from site to site and from system to > system within sites. > > Russ answered on behalf of KUMC by way of a recent HERON release contents > summary: > > - [https://informatics.kumc.edu/work/blog/heron-calhoun- > update#HERONCalhounContentsSummary HERON Calhoun Contents Summary] > > The code we use to generate the summary above is > - [https://informatics.kumc.edu/work/browser/heron_load/report_stats.sql > report_stats.sql] which draws from `concepts_stats`, which is built in > - > [https://informatics.kumc.edu/work/browser/heron_load/concept_stats.sql > concept_stats.sql] > > Actually, the numbers from that code are only part of the story; we > manually maintain info about when the various systems went live and when > is our most recent snapshot. > > Let's integrate this sort of data profiling into our quarterly data > quality review process. For bonus points, let's actually do breakdowns by > year (or quarter or month). > > But perhaps that's a large goal that we should break down into parts. A > smaller scoped task is something that I owe the breast cancer research > team: info about how fresh tumor registry data is at each site. New description: The breast cancer research team would like to know how fresh tumor registry data is at each site. -- Comment: Let's scope this ticket to just the NAACCR freshness issue and track the rest as #359. We collected these data 1 Sep (ticket:12#comment:78): 1. KUMC - July - monthly 1. ''CMH - N/A'' 1. UIOWA - every two weeks 1. WISC - July in production; Aug in QA; monthly 1. MCW - July 30; working on an update ... Taylor writes: Our latest refresh was with data extracted on July 30th 2015. We will be delayed on the next one, due to the migration of 3 hospitals to one reporting system. 1. MCRF - July; monthly 1. UMN - July; quarterly 1. UNMC - March; no regular update process yet 1. UTHSCSA - registrar provides data monthly; integration into i2b2 happens quarterly 1. UTSW - diagnoses thru 2014; an update takes about a week 1. MU - working on it (#344) -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/348#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] #356: BC Datamart Protoype - aggregated and consolidated 'REDCap Phase1 Datasets' (was: BC Datamart Protoype - aggregated and consolidated)
#356: BC Datamart Protoype - aggregated and consolidated 'REDCap Phase1 Datasets' ---+ Reporter: vleonardo | Owner: dconnolly Type: problem| Status: new Priority: major | Milestone: cohort-char-bc-db Component: data-stds | Resolution: Keywords: | Blocked By: 361 Blocking: 295| ---+ -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/356#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] #160: reproducible GPC, CDM refresh at a critical mass of GPC sites (PMO milestone 2.4)
#160: reproducible GPC, CDM refresh at a critical mass of GPC sites (PMO milestone 2.4) -+ Reporter: rwaitman | Owner: dconnolly Type: enhancement | Status: reopened Priority: minor| Milestone: data-domains3 Component: data-stds| Resolution: Keywords: cdm; enrollment | Blocked By: 145 Blocking: | -+ Changes (by dconnolly): * cc: dconnolly, ngraham, jsteinmetz, susandm (removed) * cc: gpc-dev@… (added) * status: closed => reopened * resolution: fixed => * milestone: drn-basic-query => data-domains3 Comment: As of May (ticket:240#comment:6), I had planned to use the data characterization queries (#240) to evaluate remaining gaps in our shared CDM ETL (#145, [https://bitbucket.org/gpcnetwork/gpc-pcornet-cdm gpc- pcornet-cdm]). As UNMC wraps up work on data characterization queries (#240), their annotated data dictionary does not show those gaps (e.g. diagnosis.dx_source). But their site is not using the shared GPC approach, so it's not clear how or whether their approach to addressing these gaps would apply to other sites. Meahwhile, SCILHS provides, along with their ontology (which we're exploring; see ticket:191#comment:7, #347), CDM ETL code (private communication from Jeff Klann, June 20, 2015) which may well address these gaps in a shareable fashion. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/160#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] #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: data-quality-q3 Component: data-quality | Resolution: Keywords:| Blocked By: 309, 351 Blocking:| --+-- Comment (by dconnolly): In our 1 Sep meeting (#12), the estimate was "can have the SQL by 9/14, then add time for sites to run the code/report results." What news? -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/327#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] #356: BC Datamart Protoype - aggregated and consolidated 'REDCap Phase1 Datasets'
#356: BC Datamart Protoype - aggregated and consolidated 'REDCap Phase1 Datasets' ---+ Reporter: vleonardo | Owner: vleonardo Type: problem| Status: assigned Priority: major | Milestone: cohort-char-bc-db Component: data-stds | Resolution: Keywords: | Blocked By: 361 Blocking: 295| ---+ Changes (by dconnolly): * owner: dconnolly => vleonardo * status: new => assigned Comment: Vince, you have the ball on this, right? If not, I'll need help understanding what I am to do next. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/356#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] #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: major | Milestone: data-domains3 Component: data-stds | Resolution: Keywords: | Blocked By: 109 Blocking: 317| ---+ Comment (by lv): Eric's notes from implementing SCILHS at MCRF: \PCORI\DEMOGRAPHIC\HISPANIC\ - This was using Race_CD in Patient_Dimension. We fill race with race, not ethnicity (the Race codes were also using this column). I switch this over to use our local basecode and pointed at Concept_Dimension instead. \PCORI\ENROLLMENT\ENR_BASIS\*\ - I thought the mappings in this section were a little odd… Encounter-based: would pull a count of patients that had atleast one fact that had a start_date. Insurance: would always be 0. (not available for selection in i2b2) Geography: was based on having the code LOCATION_CODE:2. We don’t have any location codes, so this would never work (again not available for selection in i2b2) Algorithmic: would be the same as Encounter-based. I switch them to be based on \i2b2\Demographics\Enrollment\ terms Encounter-based: Is in one of the two nodes: Face to Face Visit Within One Year or Two Encounters or Wellness Within 3 Years (Added two children to accomplish) Insurance: Is in Insurance Geography: Is in Patients Within 50 Miles Algorithmic: Is in MCRF Catchment \PCORI\ENROLLMENT\ENR_BASIS\ - This had a C_FACTTABLECOLUMN value of PATIENT_NUM, since I made the above changes to \PCORI\ENROLLMENT\ENR_BASIS\*\, I had to update this to concept_cd. (This node is also disable in the hierarchy) OTHER NOTES I also didn’t do much with modifier’s in the ontology. I know the ‘\PCORI_MOD\CHART\’, which is applied to ‘\PCORI\ENROLLMENT\ENR_BASIS\*\’, is all hardcoded to be true or false. So Yes to chart will always be true and all the other modifiers will always be false. There may be more examples of this, but like I said, I didn’t spend much time on modifier’s. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/191#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] #304: accuracy of ALS diagnosis data collection
#304: accuracy of ALS diagnosis data collection -+-- Reporter: rwaitman | Owner: mish Type: enhancement | Status: assigned Priority: major| Milestone: cohort-char-als Component: data-stds| Resolution: Keywords: | Blocked By: Blocking: | -+-- Changes (by dconnolly): * cc: gpc-dev@… (added) * owner: badagarla => mish * priority: minor => major Comment: Replying to [comment:2 badagarla]: > Given that the data dictionary is standardized across the sites, it should be a simple report: > ... > Looks like 15.23% of the patients selected from EMR data at KUMC was adjudicated to be ineligible by the clinician. > > If it is something that other sites also should report, please feel free to reassign it to other sites. Let's have at least one of the other DevTeams try running this REDCap report. Choosing at random... my 12 sided die nominates 2 - CMH - not participating 10 - UNMC - recently reported behing a bit behind on ALS survey deployment 5 - WISC Tom, you're adept at REDCap. Give the report in comment:2 a try, please? Feel free to nominate someone else (i.e. re-assign the ticket) if you prefer. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/304#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] #155: correlating observations with encounters
#155: correlating observations with encounters --+ Reporter: lv| Owner: mish Type: design-issue | Status: assigned Priority: major | Milestone: data-domains3 Component: data-stds | Resolution: Keywords: data-quality cdm-etl | Blocked By: Blocking:| --+ Comment (by dconnolly): A note on CDM data characterization from the PCORnet Council Call September 18, 2015: > * There’s some confusion about whether appointments are encounters. (They’re not. Encounters are interactions between patients and providers in the context of healthcare delivery.) -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/155#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] #356: BC Datamart Protoype - aggregated and consolidated 'REDCap Phase1 Datasets'
#356: BC Datamart Protoype - aggregated and consolidated 'REDCap Phase1 Datasets' ---+ Reporter: vleonardo | Owner: vleonardo Type: problem| Status: assigned Priority: major | Milestone: cohort-char-bc-db Component: data-stds | Resolution: Keywords: | Blocked By: 361 Blocking: 295| ---+ Comment (by vleonardo): Documenting this afternoon's conversation w/ Brad McDowell where discussed programming methods for the prototype datamart. Many of the NAACCR variables are 'encoded' columns (code-value pairs), Brad has asked that we embed both the code and value in the datamart cells, so that both are provided. In many cased, this may be redundant, but we both agree it's best to have both included. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/356#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] #356: BC Datamart Protoype - aggregated and consolidated 'REDCap Phase1 Datasets'
#356: BC Datamart Protoype - aggregated and consolidated 'REDCap Phase1 Datasets' ---+ Reporter: vleonardo | Owner: vleonardo Type: problem| Status: assigned Priority: major | Milestone: cohort-char-bc-db Component: data-stds | Resolution: Keywords: | Blocked By: 361 Blocking: 295| ---+ Comment (by dconnolly): Let's please stick to REDCap's conventions for managing coded/enumerated data. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/356#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] #356: BC Datamart Protoype - aggregated and consolidated 'REDCap Phase1 Datasets'
#356: BC Datamart Protoype - aggregated and consolidated 'REDCap Phase1 Datasets' ---+ Reporter: vleonardo | Owner: vleonardo Type: problem| Status: assigned Priority: major | Milestone: cohort-char-bc-db Component: data-stds | Resolution: Keywords: | Blocked By: 361 Blocking: 295| ---+ Comment (by vleonardo): Regarding 'REDCap conventions', at this point, Dan indicates these may not be documented. A separate ticket will be created to track the task of converting the codebook to REDCap data dictionary form -- using the naming conventions. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/356#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] #356: BC Datamart Protoype - aggregated and consolidated 'REDCap Phase1 Datasets'
#356: BC Datamart Protoype - aggregated and consolidated 'REDCap Phase1 Datasets' ---+ Reporter: vleonardo | Owner: vleonardo Type: problem| Status: assigned Priority: major | Milestone: cohort-char-bc-db Component: data-stds | Resolution: Keywords: | Blocked By: 361, 371 Blocking: 295| ---+ Comment (by dconnolly): Not documented? I'm not sure what gave you that impression. REDCap's data dictionary spreadsheet format is well documented. I'm sure there's more, but for example, see: https://redcap.kumc.edu/index.php?action=help#onlinedesign -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/356#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] #304: accuracy of ALS diagnosis data collection
#304: accuracy of ALS diagnosis data collection -+-- Reporter: rwaitman | Owner: mish Type: enhancement | Status: assigned Priority: major| Milestone: cohort-char-als Component: data-stds| Resolution: Keywords: | Blocked By: Blocking: | -+-- Comment (by lv): Here's an update on the process and results to date for Marshfield/MCRF: Searching by diagnosis alone results in 1219 patients, which was deemed too large to validate manually by the study team (Bob Greenlee and Deb Multerer). After discussion, the decision was made to restrict the population as follows: 335.20 OR 335.24 OR 335.29 - occurs > 1x AND Enrollment - Two Encounters or Wellness Within 3 Years AND NOT Deceased Patient Count = 89 The study team then requested that we add the location where the patient receives care from a neurologist, which would make it easier for our physician lead to review. Results weren't great. - In the past year, 34 of 89 saw a neurologist - In the past 3 years, 59 of 89 saw a neurologist. We pulled all appointments for the 89 patients over the past year and categorized as those who saw a neurologist and those that haven't. I don't have complete results, but we're seeing a lot of fallouts. Some patients are valid, but in hospice. Some are valid, but being followed at other institutions (Mayo, UW Health, New York, etc.). Some had rule-out diagnoses on the record in the distant past. Several haven't been seen at Marshfield for ALS in the past 2-3 years. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/304#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] #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: major | Milestone: data-domains3 Component: data-stds | Resolution: Keywords: | Blocked By: 109 Blocking: 317| ---+ Comment (by campbell): I have attached talking points for Tuesday presentation and for those interested included a paper we will be presenting at AMIA on the development work we have been doing on i2b2 at UNMC pertaining to query functionality Jim -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/191#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] #254: prepare Weight and Health survey contact information at all sites
#254: prepare Weight and Health survey contact information at all sites +- Reporter: sschlacter | Owner: bzschoche Type: task| Status: assigned Priority: major | Milestone: obesity-survey-def Component: data-sharing| Resolution: Keywords: obesity-cohort | Blocked By: 249, 250, 252, 253 Blocking: | +- Changes (by dconnolly): * cc: sschlacter, tmcmahon (removed) * owner: bokov => bzschoche * reporter: bokov => sschlacter Comment: Brittany offered to see that news from the LEC gets noted here. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/254#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] #284: Deploy GPC ALS Survey at GPC sites
#284: Deploy GPC ALS Survey at GPC sites ---+ Reporter: badagarla | Owner: bzschoche Type: task | Status: assigned Priority: major | Milestone: survey-redcap-als Component: data-stds | Resolution: Keywords: | Blocked By: 208 Blocking: | ---+ Changes (by dconnolly): * owner: badagarla => bzschoche Comment: Brittany offered to see that news from the LEC gets noted here. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/284#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] #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: -+- Changes (by dconnolly): * owner: campbell => lv Comment: Laurel is organizing a **GPC - Metrics and Data Characterization Review Meeting with DSSNI**. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/240#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
[gpc-informatics] #376: data builder limited to `like concept_dimension.concept_path` metadata
#376: data builder limited to `like concept_dimension.concept_path` metadata
---+---
Reporter: dconnolly | Owner: dconnolly
Type: problem | Status: new
Priority: minor | Milestone:
Component: data-sharing | Keywords:
Blocked By:| Blocking:
---+---
The data builder assumes concepts join with the concept_dimension using
LIKE in the style of the i2b2 1.4 demo metadata:
{{{
concept_cd
concept_dimension
concept_path
T
like
}}}
This is documented in a test case:
{{{
we can join back from the concept_dimension to the variables we
asked for:
>>> result_db.execute(
... """select v.name_char
...from variable v join concept_dimension cd
...on cd.concept_path like (v.concept_path || '%')
...where cd.concept_cd = :m8
... """, m8=u'KUH|MEASURE_ID:8').scalar()
u'ED Vitals'
}}}
So it doesn't support concepts that join with other dimensions, e.g.
{{{
patient_num
patient_dimension
sex_cd
T
=
M
Demographic \ Gender \ Male
}}}
Nor transitive closure style:
{{{
CONCEPT_CD
SNOMEDCT_I2B2_TC
SUPERTYPE_CONCEPTID
N
=
228282009
}}}
It also assumes just one (relevant) metadata table; i.e. that they 1st
path segment of the `item_key` can be just stripped and ignored.
--
Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/376>
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Re: [gpc-informatics] #243: GPC Procedure Ontology: CPT, HCPCS
#243: GPC Procedure Ontology: CPT, HCPCS
--+
Reporter: dconnolly | Owner: bos
Type: design-issue | Status: assigned
Priority: major | Milestone: data-domains3
Component: data-stds | Resolution:
Keywords:| Blocked By:
Blocking:|
--+
Comment (by dconnolly):
The
[https://community.i2b2.org/wiki/display/SCILHS/SCILHS+i2b2+PCORnet+Common+Data+Model+Ontology+Home
SCILHS ontology] provides another candidate (see also
ticket:191#comment:3).
Version 1.5.2 is on [https://babel.gpcnetwork.org/ babel] as "PCORnet
Procedures"; for example, HCPCS J codes:
{{{
3
\\PCORI_PROC\PCORI\PROCEDURE\HC\J9010-J\
J9010 - J: Chemotherapy Drugs
\PCORI\PROCEDURE\HC\J9010-J\
HCPCS \ Chemotherapy Drugs
}}}
--
Ticket URL:
<http://informatics.gpcnetwork.org/trac/Project/ticket/243#comment:11>
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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: closed Priority: major | Milestone: data-sec-check Component: data-sharing | Resolution: fixed Keywords: security | Blocked By: 79 Blocking: 334 | --+- Comment (by mosaa@…): MU has submitted the survey. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/80#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] #160: reproducible GPC, CDM refresh at a critical mass of GPC sites (PMO milestone 2.4)
#160: reproducible GPC, CDM refresh at a critical mass of GPC sites (PMO milestone 2.4) -+-- Reporter: rwaitman | Owner: prakashnadkarni Type: enhancement | Status: assigned Priority: minor| Milestone: data-domains3 Component: data-stds| Resolution: Keywords: cdm; enrollment | Blocked By: 145 Blocking: | -+-- Changes (by dconnolly): * owner: dconnolly => prakashnadkarni * status: reopened => assigned Comment: I our 29 Sep call (#12), Prakash offered to share code for his approach to CDM ETL. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/160#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] #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: data-quality-q3 Component: data-quality | Resolution: Keywords:| Blocked By: 309, 351, 366 Blocking:| --+-- Comment (by dconnolly): If anyone is willing to lead this while Tom is on holiday, please let me know. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/327#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] #178: determine whether last.visit is the last fulfilled visit or the last scheduled visit
#178: determine whether last.visit is the last fulfilled visit or the last scheduled visit -+--- Reporter: mish | Owner: dconnolly Type: enhancement | Status: closed Priority: minor| Milestone: cohort-char1 Component: data-stds| Resolution: invalid Keywords: | Blocked By: Blocking: | -+--- Changes (by dconnolly): * status: assigned => closed * resolution: => invalid Comment: Since our BC finder file QA (#227) is done, this is overtaken by events. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/178#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] #254: prepare Weight and Health survey contact information at all sites
#254: prepare Weight and Health survey contact information at all sites +- Reporter: sschlacter | Owner: bzschoche Type: task| Status: assigned Priority: major | Milestone: obesity-survey-def Component: data-sharing| Resolution: Keywords: obesity-cohort | Blocked By: 249, 250, 252, 253 Blocking: 379 | +- Comment (by dconnolly): Dan Hale gave an update as of Sep 25 at [http://www.gpcnetwork.org/?q=LEK2015 the LEC]: 1. **CMH: Pending** (no surveys sent) 2. MCRF: collecting responses 3. **UIOWA: Pending** 4. KUMC: Done (all responses collected) 5. MCW: collecting 6. **UNMC: Pending** 7. **UMN: Pending** 8. UTSW: collecting 9. UTHSCSA: Done 10. **WISC: Pending** He asked how much longer we should allow before we proceed without the remaining sites, suggesting the end of October as the last date to begin collecting. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/254#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] #243: GPC Procedure Ontology: CPT, HCPCS
#243: GPC Procedure Ontology: CPT, HCPCS --+ Reporter: dconnolly | Owner: dconnolly Type: design-issue | Status: assigned Priority: major | Milestone: data-domains3 Component: data-stds | Resolution: Keywords:| Blocked By: Blocking:| --+ Changes (by dconnolly): * owner: bos => dconnolly Comment: Dan is evaluating UTHSCSA's and/or SCILHS's procedure ontologies. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/243#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] #254: prepare Weight and Health survey contact information at all sites
#254: prepare Weight and Health survey contact information at all sites +- Reporter: sschlacter | Owner: bzschoche Type: task| Status: assigned Priority: major | Milestone: obesity-survey-def Component: data-sharing| Resolution: Keywords: obesity-cohort | Blocked By: 249, 250, 252, 253 Blocking: 379 | +- Comment (by dconnolly): UMN has launched, per Kathleen M. in gpc-dev today. Rita@CMH: plan to launch this week. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/254#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] #160: reproducible GPC, CDM refresh at a critical mass of GPC sites (PMO milestone 2.4)
#160: reproducible GPC, CDM refresh at a critical mass of GPC sites (PMO milestone 2.4) -+ Reporter: rwaitman | Owner: tgreen Type: enhancement | Status: assigned Priority: minor| Milestone: data-domains3 Component: data-stds| Resolution: Keywords: cdm; enrollment | Blocked By: 145, 347 Blocking: | -+ Changes (by dconnolly): * owner: prakashnadkarni => tgreen * blockedby: 145 => 145, 347 Comment: The outcome of today's call is that we'll see how the evaluation (#347) of the SCILHS ontology and their CDM ETL goes. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/160#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] #356: BC Datamart Protoype - aggregated and consolidated 'REDCap Phase1 Datasets'
#356: BC Datamart Protoype - aggregated and consolidated 'REDCap Phase1 Datasets' ---+ Reporter: vleonardo | Owner: vleonardo Type: problem| Status: assigned Priority: major | Milestone: cohort-char-bc-db Component: data-stds | Resolution: Keywords: | Blocked By: 361, 371 Blocking: 295| ---+ Comment (by vleonardo): Notes f/ 23-Sep Conf Call: Walk through prototype datamart • Code and description combined with ||? o Betsy: Possible that other sites may not have the same naming convention in place. o Brad: don’t see any issues importing it into SAS and writing some scripts to parse in SAS. o Vince will follow-up on naming conventions and REDCap. • Best to have all tumors for the patient. o Have an indicator for which was first tumor. • Add eligible tumor column o Note the eligibility dates vary by site. For example, Iowa & Nebraska went back to 1/1/2013 while some other institutions start with 5/15/2015. o Dan’s code should identify • R Report for every site? o Vince will work on a combined one in addition to one for each site. • Delete everything prior to the || shaved off? o Vince recommends the value the site reported. o We need to make certain that the actual value are at the exact same location within the string for extraction. o For REDCap conventions, this change will have to happen. o Vince will research REDCap conventions and discuss with Brad prior to making format changes for code||descriptions -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/356#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] #376: data builder limited to `like concept_dimension.concept_path` metadata
#376: data builder limited to `like concept_dimension.concept_path` metadata --+ Reporter: dconnolly | Owner: dconnolly Type: problem | Status: new Priority: major | Milestone: data-domains3 Component: data-sharing | Resolution: Keywords:| Blocked By: Blocking: 191 | --+ Changes (by dconnolly): * priority: minor => major * blocking: => 191 * milestone: => data-domains3 Comment: I just realized that this conflicts with deploying the SCILHS ontology in such a way that demographics come from `patient_dimension`. If sites do like MCRF (ticket:191#comment:15) and use the `concept_dimension`, this limitation of the DataBuilder can stay un- addressed. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/376#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] #266: CDM V3 Development for Phase 2
#266: CDM V3 Development for Phase 2 --+ Reporter: campbell | Owner: rwaitman Type: design-issue | Status: assigned Priority: minor | Milestone: adaptable-accrual Component: data-stds | Resolution: Keywords: CDM V3| Blocked By: 283 Blocking: 273 | --+ Comment (by campbell): I enclose slides from Monday DSSNI meeting this week with information on organization and timeline of CDM V3 support and deployment of SAS Jim -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/266#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] #56: shareable synthetic test data sets: Epic clarity, i2b2, NAACCR, ...
#56: shareable synthetic test data sets: Epic clarity, i2b2, NAACCR, ... --+ Reporter: dconnolly | Owner: bos Type: enhancement | Status: assigned Priority: minor | Milestone: data-domains3 Component: data-sharing | Resolution: Keywords:| Blocked By: Blocking:| --+ Comment (by dconnolly): While testing NAACCR ETL refinements for #258 and related stuff, I'm reminded that we don't have much test data. I'm interested to pursue the idea of characterizing existing data and synthesizing data based on those characteristics. - For nominal data, calculate frequencies and use the frequencies to pick random values - For numeric measures, assume a normal distribution - For dates, treat them as numeric measures by subtracting date of diagnosis for bonus points: - use primary site, stage, age, sex to influence probabilities of other data - for text, use trigrams and learn about hidden Markov models -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/56#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] #254: prepare Weight and Health survey contact information at all sites
#254: prepare Weight and Health survey contact information at all sites +- Reporter: sschlacter | Owner: bzschoche Type: task| Status: assigned Priority: major | Milestone: obesity-survey-def Component: data-sharing| Resolution: Keywords: obesity-cohort | Blocked By: 249, 250, 252, 253 Blocking: 379 | +- Comment (by dconnolly): Sarah tells us Iowa has launched (started collecting responses). This leaves - UNMC - WISC -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/254#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] #254: prepare Weight and Health survey contact information at all sites
#254: prepare Weight and Health survey contact information at all sites +- Reporter: sschlacter | Owner: bzschoche Type: task| Status: assigned Priority: major | Milestone: obesity-survey-def Component: data-sharing| Resolution: Keywords: obesity-cohort | Blocked By: 249, 250, 252, 253 Blocking: 379 | +- Comment (by bzschoche): Russ Buzalko at UNMC reports they should send surveys this week. > Ht / Wt: Last week, we requested the Spanish version of the survey from San Antonio…realized that we had only the English version. We believe we have the bugs worked out of the email system. Jim !McClay should be back in the office this week…our plan is to walk through the protocol one last time to make sure that we have all areas addressed…should release this week. ''Mon 10/12/2015 9:26 AM'' -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/254#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
[gpc-informatics] Batch modify: #196, #267, #351
Batch modification to #196, #267, #351 by dconnolly: priority to minor Comment: In our Oct 6 call (#12), we learned of a setback: TomM: I had hoped we’d get some enhancements soon, but based on some recent unforeseen events, it looks like what George has is the final version for this quarter. -- Tickets URL: <http://informatics.gpcnetwork.org/trac/Project/query?id=196%2C267%2C351> 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: bzschoche Type: task | Status: assigned Priority: major | Milestone: survey-redcap-als Component: data-stds | Resolution: Keywords: | Blocked By: 208 Blocking: 380| ---+ Comment (by bzschoche): I didn't get any ALS updates at the LEC, but I can update for UNMC. - UNMC: sent 78 initial letters; second letter / survey will go out this week I will get updated info on or before the PM call this Friday for the other sites. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/284#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] #284: Deploy GPC ALS Survey at GPC sites
#284: Deploy GPC ALS Survey at GPC sites ---+ Reporter: badagarla | Owner: bzschoche Type: task | Status: assigned Priority: major | Milestone: survey-redcap-als Component: data-stds | Resolution: Keywords: | Blocked By: 208 Blocking: 380| ---+ Comment (by lv): MCRF: No status change. Our population seems to be somewhat different; we may be more of a primary care location than a referral site. We analyzed the population to categorize as valid and invalid based on ALS dx, neurology visits in the past 12 months, and chart review (including record of hospice care). I hope to have an update in the next 5-10 days. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/284#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: bzschoche Type: task | Status: assigned Priority: major | Milestone: survey-redcap-als Component: data-stds | Resolution: Keywords: | Blocked By: 208 Blocking: 380| ---+ Comment (by lv): The date range is used (in the oracle script) on lines: 64, 239, 367, 390, 579, 611(This one is in commented code), 648, and 680. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/284#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] #254: prepare Weight and Health survey contact information at all sites
#254: prepare Weight and Health survey contact information at all sites +- Reporter: sschlacter | Owner: bzschoche Type: task| Status: assigned Priority: major | Milestone: obesity-survey-def Component: data-sharing| Resolution: Keywords: obesity-cohort | Blocked By: 249, 250, 252, 253 Blocking: 379 | +- Comment (by bzschoche): From Michelle Coady, UNM; ''Tue 10/13/2015 10:24 AM'' > Ped Obesity - 4992 surveys sent, 50 returned = 1% return rate (10/12/15) -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/254#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] #56: shareable synthetic test data sets: Epic clarity, i2b2, NAACCR, ...
#56: shareable synthetic test data sets: Epic clarity, i2b2, NAACCR, ... --+ Reporter: dconnolly | Owner: bos Type: enhancement | Status: assigned Priority: minor | Milestone: data-domains3 Component: data-sharing | Resolution: Keywords:| Blocked By: Blocking:| --+ Comment (by dconnolly): Replying to [comment:28 dconnolly]: > - For nominal data, calculate frequencies and use the frequencies to pick random values got that much done in 2f3e740c7051 on the `data_syn_g56` branch. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/56#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] #254: prepare Weight and Health survey contact information at all sites
#254: prepare Weight and Health survey contact information at all sites +- Reporter: sschlacter | Owner: bzschoche Type: task| Status: assigned Priority: major | Milestone: obesity-survey-def Component: data-sharing| Resolution: Keywords: obesity-cohort | Blocked By: 249, 250, 252, 253 Blocking: 379 | +- Comment (by bzschoche): From Brian Gryzlak, IOWA; ''Wed 10/14/2015 12:35 PM'' > •Mailing went out last week > •35 responses online > •One e-mail asking if survey should be filled out for child or self > •No phone calls > •Have student assistant assisting with data entry if needed -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/254#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] #254: prepare Weight and Health survey contact information at all sites
#254: prepare Weight and Health survey contact information at all sites +- Reporter: sschlacter | Owner: bzschoche Type: task| Status: assigned Priority: major | Milestone: obesity-survey-def Component: data-sharing| Resolution: Keywords: obesity-cohort | Blocked By: 249, 250, 252, 253 Blocking: 379 | +- Comment (by bzschoche): From Bob Greenlee, Marshfield (to Sarah Schlachter); ''Wednesday, October 14, 2015 6:41 AM'' > Our quick update is we are going to send the final reminder surveys out next week. after several weeks, the responses to the 1st reminder appear to have slowed way down now. > On the good side we have over 300 who completed survey 2, and good representation across the bins. But because of the electronic format we only have an additional 100 No’s on survey 1, so even though we are exceeding survey 2 targets, we will likely fall short of our 1000 target on survey 1. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/254#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] #356: BC Datamart Protoype - aggregated and consolidated 'REDCap Phase1 Datasets'
#356: BC Datamart Protoype - aggregated and consolidated 'REDCap Phase1 Datasets' ---+ Reporter: vleonardo | Owner: vleonardo Type: problem| Status: assigned Priority: major | Milestone: cohort-char-bc-db Component: data-stds | Resolution: Keywords: | Blocked By: 361, 362, 385 Blocking: 295| ---+ Comment (by vleonardo): Add'l 'data review' checks: - Ensure any patient w/ a second primary (NAACCR.380) also has a first primary recorded. - Each patient should have only one eligible encounter (tumor), being the one with the earliest diagnosis date that meets the inclusion criterion. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/356#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] #356: BC Datamart Protoype - aggregated and consolidated 'REDCap Phase1 Datasets'
#356: BC Datamart Protoype - aggregated and consolidated 'REDCap Phase1 Datasets' ---+ Reporter: vleonardo | Owner: vleonardo Type: problem| Status: assigned Priority: major | Milestone: cohort-char-bc-db Component: data-stds | Resolution: Keywords: | Blocked By: 361, 362, 385 Blocking: 295| ---+ Comment (by vleonardo): Following feedback received during today's conference call from Betsy & Brad: - need to go after a 'limited' dataset, which would provide actual dates, so alignment w/ study data can be made -- this will require us to get the 'date shift' from the sites, and will be done when we get the 'study id-to-order id' mapping -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/356#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] #284: Deploy GPC ALS Survey at GPC sites
#284: Deploy GPC ALS Survey at GPC sites ---+ Reporter: badagarla | Owner: bzschoche Type: task | Status: assigned Priority: major | Milestone: survey-redcap-als Component: data-stds | Resolution: Keywords: | Blocked By: 208 Blocking: 380| ---+ Comment (by bzschoche): Update from Brian Gryzlak at Iowa; ''Thu 10/15/2015 11:17 AM'': > ALS update: > “We sent out surveys to 72 patients last Thursday. I have received two calls today with questions about the survey so our patients are receiving them! No subject complaints…” -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/284#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] #284: Deploy GPC ALS Survey at GPC sites
#284: Deploy GPC ALS Survey at GPC sites ---+ Reporter: badagarla | Owner: bzschoche Type: task | Status: assigned Priority: major | Milestone: survey-redcap-als Component: data-stds | Resolution: Keywords: | Blocked By: 208 Blocking: 380| ---+ Comment (by rbuzalko): UNMC (Nebraska) sent all ALS site surveys on Friday 10/16/15. In the end, 10 went out in clinic and 59 via snail mail. Total of 69. Standing-by to see who responds and to answer questions. Thanks, Russ Buzalko. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/284#comment:17> 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: #362, #361, #356, #385
Batch modification to #362, #361, #356, #385 by dconnolly: milestone to bc-agg-1 Comment: separating milestone:bc-agg-1 out of milestone:cohort-char-bc-db to track aggregated and consolidated 'REDCap Phase1 Datasets' (#356) based on 14 Oct BC call (ticket:385#comment:3) -- Tickets URL: <http://informatics.gpcnetwork.org/trac/Project/query?id=362%2C361%2C356%2C385> 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: data-quality-q3 Component: data-quality | Resolution: Keywords:| Blocked By: 309, 351, 366 Blocking:| --+-- Comment (by gkowalski): I've submitted a pull request for the latest Oracle QA Script with fixed dates for Q3 to https://bitbucket.org/DanC/gpc-qa-quarterly/ G -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/327#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] #243: GPC Procedure Ontology: CPT, HCPCS
#243: GPC Procedure Ontology: CPT, HCPCS
--+
Reporter: dconnolly | Owner: dconnolly
Type: design-issue | Status: closed
Priority: major | Milestone: data-domains3
Component: data-stds | Resolution: fixed
Keywords:| Blocked By:
Blocking:|
--+
Changes (by dconnolly):
* status: assigned => closed
* resolution: => fixed
Comment:
PR's proposal is pretty much in line with UTHSCS work. let's go with it.
{{{
4
\\GPC_TERMS\GPC\Procedures\CPT\A23576389\A23570843\A23578991\
Other Evaluation and Management Services
N
FA
http://www.w3.org/2001/XMLSchema-
instance" xsi:nil="true" />
CPT:1013875
concept_cd
concept_dimension
concept_path
T
like
\GPC\Procedures\CPT\A23576389\A23570843\A23578991\
}}}
--
Ticket URL:
<http://informatics.gpcnetwork.org/trac/Project/ticket/243#comment:13>
gpc-informatics <http://informatics.gpcnetwork.org/>
Greater Plains Network - Informatics
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Re: [gpc-informatics] #263: Adaptable cohort query design and administration
#263: Adaptable cohort query design and administration --+ Reporter: schandaka | Owner: schandaka Type: design-issue | Status: assigned Priority: minor | Milestone: adaptable-accrual Component: data-stds | Resolution: Keywords:| Blocked By: 276 Blocking: 353 | --+ Changes (by dconnolly): * owner: rwaitman => schandaka * status: new => assigned Comment: I learned from BZ and SC that there are drafts of a CDM query in this space. I forget who told us about the drafts; I'm assigning to SC to let us know when a draft is shared with us. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/263#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] #263: Adaptable cohort query design and administration
#263: Adaptable cohort query design and administration --+ Reporter: schandaka | Owner: schandaka Type: design-issue | Status: assigned Priority: minor | Milestone: adaptable-accrual Component: data-stds | Resolution: Keywords:| Blocked By: 276 Blocking: 353 | --+ Comment (by bzschoche): From Lesley Curtis ''Thu 10/15/2015 5:06 PM'' > Hi Russ, > Sorry for the delay. > We’ll have a working version of the base eligibility phenotype for the Oct 30 ADAPTABLE data call and aim to incorporate feedback and finalize shortly thereafter. We’re working through the details of the ‘harvest’ query but I don’t know if that’s on tap for discussion on the Oct 30 call. > I’ve copied Deb, Lisa, and Shelley who are working through those details and may be able to speak to timing. > Best, > Lesley > Go Royals!!! -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/263#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] #254: prepare Weight and Health survey contact information at all sites
#254: prepare Weight and Health survey contact information at all sites +- Reporter: sschlacter | Owner: bzschoche Type: task| Status: assigned Priority: major | Milestone: obesity-survey-def Component: data-sharing| Resolution: Keywords: obesity-cohort | Blocked By: 249, 250, 252, 253 Blocking: 379 | +- Comment (by rbuzalko): UNMC (Nebraska) sent a couple test cases last night and the bulk remainder of our email surveys went out this morning. We sent 4340 email surveys via REDCap. The system appears to be working as we have received at least one response, a handful of out of office replies, two people asked to be removed from the list, and about 250 bounces due to bad email addresses. Will continue to monitor. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/254#comment:32> 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] #243: GPC Procedure Ontology: CPT, HCPCS
#243: GPC Procedure Ontology: CPT, HCPCS --+ Reporter: dconnolly | Owner: dconnolly Type: design-issue | Status: closed Priority: major | Milestone: data-domains3 Component: data-stds | Resolution: fixed Keywords:| Blocked By: Blocking:| --+ Comment (by kwanta): The following ontology example was taken from the September 2015 release of the University of Wisconsin (WISC) i2b2 instance (UW Madison and UW Health/affiliates) and compared against the GPC procedure ontology that Phillip Reeder published on Central Desktop. The GPC example was taken from the GPC ontology from Central Desktop, that Phillip uploaded per his email with subject "GPC Terminology on Central Desktop" on 10/15/2015. '''GPC example concept in CPT:''' \GPC\Procedures\CPT\A23576389\A23570843\A23578991\ 'Other Evaluation and Management Services' CPT:1013875 '''WISC example concept in CPT:''' \Procedures\cpt_codes\9-99607\99201-99499\99499-99499\99499-99499\ 'Other evaluation and management services' (this is an older version of the UMLS CPT ontology that has been modified somewhat to fit into our local UW procedure ontology.) '''SCHILS:''' It doesn't appear that the SCILHS has publicly released their CPT ontology yet. They've only released their ICD-9. http://i2b2.bioontology.org/ This page is referenced directly from the PCORnet ontology wiki. Unless they have an updated wiki page that we cannot see yet, which is likely the case with Harvard Medical School and Partners Healthcare. http://community.i2b2.org/wiki/display/SCILHS/SCILHS+i2b2+PCORnet+Common+Data+Model+Ontology+Home -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/243#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: bzschoche Type: task | Status: assigned Priority: major | Milestone: survey-redcap-als Component: data-stds | Resolution: Keywords: | Blocked By: 208 Blocking: 380| ---+ Comment (by dconnolly): I gather sites pending at this point are: **WISC**, **MCRF** UIOWA has sent stuff out. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/284#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] #165: PopMedNet node at UTSW
#165: PopMedNet node at UTSW --+ Reporter: lv| Owner: susandm Type: enhancement | Status: reopened Priority: minor | Milestone: data-agg1 Component: data-sharing | Resolution: Keywords:| Blocked By: Blocking:| --+ Changes (by lv): * status: closed => reopened * resolution: fixed => Comment: Susan is working with the DRN team to resolve some technical issues. She and I did a screensharing session on Wednesday (10/21) to clarify the process for submitting the IBQ. Kyle from DRN suggested checking her login on the querytool.pcornet.org site as a first step to move forward. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/165#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: bzschoche Type: problem | Status: assigned Priority: major | Milestone: data-quality-q3 Component: data-quality | Resolution: Keywords:| Blocked By: 309, 351, 366, 392 Blocking:| --+- Changes (by dconnolly): * owner: mish => bzschoche Comment: Brittany, I'd like your help tracking completion of this. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/327#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] #165: PopMedNet node at UTSW
#165: PopMedNet node at UTSW --+ Reporter: lv| Owner: susandm Type: enhancement | Status: reopened Priority: minor | Milestone: data-agg1 Component: data-sharing | Resolution: Keywords:| Blocked By: Blocking:| --+ Comment (by susandm): The credentials have some how changed. I am reconfiguring. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/165#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] #284: Deploy GPC ALS Survey at GPC sites
#284: Deploy GPC ALS Survey at GPC sites ---+ Reporter: badagarla | Owner: bzschoche Type: task | Status: closed Priority: major | Milestone: survey-redcap-als Component: data-stds | Resolution: fixed Keywords: | Blocked By: 208 Blocking: 380| ---+ Changes (by dconnolly): * status: assigned => closed * resolution: => fixed Comment: Let's track remaining sites individually: - #399 WISC ALS survey on regulatory stand-by - #400 ALS cohort selection query performed poorly in MCRF setting -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/284#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] #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): It doesn't appear that the network issues with PopMedNet have been resolved since October 2014. It's now October 2015. They have reset my password, and then they requested I reset my password to something new. It took over a minute to get to my Profile page, after clicking on "Profile". Then when I click "Change Password" the page spins for another minute and then I get this error: Failed to load resource: the server responded with a status of 404 (Not Found. Make sure your resource file has a build action of 'Embedded Resource') -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/166#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] #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 lv): Hi Keith, Did you report this to pcornet...@popmednet.org? What browser are you using? Have you tried using the Forgot Password link after logging out? I can't replicate the slowness loading the Profile page, but the Reset Password button doesn't seem to work for me either. Is this preventing you from receiving or responding to the IBQ? Thanks, Laurel -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/166#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
