Re: trac #411: Align Nebraska Lexicon with ACT ontology (was: Align SNOW SHRINE terminology with ACT ontology for interoperation of query)
#411: Align Nebraska Lexicon with ACT ontology --+-- Reporter: Dan Connolly | Owner: Jim Campbell Type: enhancement | Status: assigned Priority: major | Milestone: snow-shrine-3 Component: data-stds | Resolution: Keywords: ModelMashup | Blocked By: 23, 90, 201, 243, 280, 525, 583 Blocking:| Sensitive: 1 --+-- Changes (by Dan Connolly): * cc: gpc-dev@…, preeder, waitman, Matt Hoag, jay.pedersen@…, yeshwanth.narayana@…, lpatel@… (removed) * cc: GPCDEV-L@… (added) Comment: UNMC / MCW folks, I would appreciate some written material in advance of tomorrow's discussion - anything from a handful of bullet points to a detail review in the style of [http://listserv.kumc.edu/pipermail/gpc- dev/2020q3/011077.html Stoddard's CDM 6 review]. -- Ticket URL: <https://informatics.gpcnetwork.org/trac/Project/ticket/411#comment:44> gpc-informatics <https://informatics.gpcnetwork.org/trac/Project> Greater Plains Collaborative ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: trac #411: Align SNOW SHRINE terminology with ACT ontology for interoperation of query
#411: Align SNOW SHRINE terminology with ACT ontology for interoperation of query --+-- Reporter: Dan Connolly | Owner: Jim Campbell Type: enhancement | Status: assigned Priority: major | Milestone: snow-shrine-3 Component: data-stds | Resolution: Keywords: ModelMashup | Blocked By: 23, 90, 201, 243, 280, 525, 583 Blocking:| Sensitive: 1 --+-- Comment (by Dan Connolly): Replying to [comment:39 Dan Connolly]: > ... > Nebraska is Working on it [covid19 SHRINE] internally, not as part of ACT network yet; doing harmonization work with them to align ontologies. Work group meeting third Thursday of every month. Dr. Campbell, would you care to summarize progress since our Apr 28 discussion? Also, is the [https://dbmi-pitt.github.io/ACT- Network/data_harmonization.html Data Harmonization Workgroup] the relevant group? -- Ticket URL: <https://informatics.gpcnetwork.org/trac/Project/ticket/411#comment:43> gpc-informatics <https://informatics.gpcnetwork.org/trac/Project> Greater Plains Collaborative ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: trac #411: Align SNOW SHRINE terminology with ACT ontology for interoperation of query
#411: Align SNOW SHRINE terminology with ACT ontology for interoperation of query --+-- Reporter: Dan Connolly | Owner: Jim Campbell Type: enhancement | Status: assigned Priority: major | Milestone: snow-shrine-3 Component: data-stds | Resolution: Keywords: ModelMashup | Blocked By: 23, 90, 201, 243, 280, 525, 583 Blocking:| Sensitive: 1 --+-- Comment (by Dan Connolly): MCW received it. -- Ticket URL: <https://informatics.gpcnetwork.org/trac/Project/ticket/411#comment:42> gpc-informatics <https://informatics.gpcnetwork.org/trac/Project> Greater Plains Collaborative ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: trac #411: Align SNOW SHRINE terminology with ACT ontology for interoperation of query
#411: Align SNOW SHRINE terminology with ACT ontology for interoperation of query --+-- Reporter: Dan Connolly | Owner: Jim Campbell Type: enhancement | Status: assigned Priority: major | Milestone: snow-shrine-3 Component: data-stds | Resolution: Keywords: ModelMashup | Blocked By: 23, 90, 201, 243, 280, 525, 583 Blocking:| Sensitive: 1 --+-- Comment (by Dan Connolly): UNMC to send the updated ontology (RxNorm, SNOMED-CT, LOINC, ICD-10CM) to MCW, and Intermountain (from Sep 15 gpc-dev meeting) -- Ticket URL: <https://informatics.gpcnetwork.org/trac/Project/ticket/411#comment:41> gpc-informatics <https://informatics.gpcnetwork.org/trac/Project> Greater Plains Collaborative ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: trac #56: shareable synthetic test data sets: Epic clarity, i2b2, NAACCR, ...
#56: shareable synthetic test data sets: Epic clarity, i2b2, NAACCR, ... --+--- Reporter: Dan Connolly | Owner: Dan Connolly Type: enhancement | Status: assigned Priority: minor | Milestone: morning-star Component: data-sharing | Resolution: Keywords:| Blocked By: 388, 435 Blocking:| Sensitive: 1 --+--- Changes (by Dan Connolly): * sensitive: => 1 Comment: > COVID-19 Synthetic Dataset – derived from SYNTHEA, also in a DOCKER image -- https://transmartfoundation.org/agenda-modified/ -- Ticket URL: <https://informatics.gpcnetwork.org/trac/Project/ticket/56#comment:38> gpc-informatics <https://informatics.gpcnetwork.org/trac/Project> Greater Plains Collaborative ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: trac #411: Align SNOW SHRINE terminology with ACT ontology for interoperation of query
#411: Align SNOW SHRINE terminology with ACT ontology for interoperation of query --+-- Reporter: Dan Connolly | Owner: Jim Campbell Type: enhancement | Status: assigned Priority: major | Milestone: snow-shrine-3 Component: data-stds | Resolution: Keywords: ModelMashup | Blocked By: 23, 90, 201, 243, 280, 525, 583 Blocking:| Sensitive: 1 --+-- Comment (by Dan Connolly): We (Lav and I) are in receipt of medication_metadata.zip (53804323 bytes). Thanks, Jim and co. -- Ticket URL: <https://informatics.gpcnetwork.org/trac/Project/ticket/411#comment:40> gpc-informatics <https://informatics.gpcnetwork.org/trac/Project> Greater Plains Collaborative ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: trac #411: Align SNOW SHRINE terminology with ACT ontology for interoperation of query
#411: Align SNOW SHRINE terminology with ACT ontology for interoperation of query --+-- Reporter: Dan Connolly | Owner: Jim Campbell Type: enhancement | Status: assigned Priority: major | Milestone: snow-shrine-3 Component: data-stds | Resolution: Keywords: ModelMashup | Blocked By: 23, 90, 201, 243, 280, 525, 583 Blocking:| Sensitive: 1 --+-- Comment (by Dan Connolly): JRC will investigate comment:38 and report back. (from 31 Mar call) -- Ticket URL: <https://informatics.gpcnetwork.org/trac/Project/ticket/411#comment:39> gpc-informatics <https://informatics.gpcnetwork.org/trac/Project> Greater Plains Collaborative ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: trac #411: Align SNOW SHRINE terminology with ACT ontology for interoperation of query
#411: Align SNOW SHRINE terminology with ACT ontology for interoperation of query --+-- Reporter: Dan Connolly | Owner: Jim Campbell Type: enhancement | Status: assigned Priority: major | Milestone: snow-shrine-3 Component: data-stds | Resolution: Keywords: ModelMashup | Blocked By: 23, 90, 201, 243, 280, 525, 583 Blocking:| Sensitive: 1 --+-- Changes (by Dan Connolly): * cc: lpatel@… (added) * sensitive: => 1 Comment: Jim, I'm struggling to find the i2b2 metadata for medications in the Nebraska Lexicon. I downloaded `Publication_Files_20190816.zip` via https://www.unmc.edu /pathology-research/bioinformatics/campbell/tdc.html ; I don't see any i2b2 metadata in there. The cover page says that zip file includes release notes, but I don't see them in there. So I downloaded `Nebraska_Lexicon_Release_Notes_20190817.pdf`; neither "i2b2" nor "SHRINE" occurs in there. -- Ticket URL: <https://informatics.gpcnetwork.org/trac/Project/ticket/411#comment:38> gpc-informatics <https://informatics.gpcnetwork.org/trac/Project> Greater Plains Collaborative ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #411: Align SNOW SHRINE terminology with ACT ontology for interoperation of query
#411: Align SNOW SHRINE terminology with ACT ontology for interoperation of query -+-- Reporter: dconnolly| Owner: campbell Type: enhancement | Status: assigned Priority: major| Milestone: snow-shrine-3 Component: data-stds| Resolution: Keywords: ModelMashup | Blocked By: 23, 90, 201, 243, 280, 525, 583 Blocking: | -+-- Comment (by dconnolly): JRC reports regular progress continues -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/411#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
Re: [gpc-informatics] #478: ADAPTABLE monitoring
#478: ADAPTABLE monitoring --+ Reporter: schandaka | Owner: schandaka Type: enhancement | Status: closed Priority: major | Milestone: gpc-phase2-h5 Component: data-sharing | Resolution: fixed Keywords:| Blocked By: 274, 476, 496 Blocking:| --+ Changes (by dconnolly): * status: reopened => closed * resolution: => fixed Comment: In the KUMC PMO meeting this morning, we talked about "final" adaptable enrollment counts; that means this is done, if I'm not mistaken. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/478#comment:41> 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] #597: spec for crosswalk to accompany i2b2 datamarts for GROUSE
#597: spec for crosswalk to accompany i2b2 datamarts for GROUSE +--- Reporter: xsong | Owner: dconnolly Type: design-issue| Status: assigned Priority: major | Milestone: grouse-refresh-2 Component: data-sharing| Resolution: Keywords: | Blocked By: Blocking: 595, 733, 735, 737 | +--- Changes (by dconnolly): * cc: gpc-dev@… (removed) * blocking: 595 => 595, 733, 735, 737 -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/597#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] #597: spec for crosswalk to accompany i2b2 datamarts for GROUSE
#597: spec for crosswalk to accompany i2b2 datamarts for GROUSE --+--- Reporter: xsong | Owner: dconnolly Type: design-issue | Status: assigned Priority: major | Milestone: grouse-refresh-2 Component: data-sharing | Resolution: Keywords:| Blocked By: Blocking: 595 | --+--- Changes (by dconnolly): * cc: rwaitman, badagarla (removed) * reporter: lv => xsong -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/597#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] #597: spec for crosswalk to accompany i2b2 datamarts for GROUSE
#597: spec for crosswalk to accompany i2b2 datamarts for GROUSE --+--- Reporter: lv| Owner: dconnolly Type: design-issue | Status: assigned Priority: major | Milestone: grouse-refresh-2 Component: data-sharing | Resolution: Keywords:| Blocked By: Blocking: 595 | --+--- Changes (by dconnolly): * owner: lv => dconnolly * status: reopened => assigned -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/597#comment:8> gpc-informatics <http://informatics.gpcnetwork.org/> Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
[gpc-informatics] Batch modify: #120, #23, #229
Batch modification to #120, #23, #229 by dconnolly: milestone to snow-shrine-3 Comment: consolidating SHRINE milestones -- Tickets URL: <http://informatics.gpcnetwork.org/trac/Project/query?id=120%2C23%2C229> 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] #411: Align SNOW SHRINE terminology with ACT ontology for interoperation of query
#411: Align SNOW SHRINE terminology with ACT ontology for interoperation of query -+-- Reporter: dconnolly| Owner: campbell Type: enhancement | Status: assigned Priority: major| Milestone: snow-shrine-3 Component: data-stds| Resolution: Keywords: ModelMashup | Blocked By: 23, 90, 201, 243, 280, 525, 583 Blocking: | -+-- Comment (by campbell): Jay was correct; the RXCUIs listed above are of type BN (brand name) and are not orderable by specification from NLM. For the example of Norvasc above, the following are examples of orderable versions of Norvasc: RXCUI 572746 (TTY=SBDC) Norvasc 10 mg 212575 (TTY=) Norvasc 10 mg oral tablet...and several more. The NLM specifies that RXCUIs of TTY=(SCD, GPCK, BPCK, BCD, SBDC, SCDC) are orderable or prescribable and those are the only RXCUIs we map when extracting our medication orders or prescriptions. In the SHRINE metadata we publish, we index the orderable drugs to RXCUIs for their ingredients (in the case of Norvasc, the IN RXCUI = 17767 Amlodipine). We also Index to the VA drug class, both for searching of sets of medications. The orderable drugs in SHRINE metadata are, in turn, each linked to all NDC package codes that have been manufactured for that orderable drug. So, for example, the 10mg Norvasc was manufactured and packaged as (00069154030) Amlodipine 10 MG Oral Tablet Norvasc (amlodipine besylate) 100 BLISTER PACK in 1 BOX, UNIT-DOSE (0069-1540-41) > 1 TABLET in 1 BLISTER PACK [ 44 facts ]. You will not find any RXCUIs in our metadata with TTY=BN because we should not be mapping our drug orders to that set of codes. I notic in our metadata build that Jay has not used the brand names on the metadata but the brandname RXCUIs are included. We will fix that. Jim -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/411#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] #411: Align SNOW SHRINE terminology with ACT ontology for interoperation of query
#411: Align SNOW SHRINE terminology with ACT ontology for interoperation of query -+-- Reporter: dconnolly| Owner: campbell Type: enhancement | Status: assigned Priority: major| Milestone: snow-shrine-3 Component: data-stds| Resolution: Keywords: ModelMashup | Blocked By: 23, 90, 201, 243, 280, 525, 583 Blocking: | -+-- Comment (by lv): We're working with the meds ontology, and finding some RXCuis fall out. Is this what you would expect? Are brand drugs excluded? Examples listed below. ||RXCUI||STR|| ||58927||Norvasc|| ||82728||Zoloft|| ||114228||Paxil|| ||128793||Vicodin|| ||151392||Augmentin|| ||153010||Advil|| ||153165||Lipitor|| ||196474||Zithromax|| ||196503||Zocor|| ||202421||Coumadin|| ||202433||Tylenol|| ||202896||Premarin|| ||202991||Lasix|| ||203345||Prilosec|| ||215927||Celebrex|| ||224920||Synthroid|| ||789982||Sodium Chloride Solution|| ||2123072||albuterol 90 MCG/INHAL Metered Dose Inhaler, 200 A|| ||2123076||albuterol 90 MCG/INHAL Metered Dose Inhaler, 200 A|| -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/411#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] #243: GPC Procedure Ontology: CPT, HCPCS
#243: GPC Procedure Ontology: CPT, HCPCS --+ Reporter: rwaitman | Owner: lpatel Type: design-issue | Status: closed Priority: major | Milestone: snow-shrine-3 Component: data-stds | Resolution: invalid Keywords:| Blocked By: Blocking: 411 | --+ Changes (by dconnolly): * status: assigned => closed * resolution: => invalid Comment: This seems overtaken by (1) the PCORNet CDM PROCEDURES table and (2) the ACT Procedures ontology. See also - #411 regarding alignment between ACT and related GPC work. - https://github.com/kumc-bmi/h2p-mapping regarding mappings from the HERON ontology to PCORNet and, to some extent, ACT. - Note HERON has largely incorporated the ACT (nee SCILHS) ontology around July 2017. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/243#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] #597: spec for crosswalk to accompany i2b2 datamarts for GROUSE
#597: spec for crosswalk to accompany i2b2 datamarts for GROUSE --+--- Reporter: lv| Owner: lv Type: design-issue | Status: reopened Priority: major | Milestone: grouse-refresh-2 Component: data-sharing | Resolution: Keywords:| Blocked By: Blocking: 595 | --+--- Changes (by dconnolly): * milestone: gpc-phase2-h4 => grouse-refresh-2 -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/597#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] #56: shareable synthetic test data sets: Epic clarity, i2b2, NAACCR, ...
#56: shareable synthetic test data sets: Epic clarity, i2b2, NAACCR, ... --+--- Reporter: dconnolly | Owner: dconnolly Type: enhancement | Status: assigned Priority: minor | Milestone: morning-star Component: data-sharing | Resolution: Keywords:| Blocked By: 388, 435 Blocking:| --+--- Comment (by dconnolly): This Java library allows to create synthetic (fabricated) NAACCR data files. -- https://github.com/imsweb/data-generator Latest commit 24568e0 on Apr 13 -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/56#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
Re: [gpc-informatics] #597: spec for crosswalk to accompany i2b2 datamarts for GROUSE
#597: spec for crosswalk to accompany i2b2 datamarts for GROUSE --+ Reporter: lv| Owner: lv Type: design-issue | Status: reopened Priority: major | Milestone: gpc-phase2-h4 Component: data-sharing | Resolution: Keywords:| Blocked By: Blocking: 595 | --+ Comment (by dconnolly): for sites with shifted birth dates (>89 etc.) we need a 4th column. DC to clarify. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/597#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] #597: spec for crosswalk to accompany i2b2 datamarts for GROUSE
#597: spec for crosswalk to accompany i2b2 datamarts for GROUSE --+ Reporter: lv| Owner: lv Type: design-issue | Status: reopened Priority: major | Milestone: gpc-phase2-h4 Component: data-sharing | Resolution: Keywords:| Blocked By: Blocking: 595 | --+ Changes (by dconnolly): * status: closed => reopened * resolution: fixed => -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/597#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] #411: Align SNOW SHRINE terminology with ACT ontology for interoperation of query
#411: Align SNOW SHRINE terminology with ACT ontology for interoperation of query -+-- Reporter: dconnolly| Owner: campbell Type: enhancement | Status: assigned Priority: major| Milestone: snow-shrine-3 Component: data-stds| Resolution: Keywords: ModelMashup | Blocked By: 23, 90, 201, 243, 280, 525, 583 Blocking: | -+-- Comment (by campbell): I attach a working draft of our Research user data dictionary which documents CDMV4 data model with expanded tables including ALLERGY and terminology support for folder searches (ie valuesets) in SNOMED CT and RXNORM/NDC. ICD and others under development. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/411#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] #745: Grant funding request to NCI
#745: Grant funding request to NCI -+ Reporter: campbell | Owner: dconnolly Type: enhancement | Status: closed Priority: minor| Milestone: Component: data-stds| Resolution: fixed Keywords: | Blocked By: Blocking: | -+ Changes (by dconnolly): * status: new => closed * resolution: => fixed Comment: JRC notes it's a follow-up to [[CancerRCR#Aim2]] Noted. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/745#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
[gpc-informatics] #745: Grant funding request to NCI
#745: Grant funding request to NCI --+--- Reporter: campbell | Owner: dconnolly Type: enhancement | Status: new Priority: minor| Milestone: Component: data-stds| Keywords: Blocked By: | Blocking: --+--- UNMC is preparing a grant submission to NCI for standardization of data encoding for synoptic cancer reports. We will be implementing standard SNOMED CT in CAP Cancer Protocol datasets. The Cancer Protocols will be deployed into pathologist workflow by implementing eCC (electronic checksheet format) into the pathology system. Epic Beaker and Cerner COPATH both support eCC workflow deployment. UNMC will be offering contract funding within the grant collaborators whose pathology departments agree to implement and use the Cancer Protocols in recording new cases of cancer. Any GPC or affiliate sites who may have interest in this collaboration should contact Jim (campb...@unmc.edu) or Scott (wcamp...@unmc.edu) for discussion. Deadline for grant submission is June 11. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/745> 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] #411: Align SNOW SHRINE terminology with ACT ontology for interoperation of query
#411: Align SNOW SHRINE terminology with ACT ontology for interoperation of query -+-- Reporter: dconnolly| Owner: campbell Type: enhancement | Status: assigned Priority: major| Milestone: snow-shrine-3 Component: data-stds| Resolution: Keywords: ModelMashup | Blocked By: 23, 90, 201, 243, 280, 525, 583 Blocking: | -+-- Comment (by dconnolly): I see "Full Release of Snow Shrine metadata, version 1.2 (20190430)" -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/411#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] #715: NextD request on mapping payer_type variable
#715: NextD request on mapping payer_type variable --+- Reporter: afurmanchuck | Owner: meiliu Type: problem | Status: closed Priority: critical | Milestone: next-d Component: data-stds | Resolution: fixed Keywords:| Blocked By: Blocking: 713 | --+- Changes (by xsong): * status: assigned => closed * resolution: => fixed Old description: > The aim of NextD project is evaluation of Affordable Act Effect on health > outcomes of patients with type 2 diabetes. In oversimplified language, > effect on health from having Medicaid insurance. One must must know > effects of other insurances or their absence in order to definitively say > if ACA expansion actually effective. > > In last PCORI cdm 4.1 refresh sites reported from 80% to 100% of > encounters missing information on insurance used. Clearly, PCORI table > ENCOUNTER could not be used for next-D project to report insurance. > > We ask sites to respond to this ticket with timelines they might need in > order to remap source insurance values to PCORI categories. > For Next-D purposes we would ask to remap into following categories: > 1.Medicare > 2.Medicaid > 3.Other Government > 4.Department of corrections > 5.Private health insurance > 6.Blue cross/Blue shield > 7.Managed care, unspecified > 8.No payment > 9.Miscellaneous/Other > .Unavailable/No payer specified/blank > NI.No information > UN.Unknown > OT.Other > > Categories 9,,NI,UN,OT could not contribute more than 20% total. > Explanations must be provided if your site face this situation. NU team > will be offering help on remapping or extra allocation if requested. > > Respond to this ticket by September 21st, 2018. New description: The aim of NextD project is evaluation of Affordable Act Effect on health outcomes of patients with type 2 diabetes. In oversimplified language, effect on health from having Medicaid insurance. One must must know effects of other insurances or their absence in order to definitively say if ACA expansion actually effective. In last PCORI cdm 4.1 refresh sites reported from 80% to 100% of encounters missing information on insurance used. Clearly, PCORI table ENCOUNTER could not be used for next-D project to report insurance. We ask sites to respond to this ticket with timelines they might need in order to remap source insurance values to PCORI categories. For Next-D purposes we would ask to remap into following categories: 1.Medicare 2.Medicaid 3.Other Government 4.Department of corrections 5.Private health insurance 6.Blue cross/Blue shield 7.Managed care, unspecified 8.No payment 9.Miscellaneous/Other .Unavailable/No payer specified/blank NI.No information UN.Unknown OT.Other Categories 9,,NI,UN,OT could not contribute more than 20% total. Explanations must be provided if your site face this situation. NU team will be offering help on remapping or extra allocation if requested. Respond to this ticket by September 21st, 2018. See ticket #713 for timelines on extraction of ENROLLMENT table -- -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/715#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] #411: Align SNOW SHRINE terminology with ACT ontology for interoperation of query
#411: Align SNOW SHRINE terminology with ACT ontology for interoperation of query -+-- Reporter: dconnolly| Owner: campbell Type: enhancement | Status: assigned Priority: major| Milestone: snow-shrine-3 Component: data-stds| Resolution: Keywords: ModelMashup | Blocked By: 23, 90, 201, 243, 280, 525, 583 Blocking: | -+-- Comment (by campbell): SNOW SHRINE metadat and Nebraska Lexicon are back online and available at: https://www.unmc.edu/pathology-research/bioinformatics/campbell/tdc.html Nebraska plans for April 15 publication of spring release including new CDMV4 supplemental tables for medications-RXNORM and NDC, diagnoses - ICD-10-CM and SNOMED CT. Jim -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/411#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] #411: Align SNOW SHRINE terminology with ACT ontology for interoperation of query
#411: Align SNOW SHRINE terminology with ACT ontology for interoperation of query -+-- Reporter: dconnolly| Owner: campbell Type: enhancement | Status: assigned Priority: major| Milestone: snow-shrine-3 Component: data-stds| Resolution: Keywords: ModelMashup | Blocked By: 23, 90, 201, 243, 280, 525, 583 Blocking: | -+-- Old description: > reference: https://www.unmc.edu/pathology/informatics/tdc > Full release of SNOW SHRINE metadata 20181001 > > Hackathon6 discussion converged on NOT deploying SNOW SHRINE hub for GPC > given Wisconsin departure but UNMC will continue to promote convergence > of metadata maintenance with ACT network given the number of GPC sites > which will be participating in that SHRINE network. ARCH > network(formerly SCILHS) due to retire as Harvard joins ACT. New description: reference: https://www.unmc.edu/pathology- research/bioinformatics/campbell/tdc.html Full release of SNOW SHRINE metadata 20181001 Hackathon6 discussion converged on NOT deploying SNOW SHRINE hub for GPC given Wisconsin departure but UNMC will continue to promote convergence of metadata maintenance with ACT network given the number of GPC sites which will be participating in that SHRINE network. ARCH network(formerly SCILHS) due to retire as Harvard joins ACT. -- Comment (by campbell): Apologies to GPC colleagues. SNOW SHRINE publications have been moved to: https://www.unmc.edu/pathology-research/bioinformatics/campbell/tdc.html -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/411#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] #716: Create Trac Accounts
#716: Create Trac Accounts ---+ Reporter: lv | Owner: dconnolly Type: task | Status: closed Priority: major | Milestone: Component: data-stds | Resolution: fixed Keywords: trac, account | Blocked By: Blocking: | ---+ Changes (by dconnolly): * status: assigned => closed * resolution: => fixed Comment: Gak! I just realized Gorkski's account was yet to be created. Done. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/716#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] #719: Oracle is changing their licensing fees
#719: Oracle is changing their licensing fees ---+- Reporter: campbell | Owner: dconnolly Type: problem| Status: closed Priority: major | Milestone: Component: data-stds | Resolution: worksforme Keywords: | Blocked By: Blocking: | ---+- Changes (by dconnolly): * status: new => closed * resolution: => worksforme -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/719#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] #243: GPC Procedure Ontology: CPT, HCPCS
#243: GPC Procedure Ontology: CPT, HCPCS --+ Reporter: rwaitman | Owner: lpatel Type: design-issue | Status: assigned Priority: major | Milestone: snow-shrine-3 Component: data-stds | Resolution: Keywords:| Blocked By: Blocking: 411 | --+ Changes (by dconnolly): * milestone: snow-shrine-2 => snow-shrine-3 -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/243#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] #718: DROC Request #42 - BC data to MCW
#718: DROC Request #42 - BC data to MCW --+ Reporter: kosinski | Owner: campbell Type: problem | Status: closed Priority: major | Milestone: pcornet-cdm-6 Component: data-sharing | Resolution: fixed Keywords: BC breast-cancer | Blocked By: Blocking:| --+ Changes (by dconnolly): * cc: gpc-dev@… (removed) * status: assigned => closed * resolution: => fixed Comment: Nice work, everybody. Kristen, if I missed something and there's more to do, feel free to reopen this. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/718#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] #718: DROC Request #42 - BC data to MCW
#718: DROC Request #42 - BC data to MCW --+ Reporter: kosinski | Owner: campbell Type: problem | Status: assigned Priority: major | Milestone: pcornet-cdm-6 Component: data-sharing | Resolution: Keywords: BC breast-cancer | Blocked By: Blocking:| --+ Comment (by ynarayana): UNMC submitted the data using the redcap link in comment#3. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/718#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] #718: DROC Request #42 - BC data to MCW
#718: DROC Request #42 - BC data to MCW --+ Reporter: kosinski | Owner: campbell Type: problem | Status: assigned Priority: major | Milestone: pcornet-cdm-6 Component: data-sharing | Resolution: Keywords: BC breast-cancer | Blocked By: Blocking:| --+ Changes (by schandaka): * owner: mwennberg => campbell Comment: I sent the data on 02/19 via securefiles.kumc and I also received an acknowledgement that Yesh downloaded it on 02/21. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/718#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] #718: DROC Request #42 - BC data to MCW
#718: DROC Request #42 - BC data to MCW --+ Reporter: kosinski | Owner: mwennberg Type: problem | Status: assigned Priority: major | Milestone: pcornet-cdm-6 Component: data-sharing | Resolution: Keywords: BC breast-cancer | Blocked By: Blocking:| --+ Changes (by dconnolly): * owner: campbell => mwennberg Comment: Maren, Sravani, did we send the survey data to UNMC? -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/718#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] #718: DROC Request #42 - BC data to MCW
#718: DROC Request #42 - BC data to MCW --+ Reporter: kosinski | Owner: campbell Type: problem | Status: assigned Priority: major | Milestone: pcornet-cdm-6 Component: data-sharing | Resolution: Keywords: BC breast-cancer | Blocked By: Blocking:| --+ Comment (by ynarayana): Can someone help me find the Breast Cancer Survey Data? Thanks, Yesh(UNMC) -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/718#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] #718: DROC Request #42 - BC data to MCW
#718: DROC Request #42 - BC data to MCW --+ Reporter: kosinski | Owner: campbell Type: problem | Status: assigned Priority: major | Milestone: pcornet-cdm-6 Component: data-sharing | Resolution: Keywords: BC breast-cancer | Blocked By: Blocking:| --+ Comment (by nsmith): Replying to [comment:9 bgryzlak]: > UIOWAs revised ETA is COB 2/18/19. UIOWA just submitted. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/718#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] #718: DROC Request #42 - BC data to MCW
#718: DROC Request #42 - BC data to MCW --+ Reporter: kosinski | Owner: campbell Type: problem | Status: assigned Priority: major | Milestone: pcornet-cdm-6 Component: data-sharing | Resolution: Keywords: BC breast-cancer | Blocked By: Blocking:| --+ Comment (by bgryzlak): UIOWAs revised ETA is COB 2/18/19. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/718#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] #718: DROC Request #42 - BC data to MCW
#718: DROC Request #42 - BC data to MCW --+ Reporter: kosinski | Owner: campbell Type: problem | Status: assigned Priority: major | Milestone: pcornet-cdm-6 Component: data-sharing | Resolution: Keywords: BC breast-cancer | Blocked By: Blocking:| --+ Changes (by dconnolly): * owner: lv => campbell * status: new => assigned Comment: UNMC, UTSW, UIOWA folks what news on this? Recall the Jan 15 plan was to deliver by end of Jan. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/718#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] #718: DROC Request #42 - BC data to MCW
#718: DROC Request #42 - BC data to MCW --+ Reporter: kosinski | Owner: lv Type: problem | Status: new Priority: major | Milestone: pcornet-cdm-6 Component: data-sharing | Resolution: Keywords: BC breast-cancer | Blocked By: Blocking:| --+ Comment (by schandaka): KUMC submitted their results today. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/718#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] #711: External Validation for Acute Kidney Injury(AKI) Predictive Models using PCORnet CDM data (Part I)
#711: External Validation for Acute Kidney Injury(AKI) Predictive Models using PCORnet CDM data (Part I) --+ Reporter: meiliu| Owner: xsong Type: task | Status: new Priority: major | Milestone: Component: data-sharing | Resolution: Keywords: aki cdm | Blocked By: Blocking: 742 | --+ Description changed by xsong: Old description: > We propose to build predictive models to identify patients at risk for > hospital-acquired AKI and externally validate the models using the > PCORnet (Patient Centered Outcomes Research Network) 13 common data model > (CDM) infrastructure. This ticket is to **track working progress** and > **report bugs** for the first part of exploration. > > Part I objective: data extraction and quality check > [https://github.com/sxinger/AKI_CDM#background Task 1.1 and Task 2.1] > > For more details, please visit: https://github.com/kumc-bmi/AKI_CDM or > xsong's branch: https://github.com/sxinger/AKI_CDM New description: We propose to build predictive models to identify patients at risk for hospital-acquired AKI and externally validate the models using the PCORnet (Patient Centered Outcomes Research Network) 13 common data model (CDM) infrastructure. This ticket is to **track working progress** and **report bugs** for the **first** part of exploration. Part I objective: data extraction and quality check [https://github.com/sxinger/AKI_CDM#background Task 1.1 and Task 2.1] For more details, please visit: https://github.com/kumc-bmi/AKI_CDM or xsong's branch: https://github.com/sxinger/AKI_CDM -- -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/711#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
[gpc-informatics] #742: External Validation for Acute Kidney Injury(AKI) Predictive Models using PCORnet CDM data (Part II)
#742: External Validation for Acute Kidney Injury(AKI) Predictive Models using PCORnet CDM data (Part II) ---+- Reporter: meiliu| Owner: xsong Type: problem | Status: new Priority: major | Milestone: Component: data-sharing | Keywords: aki cdm Blocked By: 711 | Blocking: ---+- This ticket is a continuation of ticket #711 and is to track working progress and report bugs for the **second** part of exploration. Part II objective: exploratory data analysis and deploying R codes for external validations of predictive models [https://github.com/kumc- bmi/AKI_CDM Task 1.2 and Task 2.2] For more details, please visit: https://github.com/kumc-bmi/AKI_CDM or xsong's branch: https://github.com/sxinger/AKI_CDM -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/742> 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] #711: External Validation for Acute Kidney Injury(AKI) Predictive Models using PCORnet CDM data (Part I) (was: External Validation for Acute Kidney Injury(AKI) Predictive Models
#711: External Validation for Acute Kidney Injury(AKI) Predictive Models using PCORnet CDM data (Part I) --+ Reporter: meiliu| Owner: xsong Type: task | Status: new Priority: major | Milestone: Component: data-sharing | Resolution: Keywords: aki cdm | Blocked By: Blocking:| --+ Description changed by xsong: Old description: > We propose to build predictive models to identify patients at risk for > hospital-acquired AKI and externally validate the models using the > PCORnet (Patient Centered Outcomes Research Network) 13 common data model > (CDM) infrastructure. This ticket is to **track working progress** and > **report bugs**. > > We are currently at stage 1: data extraction and quality check > [https://github.com/sxinger/AKI_CDM#background Task 1.1 and Task 2.1] > > For more details, please visit: https://github.com/kumc-bmi/AKI_CDM or > xsong's branch: https://github.com/sxinger/AKI_CDM New description: We propose to build predictive models to identify patients at risk for hospital-acquired AKI and externally validate the models using the PCORnet (Patient Centered Outcomes Research Network) 13 common data model (CDM) infrastructure. This ticket is to **track working progress** and **report bugs** for the first part of exploration. Part I objective: data extraction and quality check [https://github.com/sxinger/AKI_CDM#background Task 1.1 and Task 2.1] For more details, please visit: https://github.com/kumc-bmi/AKI_CDM or xsong's branch: https://github.com/sxinger/AKI_CDM -- -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/711#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] #738: real dates in PCORNet CDM: confirm or describe plan
#738: real dates in PCORNet CDM: confirm or describe plan -+ Reporter: dconnolly| Owner: manuells Type: enhancement | Status: closed Priority: major| Milestone: pcornet-cdm-6 Component: data-stds| Resolution: fixed Keywords: | Blocked By: Blocking: | -+ Changes (by dconnolly): * status: assigned => closed * resolution: => fixed Comment: Thanks, everybody. Steve, comment:7 has a summary. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/738#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] #738: real dates in PCORNet CDM: confirm or describe plan
#738: real dates in PCORNet CDM: confirm or describe plan -+ Reporter: dconnolly| Owner: manuells Type: enhancement | Status: assigned Priority: major| Milestone: pcornet-cdm-6 Component: data-stds| Resolution: Keywords: | Blocked By: Blocking: | -+ Comment (by kosinski): MCW will generate an unshifted CDM for the April 2019 C6R2 release. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/738#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] #738: real dates in PCORNet CDM: confirm or describe plan
#738: real dates in PCORNet CDM: confirm or describe plan -+ Reporter: dconnolly| Owner: manuells Type: enhancement | Status: assigned Priority: major| Milestone: pcornet-cdm-6 Component: data-stds| Resolution: Keywords: | Blocked By: Blocking: | -+ Comment (by mosaa@…): MU has unshift capability. We plan for C6R2 refresh in April. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/738#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] #738: real dates in PCORNet CDM: confirm or describe plan
#738: real dates in PCORNet CDM: confirm or describe plan -+ Reporter: dconnolly| Owner: manuells Type: enhancement | Status: assigned Priority: major| Milestone: pcornet-cdm-6 Component: data-stds| Resolution: Keywords: | Blocked By: Blocking: | -+ Comment (by manuells): UTHSCSA- We have already updated our protocol to include no longer date shifting CDM and it's a simple matter to strip it out of our ETL. We'll have no trouble getting this set up by the April refresh. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/738#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] #718: DROC Request #42 - BC data to MCW
#718: DROC Request #42 - BC data to MCW --+ Reporter: kosinski | Owner: lv Type: problem | Status: new Priority: major | Milestone: pcornet-cdm-6 Component: data-sharing | Resolution: Keywords: BC breast-cancer | Blocked By: Blocking:| --+ Changes (by dconnolly): * keywords: BC => BC breast-cancer * priority: minor => major * reporter: lv => kosinski * milestone: gpc-phase2-h5 => pcornet-cdm-6 Comment: Jan 15 status: - **UNMC, UTSW** to deliver by end of the month - **UIOWA** - end of Jan OK - **KUMC** - Maren OK end of Jan -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/718#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] #715: NextD request on mapping payer_type variable
#715: NextD request on mapping payer_type variable --+--- Reporter: afurmanchuck | Owner: meiliu Type: problem | Status: assigned Priority: critical | Milestone: next-d Component: data-stds | Resolution: Keywords:| Blocked By: Blocking: 713 | --+--- Comment (by afurmanchuck): Please, see ticket #713 for timelines on extraction of ENROLLMENT table. Sites are currently working on mappings. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/715#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] #715: NextD request on mapping payer_type variable
#715: NextD request on mapping payer_type variable --+--- Reporter: afurmanchuck | Owner: meiliu Type: problem | Status: assigned Priority: critical | Milestone: next-d Component: data-stds | Resolution: Keywords:| Blocked By: Blocking: 713 | --+--- Comment (by dconnolly): Is this done? If not, who has the ball? What's the next step? -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/715#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] #738: real dates in PCORNet CDM: confirm or describe plan
#738: real dates in PCORNet CDM: confirm or describe plan -+ Reporter: dconnolly| Owner: manuells Type: enhancement | Status: assigned Priority: major| Milestone: pcornet-cdm-6 Component: data-stds| Resolution: Keywords: | Blocked By: Blocking: | -+ Changes (by dconnolly): * owner: lv => manuells Comment: Laura, notes (#12) from Jan 15 say UTHSCSA "can give a plan this week". By site, from what I can find just now: 1. KUMC - planned for C6R2 April (comment:2) 1. UIOWA - April, pending IRB modification (comment:4) 1. **MCW** - ??? 1. **MCRI** - ??? 1. UNMC - April, pending IRB modification (comment:6) 1. **UTHSCSA** - ??? 1. UTSW - plans to build from identified (Jan 15 call) 1. MU - has unshift-capability (Jan 15 call, comment:3) 1. IU - April, pending IRB mod (comment:5) 1. **Utah** - ??? 1. **Allina** - ??? 1. **Intermountain** - ??? -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/738#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] #738: real dates in PCORNet CDM: confirm or describe plan
#738: real dates in PCORNet CDM: confirm or describe plan -+ Reporter: dconnolly| Owner: lv Type: enhancement | Status: assigned Priority: major| Milestone: pcornet-cdm-6 Component: data-stds| Resolution: Keywords: | Blocked By: Blocking: | -+ Comment (by jmcclay): UNMC needs to submit a modification to our existing IRB. There is no technical obstacle to providing a non-date shifted CDM tables by the April release. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/738#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] #738: real dates in PCORNet CDM: confirm or describe plan
#738: real dates in PCORNet CDM: confirm or describe plan -+ Reporter: dconnolly| Owner: lv Type: enhancement | Status: assigned Priority: major| Milestone: pcornet-cdm-6 Component: data-stds| Resolution: Keywords: | Blocked By: Blocking: | -+ Comment (by jhamer): Indiana University will provide a cross-walk file for dates that are shifted. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/738#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] #738: real dates in PCORNet CDM: confirm or describe plan
#738: real dates in PCORNet CDM: confirm or describe plan -+ Reporter: dconnolly| Owner: lv Type: enhancement | Status: assigned Priority: major| Milestone: pcornet-cdm-6 Component: data-stds| Resolution: Keywords: | Blocked By: Blocking: | -+ Comment (by bgryzlak): UIOWA needs to submit a modification to the existing IRB approval before making this change. Currently not sure of a timeline but am estimating mid-February. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/738#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] #738: real dates in PCORNet CDM: confirm or describe plan
#738: real dates in PCORNet CDM: confirm or describe plan -+ Reporter: dconnolly| Owner: lv Type: enhancement | Status: assigned Priority: major| Milestone: pcornet-cdm-6 Component: data-stds| Resolution: Keywords: | Blocked By: Blocking: | -+ Comment (by tmcneeley): MU should be able to setup non-date shifting by unshifting using our crosswalk table. We should have a completed process written for this by the April refresh cycle. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/738#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] #411: Align SNOW SHRINE terminology with ACT ontology for interoperation of query
#411: Align SNOW SHRINE terminology with ACT ontology for interoperation of query -+-- Reporter: dconnolly| Owner: campbell Type: enhancement | Status: assigned Priority: major| Milestone: snow-shrine-3 Component: data-stds| Resolution: Keywords: ModelMashup | Blocked By: 23, 90, 201, 243, 280, 525, 583 Blocking: | -+-- Comment (by campbell): Upload of RXCUI-NDC maps for discussion and demo on 20180115 -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/411#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] #411: Align SNOW SHRINE terminology with ACT ontology for interoperation of query (was: Align SNOW SHRINE terminology with ARCH and ACT ontology for interoperation of query)
#411: Align SNOW SHRINE terminology with ACT ontology for interoperation of query -+-- Reporter: dconnolly| Owner: campbell Type: enhancement | Status: assigned Priority: major| Milestone: snow-shrine-3 Component: data-stds| Resolution: Keywords: ModelMashup | Blocked By: 23, 90, 201, 243, 280, 525, 583 Blocking: | -+-- Description changed by campbell: Old description: > reference: https://www.unmc.edu/pathology/informatics/tdc > Full release of SNOW SHRINE metadata 20181001 > > Hackathon6 discussion converged on NOT deploying SNOW SHRINE hub for GPC > given Wisconsin departure but UNMC will continue to promote convergence > of metadata maintenance with ACT network given the number of GPC sites > which will be participating in that SHRINE network. New description: reference: https://www.unmc.edu/pathology/informatics/tdc Full release of SNOW SHRINE metadata 20181001 Hackathon6 discussion converged on NOT deploying SNOW SHRINE hub for GPC given Wisconsin departure but UNMC will continue to promote convergence of metadata maintenance with ACT network given the number of GPC sites which will be participating in that SHRINE network. ARCH network(formerly SCILHS) due to retire as Harvard joins ACT. -- -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/411#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] #738: real dates in PCORNet CDM: confirm or describe plan
#738: real dates in PCORNet CDM: confirm or describe plan -+ Reporter: dconnolly| Owner: lv Type: enhancement | Status: assigned Priority: major| Milestone: pcornet-cdm-6 Component: data-stds| Resolution: Keywords: | Blocked By: Blocking: | -+ Comment (by schandaka): Replying to [comment:1 dconnolly]: > At KUMC, we plan to use real dates in cycle 6 this month; due to some hardware shuffling, we first built our datamart with date shifting and we are now ready to run it without date shifting. > > Laurel, how about Marshfield? > > After you give your answer, please re-assign to another site. I may have confused Dan earlier, KUMC is '''NOT''' date shifting for C6R1. We plan to implement the 'no date shift' logic this month though in preparation for the C6R2 in April. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/738#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] #738: real dates in PCORNet CDM: confirm or describe plan
#738: real dates in PCORNet CDM: confirm or describe plan -+ Reporter: dconnolly| Owner: lv Type: enhancement | Status: assigned Priority: major| Milestone: pcornet-cdm-6 Component: data-stds| Resolution: Keywords: | Blocked By: Blocking: | -+ Changes (by dconnolly): * owner: dconnolly => lv * status: new => assigned Comment: At KUMC, we plan to use real dates in cycle 6 this month; due to some hardware shuffling, we first built our datamart with date shifting and we are now ready to run it without date shifting. Laurel, how about Marshfield? After you give your answer, please re-assign to another site. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/738#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
[gpc-informatics] #738: real dates in PCORNet CDM: confirm or describe plan
#738: real dates in PCORNet CDM: confirm or describe plan --+--- Reporter: dconnolly| Owner: dconnolly Type: enhancement | Status: new Priority: major| Milestone: pcornet-cdm-6 Component: data-stds| Keywords: Blocked By: | Blocking: --+--- For a PCRF Quarterly Report we are to: Confirm that dates are not shifted or obfuscated in each DataMart. If dates are currently shifted, CRNs must describe the plan and timeline for remediating. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/738> 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] #716: Create Trac Accounts
#716: Create Trac Accounts ---+ Reporter: lv | Owner: dconnolly Type: task | Status: assigned Priority: major | Milestone: Component: data-stds | Resolution: Keywords: trac, account | Blocked By: Blocking: | ---+ Changes (by lv): * owner: hweedman => dconnolly Comment: Please create an account for Marshall - marshall.gor...@cerner.com; he's part of the MU team (comment 1 above). Dan - who will cover this while Hillary is out? -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/716#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] #718: DROC Request #42 - BC data to MCW
#718: DROC Request #42 - BC data to MCW --+ Reporter: lv| Owner: lv Type: problem | Status: new Priority: minor | Milestone: gpc-phase2-h5 Component: data-sharing | Resolution: Keywords: BC| Blocked By: Blocking:| --+ Comment (by mwennberg): The instructions have not changed and are attached to the REDCap used for submission found [https://redcap.gpcnetwork.org/surveys/?s=YNR38TJ9RF here] I sent an email on 12/20 to those on the IRB who should be working on this submission: • UIOWA - Nick Smith • KUMC – Maren and Sravani • UNMC - Yesh • UTSW – Phillip, Shiby -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/718#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] #718: DROC Request #42 - BC data to MCW
#718: DROC Request #42 - BC data to MCW --+ Reporter: lv| Owner: lv Type: problem | Status: new Priority: minor | Milestone: gpc-phase2-h5 Component: data-sharing | Resolution: Keywords: BC| Blocked By: Blocking:| --+ Comment (by lv): Are there revised instructions to support the 11 Jan deadline? Per gpc-dev 18 Dec, work would progress by email/ticket updates. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/718#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] #711: External Validation for Acute Kidney Injury(AKI) Predictive Models using PCORnet CDM data
#711: External Validation for Acute Kidney Injury(AKI) Predictive Models using PCORnet CDM data --+ Reporter: meiliu| Owner: xsong Type: task | Status: new Priority: major | Milestone: Component: data-sharing | Resolution: Keywords: aki cdm | Blocked By: Blocking:| --+ Comment (by xsong): Reports from IU received on 12/24/2018. ||sites||implementation preference||progress notes|| ||UIOWA||R (sql developer, JDBC)||received|| ||UTHSCSA||R (Oracle, OCI)||received|| ||MCRI||R (sql developer, JDBC)||received (1-yr data)|| ||IU||R (Oracle, JDBC)||received|| ||Utah||R ||VA*(non-GPC)||R (sql developer, JDBC) ||MCW||GROUSE lite ||UNMC||GROUSE lite ||MU||GROUSE lite ||UTSW||GROUSE lite -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/711#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] #711: External Validation for Acute Kidney Injury(AKI) Predictive Models using PCORnet CDM data
#711: External Validation for Acute Kidney Injury(AKI) Predictive Models using PCORnet CDM data --+ Reporter: meiliu| Owner: xsong Type: task | Status: new Priority: major | Milestone: Component: data-sharing | Resolution: Keywords: aki cdm | Blocked By: Blocking:| --+ Changes (by xsong): * cc: jtvansch@… (added) -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/711#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] #715: NextD request on mapping payer_type variable
#715: NextD request on mapping payer_type variable --+--- Reporter: afurmanchuck | Owner: meiliu Type: problem | Status: assigned Priority: critical | Milestone: next-d Component: data-stds | Resolution: Keywords:| Blocked By: Blocking: 713 | --+--- Comment (by afurmanchuck): ENR_BASIS='I' is one of permitted values from PCORI CDM (please, see page 31 in https://pcornet.org/wp-content/uploads/2018/05 /PCORnet-Common-Data-Model-v4-1-2018_05_15.pdf ). New variable (ENR_VALUE) was introduced to ENROLLMENT table (and Next-D data dictionary) in order to incorporate information on patient insurance coverage (when extracting from Epic, please adopt to your system prototype of the extraction code from https://github.com/afurmanchuk/NextD/blob/master /NextD_Epic_InsuranceCoveragePerPatient_pro-ENROLLMENTtable.sql For details on ENROLLMENT table structure, please see page 20 from https://www.dropbox.com/home/diabetes%20project%20(working%20docs)/Definitions_StudySamples%26Variables?preview=Definitions_Part2-2018-12-06-af.docx ). Sites should not send raw insurance payer records to NU. When reporting ENR_VALUE, please, remap your raw values into following categories: 1.Medicare 2.Medicaid 3.Other Government 4.Department of corrections 5.Private health insurance 6.Blue cross/Blue shield 7.Managed care, unspecified 8.No payment 9.Miscellaneous/Other .Unavailable/No payer specified/blank NI.No information UN.Unknown OT.Other Listed insurance categories is subset of value set from PCORI CDM v4.1 (please, refer to tab PAYER_TYPE in https://pcornet.org/wp- content/uploads/2018/05/PCORnet_CDM_ValueSet_ReferenceFile_v1.4.xlsx). Let NU know if assistance in mapping from raw payer categories into PCORI categories is needed. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/715#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] #715: NextD request on mapping payer_type variable
#715: NextD request on mapping payer_type variable
--+---
Reporter: afurmanchuck | Owner: meiliu
Type: problem | Status: assigned
Priority: critical | Milestone: next-d
Component: data-stds | Resolution:
Keywords:| Blocked By:
Blocking: 713 |
--+---
Comment (by campbell):
I cannot locate a specification of ENR_BASIS which we will use for
ENROLLMENT table. I suggest that we use CONCAT('I:', PAYOR_CLASS) for the
entries in ENROLLMENT. Northwestern to please respond and agree on data
formatting for ENROLLMENT.ENR_BASIS attribute
Jim Campbell
--
Ticket URL:
<http://informatics.gpcnetwork.org/trac/Project/ticket/715#comment:29>
gpc-informatics <http://informatics.gpcnetwork.org/>
Greater Plains Network - Informatics
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Re: [gpc-informatics] #411: Align SNOW SHRINE terminology with ARCH and ACT ontology for interoperation of query
#411: Align SNOW SHRINE terminology with ARCH and ACT ontology for interoperation of query -+-- Reporter: dconnolly| Owner: campbell Type: enhancement | Status: assigned Priority: major| Milestone: snow-shrine-3 Component: data-stds| Resolution: Keywords: ModelMashup | Blocked By: 23, 90, 201, 243, 280, 525, 583 Blocking: | -+-- Description changed by campbell: Old description: > ref > - [https://unmc.edu/pathology/informatics/tdc.html Nebraska Lexicon©] > - [http://listserv.kumc.edu/pipermail/gpc-dev/2018q2/004608.html > SHRINE Metadata -- UNMC release of SHRINE metadata -- with updated > Medications] Pedersen, Jay G Tue Apr 3 > > > > We considered exact path alignment between the GPC ontologies and the > SCILHS PCORnet ontologies (ticket:67#comment:38) but to date, the benefit > is not worth the cost. > > Mosa @ MU reports successfully using both ontologies simultaneously, and > Reeder @ UTSW notes SHRINE mappings should work, so we can postpone this > indefinitely. New description: reference: https://www.unmc.edu/pathology/informatics/tdc Full release of SNOW SHRINE metadata 20181001 Hackathon6 discussion converged on NOT deploying SNOW SHRINE hub for GPC given Wisconsin departure but UNMC will continue to promote convergence of metadata maintenance with ACT network given the number of GPC sites which will be participating in that SHRINE network. -- -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/411#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] #583: SNOW SCILHS Lab Metadata Expansion
#583: SNOW SCILHS Lab Metadata Expansion ---+--- Reporter: campbell | Owner: campbell Type: enhancement| Status: closed Priority: major | Milestone: snow- Component: data-stds | shrine-3 Keywords: LOINC Lab_PRO_CM SCILHS all-sites | Resolution: fixed Blocking: 411| Blocked By: ---+--- Changes (by dconnolly): * status: assigned => closed * resolution: => fixed Comment: This has shipped twice: March and now Dec. https://www.unmc.edu/pathology/informatics/tdc -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/583#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] #715: NextD request on mapping payer_type variable
#715: NextD request on mapping payer_type variable --+--- Reporter: afurmanchuck | Owner: meiliu Type: problem | Status: assigned Priority: critical | Milestone: next-d Component: data-stds | Resolution: Keywords:| Blocked By: Blocking: 713 | --+--- Changes (by dconnolly): * owner: nsmith => meiliu Comment: Mei, UIOWA is done; please assign this to somebody who is not done. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/715#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] #719: Oracle is changing their licensing fees
#719: Oracle is changing their licensing fees ---+ Reporter: campbell | Owner: dconnolly Type: problem| Status: new Priority: major | Milestone: Component: data-stds | Resolution: Keywords: | Blocked By: Blocking: | ---+ Comment (by dconnolly): In preparation for HackathonSix, sites are requested to update hardware info in the slide deck: - [https://docs.google.com/presentation/d/1LkZNvjSEjXkCwo0a0rLigqlSFS_ZOHS8QQiJfL8K_-Q/edit#slide=id.p DevTeams Tools and Techniques] -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/719#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] #711: External Validation for Acute Kidney Injury(AKI) Predictive Models using PCORnet CDM data
#711: External Validation for Acute Kidney Injury(AKI) Predictive Models using PCORnet CDM data --+ Reporter: meiliu| Owner: xsong Type: task | Status: new Priority: major | Milestone: Component: data-sharing | Resolution: Keywords: aki cdm | Blocked By: Blocking:| --+ Comment (by xsong): Marshfield reported the results after a successful run of the updated package on 1-year worth of data (start_date="2017-01-01") -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/711#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] #717: OBS_CLIN coding for CDMV41
#717: OBS_CLIN coding for CDMV41 -+ Reporter: campbell | Owner: dconnolly Type: enhancement | Status: closed Priority: major| Milestone: pcornet-cdm-5 Component: data-stds| Resolution: worksforme Keywords: Clinical LOINC OBS_CLIN | Blocked By: Blocking: | -+ Changes (by dconnolly): * status: new => closed * resolution: => worksforme Comment: It's not clear to me what was supposed to happen with this. I suppose it happened. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/717#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] #715: NextD request on mapping payer_type variable
#715: NextD request on mapping payer_type variable --+--- Reporter: afurmanchuck | Owner: nsmith Type: problem | Status: assigned Priority: critical | Milestone: next-d Component: data-stds | Resolution: Keywords:| Blocked By: Blocking: 713 | --+--- Comment (by afurmanchuck): After extensive investigation by KUMC team, Prof. James Campbell & NU team it was decided to '''remove insurance information from ENCOUNTER table'''. Insurance information will be extracted for each patient (not each encounter!) form clarity.COVERAGE_MEM_LIST (in Epic). For each patient following elements will be collected: '''PATID, Insurance, MEM_EFF_FROM_DATE, MEM_EFF_TO_DATE''' Those '''will be added to ENROLLMENT table'''. Please, see all details in new data dictionary in drop box: https://www.dropbox.com/home/diabetes%20project%20(working%20docs)/Definitions_StudySamples%26Variables?preview=Definitions_Part2-2018-11-20-af.docx Updates in corresponding SQL extraction codes will be announced separately. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/715#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] #719: Oracle is changing their licensing fees
#719: Oracle is changing their licensing fees ---+ Reporter: campbell | Owner: dconnolly Type: problem| Status: new Priority: major | Milestone: Component: data-stds | Resolution: Keywords: | Blocked By: Blocking: | ---+ Changes (by dconnolly): * cc: gpc-dev (removed) * cc: gpc-dev@… (added) -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/719#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] #718: DROC Request #42 - BC data to MCW
#718: DROC Request #42 - BC data to MCW --+ Reporter: lv| Owner: lv Type: problem | Status: new Priority: minor | Milestone: gpc-phase2-h5 Component: data-sharing | Resolution: Keywords: BC| Blocked By: Blocking:| --+ Comment (by mwennberg): I updated the description of this ticket. Instead of using box, please submit results via [https://redcap.gpcnetwork.org/redcap_v6.11.5/Surveys/invite_participants.php?pid=100 GPC REDCap Request#42_Comparison of Outcomes of Unilateral Mastectomy and Contralateral Prophylactic Mastectomy with Reconstruction in a Multicenter Cohort] If sites need a create table statement to load data into SQL, please reach out to Kris Osinski (kosin...@mcw.edu) or Maren at KUMC (mlowra...@kumc.edu). -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/718#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] #718: DROC Request #42 - BC data to MCW
#718: DROC Request #42 - BC data to MCW --+ Reporter: lv| Owner: lv Type: problem | Status: new Priority: minor | Milestone: gpc-phase2-h5 Component: data-sharing | Resolution: Keywords: BC| Blocked By: Blocking:| --+ Description changed by mwennberg: Old description: > Comparison of Outcomes of Unilateral Mastectomy and Contralateral > Prophylactic Mastectomy with Reconstruction in a Multicenter Cohort > > Code distributed by Kris O using MCW box account. > De-identified response should also be posted to box. New description: Comparison of Outcomes of Unilateral Mastectomy and Contralateral Prophylactic Mastectomy with Reconstruction in a Multicenter Cohort Code distributed by Kris O using MCW box account. De-identified response should be sent via REDCap: [https://redcap.gpcnetwork.org/surveys/?s=YNR38TJ9RF Request#42_Comparison of Outcomes of Unilateral Mastectomy and Contralateral Prophylactic Mastectomy with Reconstruction in a Multicenter Cohort] -- -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/718#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] #711: External Validation for Acute Kidney Injury(AKI) Predictive Models using PCORnet CDM data
#711: External Validation for Acute Kidney Injury(AKI) Predictive Models using PCORnet CDM data --+ Reporter: meiliu| Owner: xsong Type: task | Status: new Priority: major | Milestone: Component: data-sharing | Resolution: Keywords: aki cdm | Blocked By: Blocking:| --+ Comment (by xsong): **Enhancements**: 1. added parameters `start_date` and `end_date` so that inclusion time window can be customized. 2. added parameters `driver_type` for oracle sites who may have different preferences on db drivers between **OCI** and **JDBC**. Note that **JDBC** is currently the only option for sql server sites. **Defects**: 1. sites may run into "Java heap space" error, which is an out-of-memory error whenever the JVM reaches the heap size limit. If that occurs, site can decide to restrict collection window by resetting `start_date` and `end_date` (e.g. start_date = "2014-01-01") -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/711#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] #715: NextD request on mapping payer_type variable
#715: NextD request on mapping payer_type variable --+--- Reporter: afurmanchuck | Owner: nsmith Type: problem | Status: assigned Priority: critical | Milestone: next-d Component: data-stds | Resolution: Keywords:| Blocked By: Blocking: 713 | --+--- Comment (by campbell): Alona, Abel, Mei Liu and I had a discussion yesterday what Northwestern needs for insurance coverage data from each of our sites for purposes of the next-D trial. Abel confirmed that a chronological history file by patient with a list of all insuror policies that have had contracts with the patient account would be the optimal data for their purposes. This would mean accessing the billing office records for each patient and generating a table such as below with mapping to the carrier classification provided by Alona in the past. I have attached an exemplar to this ticket and ask Abel to confirm that this indeed is it for their purpose? I have code for those sites with Epic billing if you would bnefit from the SQL Jim PATIENT_NUM COVERAGE_NAME PAYOR_NAME PAYOR_CLASS EFFECTIVE_DATE TERMINATION_DATE NN EYEMED VISION CARE EYEMED VISION CARE 5 1/1/2008 0:00 (null) NN MEDICARE PART A ONLYMEDICARE1 10/1/2011 0:00 (null) NN BC BLUECARD PPO PLANBCBS6 1/1/2012 0:00 3/31/2014 0:00 NN BCBS NETWORK BLUE BCBS6 4/1/2014 0:00 (null) -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/715#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] #716: Create Trac Accounts
#716: Create Trac Accounts ---+--- Reporter: lv | Owner: hweedman Type: task | Status: assigned Priority: major | Milestone: Component: data-stds | Resolution: Keywords: trac, account | Blocked By: Blocking: | ---+--- Comment (by lv): Hillary created an account for Steffani on 10/18. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/716#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] #711: External Validation for Acute Kidney Injury(AKI) Predictive Models using PCORnet CDM data
#711: External Validation for Acute Kidney Injury(AKI) Predictive Models using PCORnet CDM data --+ Reporter: meiliu| Owner: xsong Type: task | Status: new Priority: major | Milestone: Component: data-sharing | Resolution: Keywords: aki cdm | Blocked By: Blocking:| --+ Comment (by xsong): **Debugged**: Steffani helped me figure out that the underpopulation of med table is caused by low counts of eligible patients, which is further caused by collecting **serum creatinine labs** by matching on `ENCOUNTERID`. I updated both tSQL and Oracle collection codes (in particular, collect_all_SCr, collect_lab, collect_med) by matching on **(patient, day)** [https://github.com/kumc-bmi/AKI_CDM/pull/38 commit#38]. New codes are ready to be tested. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/711#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] #711: External Validation for Acute Kidney Injury(AKI) Predictive Models using PCORnet CDM data
#711: External Validation for Acute Kidney Injury(AKI) Predictive Models using PCORnet CDM data --+ Reporter: meiliu| Owner: xsong Type: task | Status: new Priority: major | Milestone: Component: data-sharing | Resolution: Keywords: aki cdm | Blocked By: Blocking:| --+ Comment (by xsong): Also, is roush.steff...@marshfieldresearch.org the correct email address for Steffani? Replying to [comment:24 lv]: > From Steffani (and I'm hoping a Trac account can be created for her): > > Collect_med.sql creates 54 records when I run just the SQL, but I’m returning this error when running the test code: > > Error during wrapup: Unable to retrieve JDBC result set for select distinctpat.PATID ,pat.ENCOUNTERID ,convert(datetime, convert(CHAR(8), p.RX_ORDER_DATE, 112)+ ' ' + CONVERT(CHAR(8), p.RX_ORDER_TIME, 108)) RX_ORDER_DATE_TIME ,p.RX_START_DATE ,case when pat.DISCHARGE_DATE < p.RX_END_DATE THEN pat.DISCHARGE_DATE else p.RX_END_DATE end as RX_END_DATE ,p.RX_BASIS ,p.RXNORM_CUI /*,regexp_substr(p.RAW_RX_MED_NAME,'[^\[]+',1,1) RX_MED_NAME */ ,p.RX_QUANTITY /*,p.RX_QUANTITY_UNIT */ ,p.RX_REFILLS ,p.RX_DAYS_SUPPLY ,p.RX_FREQUENCY ,case when p.RX_DAYS_SUPPLY is not null and p.RX_DAYS_SUPPLY is not null then round(p.RX_QUANTITY/p.RX_DAYS_SUPPLY,0) else nullend as RX_QUANTITY_DAILY ,datediff(dd,pat.ADMIT_DATE,p.RX_START_DATE) DAYS_SINCE_ADMIT from #AKI_onsets pat join [PopMedNet].[dbo].PRESCRIBING p on pat.ENCOUNTERID = p.ENCOUNTERID where p.RXNORM_CUI is not null and p.RX_START_DATE is not null and p.RX_ORDER_DATE is not null and p.RX_ORDER_TIME is not null and p.RX_ORDER_DATE between dateadd(day,-30,pat.ADMIT_DATE) and pat.DISCHARGE_DATE order by PATID, ENCOUNTERID, RXNORM_CUI, RX_START_DATE (Invalid object name '#AKI_onsets'.) > -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/711#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] #711: External Validation for Acute Kidney Injury(AKI) Predictive Models using PCORnet CDM data
#711: External Validation for Acute Kidney Injury(AKI) Predictive Models using PCORnet CDM data --+ Reporter: meiliu| Owner: xsong Type: task | Status: new Priority: major | Milestone: Component: data-sharing | Resolution: Keywords: aki cdm | Blocked By: Blocking:| --+ Comment (by xsong): Oops,I forgot that #AKI_onset was only a temporary table on sql server, which should be recreated every time we need to call it. However, I think we could confirm that the issue is caused by the low counts of records for the med table. May I know if that can possibly be caused by RXNORM_CUI not being well populated (since we are only collecting med with `RXNORM_CUI is not null`)?. Replying to [comment:24 lv]: > From Steffani (and I'm hoping a Trac account can be created for her): > > Collect_med.sql creates 54 records when I run just the SQL, but I’m returning this error when running the test code: > > Error during wrapup: Unable to retrieve JDBC result set for select distinctpat.PATID ,pat.ENCOUNTERID ,convert(datetime, convert(CHAR(8), p.RX_ORDER_DATE, 112)+ ' ' + CONVERT(CHAR(8), p.RX_ORDER_TIME, 108)) RX_ORDER_DATE_TIME ,p.RX_START_DATE ,case when pat.DISCHARGE_DATE < p.RX_END_DATE THEN pat.DISCHARGE_DATE else p.RX_END_DATE end as RX_END_DATE ,p.RX_BASIS ,p.RXNORM_CUI /*,regexp_substr(p.RAW_RX_MED_NAME,'[^\[]+',1,1) RX_MED_NAME */ ,p.RX_QUANTITY /*,p.RX_QUANTITY_UNIT */ ,p.RX_REFILLS ,p.RX_DAYS_SUPPLY ,p.RX_FREQUENCY ,case when p.RX_DAYS_SUPPLY is not null and p.RX_DAYS_SUPPLY is not null then round(p.RX_QUANTITY/p.RX_DAYS_SUPPLY,0) else nullend as RX_QUANTITY_DAILY ,datediff(dd,pat.ADMIT_DATE,p.RX_START_DATE) DAYS_SINCE_ADMIT from #AKI_onsets pat join [PopMedNet].[dbo].PRESCRIBING p on pat.ENCOUNTERID = p.ENCOUNTERID where p.RXNORM_CUI is not null and p.RX_START_DATE is not null and p.RX_ORDER_DATE is not null and p.RX_ORDER_TIME is not null and p.RX_ORDER_DATE between dateadd(day,-30,pat.ADMIT_DATE) and pat.DISCHARGE_DATE order by PATID, ENCOUNTERID, RXNORM_CUI, RX_START_DATE (Invalid object name '#AKI_onsets'.) > -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/711#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] #711: External Validation for Acute Kidney Injury(AKI) Predictive Models using PCORnet CDM data
#711: External Validation for Acute Kidney Injury(AKI) Predictive Models using PCORnet CDM data --+ Reporter: meiliu| Owner: xsong Type: task | Status: new Priority: major | Milestone: Component: data-sharing | Resolution: Keywords: aki cdm | Blocked By: Blocking:| --+ Comment (by lv): From Steffani (and I'm hoping a Trac account can be created for her): Collect_med.sql creates 54 records when I run just the SQL, but I’m returning this error when running the test code: Error during wrapup: Unable to retrieve JDBC result set for select distinctpat.PATID ,pat.ENCOUNTERID ,convert(datetime, convert(CHAR(8), p.RX_ORDER_DATE, 112)+ ' ' + CONVERT(CHAR(8), p.RX_ORDER_TIME, 108)) RX_ORDER_DATE_TIME ,p.RX_START_DATE ,case when pat.DISCHARGE_DATE < p.RX_END_DATE THEN pat.DISCHARGE_DATE else p.RX_END_DATE end as RX_END_DATE ,p.RX_BASIS ,p.RXNORM_CUI /*,regexp_substr(p.RAW_RX_MED_NAME,'[^\[]+',1,1) RX_MED_NAME */ ,p.RX_QUANTITY /*,p.RX_QUANTITY_UNIT */ ,p.RX_REFILLS ,p.RX_DAYS_SUPPLY ,p.RX_FREQUENCY ,case when p.RX_DAYS_SUPPLY is not null and p.RX_DAYS_SUPPLY is not null then round(p.RX_QUANTITY/p.RX_DAYS_SUPPLY,0) else nullend as RX_QUANTITY_DAILY ,datediff(dd,pat.ADMIT_DATE,p.RX_START_DATE) DAYS_SINCE_ADMIT from #AKI_onsets pat join [PopMedNet].[dbo].PRESCRIBING p on pat.ENCOUNTERID = p.ENCOUNTERID where p.RXNORM_CUI is not null and p.RX_START_DATE is not null and p.RX_ORDER_DATE is not null and p.RX_ORDER_TIME is not null and p.RX_ORDER_DATE between dateadd(day,-30,pat.ADMIT_DATE) and pat.DISCHARGE_DATE order by PATID, ENCOUNTERID, RXNORM_CUI, RX_START_DATE (Invalid object name '#AKI_onsets'.) -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/711#comment:24> gpc-informatics <http://informatics.gpcnetwork.org/> Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #716: Create Trac Accounts
#716: Create Trac Accounts ---+--- Reporter: lv | Owner: hweedman Type: task | Status: assigned Priority: major | Milestone: Component: data-stds | Resolution: Keywords: trac, account | Blocked By: Blocking: | ---+--- Comment (by lv): Account needed for Steffani Roush - roush.steff...@marshfieldresearch.org -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/716#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] #711: External Validation for Acute Kidney Injury(AKI) Predictive Models using PCORnet CDM data
#711: External Validation for Acute Kidney Injury(AKI) Predictive Models using
PCORnet CDM data
--+
Reporter: meiliu| Owner: xsong
Type: task | Status: new
Priority: major | Milestone:
Component: data-sharing | Resolution:
Keywords: aki cdm | Blocked By:
Blocking:|
--+
Comment (by xsong):
Awesome, we are so close!
**Debugging**: Just based on the error, it seems that the collected
medication table is likely to be empty. To be sure about it, would you
please help me refresh the package and run a new script
`./test/debug_collect_med.R` and report the summaries generated in the
**console**, which will be something like
{{{
9479020 rows are collected.
145345 distinct encounters are covered.
11539 distinct rxnorm are identified.
exposure quantiles are 1,1,1,1,1,1,2,3,5,8,771 .
}}}
This stats can help me better identify the problem.
Replying to [comment:22 lv]:
> That helped! Now we're getting the following:
>
> Quitting from lines 780-889 (AKI_CDM_EXT_VALID_p1_QA.Rmd)
>
> Error in mutate_impl(.data, dots) :
> Column `expos_daily` must be length 0 (the number of rows) or one, not
2
--
Ticket URL:
<http://informatics.gpcnetwork.org/trac/Project/ticket/711#comment:23>
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Re: [gpc-informatics] #711: External Validation for Acute Kidney Injury(AKI) Predictive Models using PCORnet CDM data
#711: External Validation for Acute Kidney Injury(AKI) Predictive Models using PCORnet CDM data --+ Reporter: meiliu| Owner: xsong Type: task | Status: new Priority: major | Milestone: Component: data-sharing | Resolution: Keywords: aki cdm | Blocked By: Blocking:| --+ Comment (by lv): That helped! Now we're getting the following: Quitting from lines 780-889 (AKI_CDM_EXT_VALID_p1_QA.Rmd) Error in mutate_impl(.data, dots) : Column `expos_daily` must be length 0 (the number of rows) or one, not 2 -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/711#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] #711: External Validation for Acute Kidney Injury(AKI) Predictive Models using PCORnet CDM data
#711: External Validation for Acute Kidney Injury(AKI) Predictive Models using PCORnet CDM data --+ Reporter: meiliu| Owner: xsong Type: task | Status: new Priority: major | Milestone: Component: data-sharing | Resolution: Keywords: aki cdm | Blocked By: Blocking:| --+ Comment (by xsong): **Debugged**: It seems that there could be no labs initiated on the 2nd day since admission (that's why `2` is not found). So I removed the column of collecting summaries of labs initiated within the first 3 days since admission. [https://github.com/kumc-bmi/AKI_CDM/pull/36 commit:36]. Please refresh and rerun the package. Replying to [comment:20 lv]: > The error that Steffani reports is below: > > Quitting from lines 479-551 (AKI_CDM_EXT_VALID_p1_QA.Rmd) > Error in mutate_impl(.data, dots) : > Evaluation error: object '2' not found. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/711#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] #711: External Validation for Acute Kidney Injury(AKI) Predictive Models using PCORnet CDM data
#711: External Validation for Acute Kidney Injury(AKI) Predictive Models using PCORnet CDM data --+ Reporter: meiliu| Owner: xsong Type: task | Status: new Priority: major | Milestone: Component: data-sharing | Resolution: Keywords: aki cdm | Blocked By: Blocking:| --+ Changes (by lv): * cc: roush.steffani@… (added) Comment: The error that Steffani reports is below: Quitting from lines 479-551 (AKI_CDM_EXT_VALID_p1_QA.Rmd) Error in mutate_impl(.data, dots) : Evaluation error: object '2' not found. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/711#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] #714: NextD aggregate counts request
#714: NextD aggregate counts request --+- Reporter: afurmanchuck | Owner: nsmith Type: task | Status: closed Priority: major | Milestone: next-d Component: data-stds | Resolution: fixed Keywords:| Blocked By: Blocking: 713 | --+- Changes (by lv): * status: assigned => closed * resolution: => fixed Comment: Per GPC-DEV call on 10/16, this is resolved. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/714#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] #715: NextD request on mapping payer_type variable
#715: NextD request on mapping payer_type variable --+--- Reporter: afurmanchuck | Owner: nsmith Type: problem | Status: assigned Priority: critical | Milestone: next-d Component: data-stds | Resolution: Keywords:| Blocked By: Blocking: 713 | --+--- Comment (by campbell): Nebraska inadvertenbtly filed these results onn ticket 714 two weeks ago. See enclosed payor stats for our site Jim Campbell -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/715#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] #715: NextD request on mapping payer_type variable
#715: NextD request on mapping payer_type variable --+--- Reporter: afurmanchuck | Owner: nsmith Type: problem | Status: assigned Priority: critical | Milestone: next-d Component: data-stds | Resolution: Keywords:| Blocked By: Blocking: 713 | --+--- Comment (by astoddard): MCW encounter type results: ||= enc_type =||= enc_cnt =||= enc_prop =||= with_primary_payor_cnt =||= with_primary_payor_prop =|| || OA || 20,382,600 ||27.0%||2,040,187 || 10.0% || || NI || 19,406,742 ||25.7%|| 19,406,742 || 100% || ||OT || 18,080,152 ||23.9%|| 15,731 || 0.1% || ||AV || 16,724,650 ||22.1%|| 11,341,298 || 67.8% || ||ED || 626,775 ||0.8%|| 555,209 || 88.6% || ||IP || 290,846 ||0.4%|| 288,443 || 99.2% || ||OS ||61,610 ||0.1%|| 60,944 || 98.9% || ||UN || 2,735 ||< 0.1%|| 2,316 || 84.7% || ||IS || 761 ||< 0.1%||661 || 86.9% || -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/715#comment:24> gpc-informatics <http://informatics.gpcnetwork.org/> Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #711: External Validation for Acute Kidney Injury(AKI) Predictive Models using PCORnet CDM data
#711: External Validation for Acute Kidney Injury(AKI) Predictive Models using PCORnet CDM data --+ Reporter: meiliu| Owner: xsong Type: task | Status: new Priority: major | Milestone: Component: data-sharing | Resolution: Keywords: aki cdm | Blocked By: Blocking:| --+ Comment (by xsong): The r codes updated on 10/10/2018 have merged all changes for tSQL based on the feedback from UIOWA. Please download the revised package and give it another try. Btw, did you set the `DBMS_type` to "tSQL" and was the connection between r and sql server successful? Replying to [comment:18 lv]: > Is there a place to access the code that Iowa ran? > > We're having a lot of trouble getting this to run on SQL server. It seems like the tSQL on Github was not updated fully (certain functions native to oracle still exist in the updated files). -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/711#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] #714: NextD aggregate counts request
#714: NextD aggregate counts request --+--- Reporter: afurmanchuck | Owner: nsmith Type: task | Status: assigned Priority: major | Milestone: next-d Component: data-stds | Resolution: Keywords:| Blocked By: Blocking: 713 | --+--- Comment (by jhamer): Hi Zahra, Below are Regenstrief's NextD aggregate counts per your request: 1.PAT_PREF_LANGUAGE_SPOKEN RECORD_NRECORD_PCT NULL or missing 2811874 100.0 2. PAYER_TYPE_PRIMARY RECORD_NRECORD_PCT NULL or missing 41628148100.0 3. PAYER_TYPE_SECONDARYRECORD_NRECORD_PCT NULL or missing 41628148100.0 -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/714#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] #711: External Validation for Acute Kidney Injury(AKI) Predictive Models using PCORnet CDM data
#711: External Validation for Acute Kidney Injury(AKI) Predictive Models using PCORnet CDM data --+ Reporter: meiliu| Owner: xsong Type: task | Status: new Priority: major | Milestone: Component: data-sharing | Resolution: Keywords: aki cdm | Blocked By: Blocking:| --+ Comment (by lv): Is there a place to access the code that Iowa ran? We're having a lot of trouble getting this to run on SQL server. It seems like the tSQL on Github was not updated fully (certain functions native to oracle still exist in the updated files). -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/711#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] #715: NextD request on mapping payer_type variable
#715: NextD request on mapping payer_type variable
--+---
Reporter: afurmanchuck | Owner: nsmith
Type: problem | Status: assigned
Priority: critical | Milestone: next-d
Component: data-stds | Resolution:
Keywords:| Blocked By:
Blocking: 713 |
--+---
Comment (by xsong):
`when PAYER_TYPE_PRIMARY in (NULL, 'OT','NI')` doesn't work, the predicate
should be `case when PAYER_TYPE_PRIMARY in ('OT','NI') or
PAYER_TYPE_PRIMARY is null then 0 else 1 end`.
Replying to [comment:22 xsong]:
> No, if "NI" and "OT" are imputed automatically for all non-mapped
encounters. But if that's the case, should we always have 100% mapping for
primary payer (when NULL is assigned with an "NI" or "OT")?
>
> But I think it does make more sense to collect summaries just for
meaningful payer info. I will update the summary codes by using `when
PAYER_TYPE_PRIMARY in (NULL, 'OT','NI')` instead.
> Replying to [comment:21 dconnolly]:
> > Song, I see `when PAYER_TYPE_PRIMARY is not null`... that succeed for
`NI` and `OT`. Is that on purpose? That is: do you want to count "no
information" and "other" as successfully mapped payer types?
--
Ticket URL:
<http://informatics.gpcnetwork.org/trac/Project/ticket/715#comment:23>
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Re: [gpc-informatics] #715: NextD request on mapping payer_type variable
#715: NextD request on mapping payer_type variable --+--- Reporter: afurmanchuck | Owner: nsmith Type: problem | Status: assigned Priority: critical | Milestone: next-d Component: data-stds | Resolution: Keywords:| Blocked By: Blocking: 713 | --+--- Comment (by xsong): No, if "NI" and "OT" are imputed automatically for all non-mapped encounters. But if that's the case, should we always have 100% mapping for primary payer (when NULL is assigned with an "NI" or "OT")? But I think it does make more sense to collect summaries just for meaningful payer info. I will update the summary codes by using `when PAYER_TYPE_PRIMARY in (NULL, 'OT','NI')` instead. Replying to [comment:21 dconnolly]: > Song, I see `when PAYER_TYPE_PRIMARY is not null`... that succeed for `NI` and `OT`. Is that on purpose? That is: do you want to count "no information" and "other" as successfully mapped payer types? -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/715#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] #715: NextD request on mapping payer_type variable
#715: NextD request on mapping payer_type variable --+--- Reporter: afurmanchuck | Owner: nsmith Type: problem | Status: assigned Priority: critical | Milestone: next-d Component: data-stds | Resolution: Keywords:| Blocked By: Blocking: 713 | --+--- Changes (by dconnolly): * milestone: => next-d Comment: Song, I see `when PAYER_TYPE_PRIMARY is not null`... that succeed for `NI` and `OT`. Is that on purpose? That is: do you want to count "no information" and "other" as successfully mapped payer types? -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/715#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] #715: NextD request on mapping payer_type variable
#715: NextD request on mapping payer_type variable --+--- Reporter: afurmanchuck | Owner: nsmith Type: problem | Status: assigned Priority: critical | Milestone: Component: data-stds | Resolution: Keywords:| Blocked By: Blocking: 713 | --+--- Comment (by nsmith): Here are the encounter type numbers for UIOWA with primary insurnace... ||Enc_Type||Enc_Cnt ||Enc_Prop||With_Primary_Payor_Cnt||With_Primary_Payor_Prop|| ||**AV** ||10,697,262 ||56.97% ||9,908,916||92.63% || ||OA ||5,481,164 ||29.19% ||0||0.00% || ||UN ||1,845,414 ||9.83%||0||0.00% || ||**ED** ||393,093||2.09%||356,894 ||90.79% || ||**IP** ||198,647||1.06%||179,964 ||90.59% || ||**EI** ||122,957||0.65%||118,485 ||96.36% || ||**OS** ||31,796 ||0.17%||28,619 ||90.01% || ||OT ||6,387 ||0.03%||5,975||93.55% || -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/715#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] #718: DROC Request #42 - BC data to MCW
#718: DROC Request #42 - BC data to MCW --+ Reporter: lv| Owner: lv Type: problem | Status: new Priority: minor | Milestone: gpc-phase2-h5 Component: data-sharing | Resolution: Keywords: BC| Blocked By: Blocking:| --+ Comment (by lv): Per DEV call on 10/2: KU (Sravani) - approved, queries delivered Iowa (Nick) - email approval, Box invitation pending Wisconsin (Jiqiang) - email approval, queries delivered Marshfield (Laurel) - done Minnesota (?) - no droc approval yet Nebraska (Yesh) - approved, queries delivered; only located files sent to Iowa initially and not certain of location of Iowa processed results UTSW (Phillip) - approved, queries delivered -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/718#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
