I would like to discuss on our Dev call. I spent time as we approached this CDM refresh cycle to get a final answer for the documentation in Duke Redcap. Was our lapse (~78% complete on normal ranges) something we could remediate? We had a unique problem: our central lab lost a section of historic normal range data when they upgraded software. Our Data Curation report caught this, although no one else noticed. Discussing with the lab, they could not restore it after time had passed and their data had changed. Since these results had already been reported out a while back, so were historic lab results, no one else at Intermountain Healthcare has found this to be a problem. Normal ranges may have been stored in up to 3 EMRs during the time this occurred. We don’t have resources to try to put these normal ranges back into the CDM from the EMRs: we load from the central lab. Especially just to gain back 2% coverage on the Data Curation report: we think over time that gap will fill in and we will be back above 80%. Our usual coverage of Lab Normal ranges for quantitative labs is ~95%.
So, I wonder what the consumers of lab data, investigators, need? We sometimes use the Abnormal Flags to identify abnormal labs; as these don’t vary with the normal ranges used by the particular equipment or by age, sex or other variables. The Abnormal Flag status was not lost in the problem described above for normal ranges. Or sometimes the investigator will specify the ranges they consider interesting. I cannot say that I have ever had to compare the lab results to the normal ranges and generate my own “high” or “low” determination for a study data set. We have been asked to dump all of our lab data into the CDM. It would make much more sense for either selective, highly used labs (as LOINC makes available) or add labs as the various clinical research teams define those that are important in their domains. Wading through so many lab results in the CDM takes so much disk space, data transfer time from storage to local memory and makes our run times very long. I like the characterization they have done for common labs across sites, and they did point out a few we were missing. That is helpful. It would be useful if DRNOC could articulate why it seems useful – or have they found it useful in practice – to ask for every site’s entire lab data holdings. I believe DRNOC would need to justify why these Lab Normal tables in the CDM are needed. For us, this is a lot of work, if even possible. We are a hospital system across Utah. Different labs in the system may have different ranges for the same LOINC. We also use reference labs. One must know that clinical labs calibrate whatever machines they are using and ranges may change upon calibration. We have no process for keeping up with all changes: this is what the LIMS does. I think a more reasonable approach for research purposes, not for purposes of patient care where one might need to be exacting: use standard normal ranges for each LOINC. Does LOINC provide those? Thanks, Susan Susan Rea, Medical Informaticist Data Administrator, PCORnet Intermountain Enterprise Analytics Intermountain Healthcare [email protected]<mailto:[email protected]> 801-694-6343 (cell) From: Gpc-dev <[email protected]> On Behalf Of Mei Liu Sent: Monday, July 20, 2020 8:16 AM To: Dan Connolly <[email protected]>; [email protected] Subject: RE: gpc-dev 21 July agenda and meeting notes BE ALERT. External Sender. Be cautious. Just to share with the GPC-dev group notes from the PCORnet Data WG meeting on July 17. Discussion on data quality checks on labs * Problem: lab completeness check requires >80% of labs reported with normal ranges, which many sites feel uncomfortable in assigning one if it does not come automatically from the EMR. * Proposed easy solution: simplify the check by reporting whether a lab is a clinical vs statistical outlier (defined based on PCORnet population). * Long-term fix (CDM 6.0): introduce a new CDM table to be called “reference range history” that would contain following elements for each lab: o Lab (LOINC) o Gender o Age (go/from) o Race o Normal range o Units o Effective dates When reporting normal ranges of labs, indicate whether it is derived from the EMR or the reference range table. Note that the long-term fix of adding a reference range history table will require extra work from the sites. The timeline for the work is not confirmed yet, but sites can start working on it. Please let me know if you would like to discuss during the gpc-dev call. Thanks, Mei From: Gpc-dev <[email protected]<mailto:[email protected]>> On Behalf Of Dan Connolly Sent: Monday, July 20, 2020 8:55 AM To: [email protected]<mailto:[email protected]> Subject: gpc-dev 21 July agenda and meeting notes What else for tomorrow? UTHSCSA is scheduled to scribe https://docs.google.com/document/d/18NSOQU1dKCc6Hzv_-TpJQnNQ_TBo-zs5Af1AfXH051Y/edit<https://urldefense.proofpoint.com/v2/url?u=https-3A__docs.google.com_document_d_18NSOQU1dKCc6Hzv-5F-2DTpJQnNQ-5FTBo-2Dzs5Af1AfXH051Y_edit&d=DwMGaQ&c=II16XUCNF0uj2WHDMBdftpHZzyfqZU4E6o4J8m7Yfh-XF5deecOtjPXuMFvj1uWy&r=MwmdyHUR1MNPWZBi1oQ_Ksh4XI39nGu45nleZO875iA&m=MGu-SjJKVwwntFL9bvGvKZpsX-4j1sIPaTqQFBJxj7M&s=XvvcSYp8IA_VTVPP6rAomSy8vcYn_BJO9EtAN4pimN0&e=> 1. Convene, take roll, review records and plan the next meeting(s). * 11:00 a.m. Central Time. Meeting ID and access code: 817-393-381<https://global.gotomeeting.com/meeting/join/817393381>; call +1 (571) 317-3131 * Roll; Reminder - put site after your name in GoToMeeting<https://global.gotomeeting.com/meeting/join/817393381> preferences GPC DevTeams<https://urldefense.proofpoint.com/v2/url?u=https-3A__informatics.gpcnetwork.org_trac_Project_wiki_DevTeams&d=DwMGaQ&c=II16XUCNF0uj2WHDMBdftpHZzyfqZU4E6o4J8m7Yfh-XF5deecOtjPXuMFvj1uWy&r=MwmdyHUR1MNPWZBi1oQ_Ksh4XI39nGu45nleZO875iA&m=MGu-SjJKVwwntFL9bvGvKZpsX-4j1sIPaTqQFBJxj7M&s=rqJOroiCzviMQVzJr6SdxDwhaaYS30hhI8n61JJxfeo&e=> represented? KUMC (chair), UIOWA, MCW, MCRI, UNMC, UTHSCSA (scribe), UTSW, MU, IndianaU, Utah, Allina, Intermountain, UTH * Comments on the agenda? (ref SoftwareDev#tracking<https://urldefense.proofpoint.com/v2/url?u=https-3A__informatics.gpcnetwork.org_trac_Project_wiki_SoftwareDev-23tracking&d=DwMGaQ&c=II16XUCNF0uj2WHDMBdftpHZzyfqZU4E6o4J8m7Yfh-XF5deecOtjPXuMFvj1uWy&r=MwmdyHUR1MNPWZBi1oQ_Ksh4XI39nGu45nleZO875iA&m=MGu-SjJKVwwntFL9bvGvKZpsX-4j1sIPaTqQFBJxj7M&s=p9mhgK5--aEydcBYdX0zmsqMGDd3-RCwN10JKc7jfDM&e=>) On last week’s notes?<https://urldefense.proofpoint.com/v2/url?u=https-3A__docs.google.com_document_d_18NSOQU1dKCc6Hzv-5F-2DTpJQnNQ-5FTBo-2Dzs5Af1AfXH051Y_edit-23heading-3Dh.9ioc8gnd1ijp&d=DwMGaQ&c=II16XUCNF0uj2WHDMBdftpHZzyfqZU4E6o4J8m7Yfh-XF5deecOtjPXuMFvj1uWy&r=MwmdyHUR1MNPWZBi1oQ_Ksh4XI39nGu45nleZO875iA&m=MGu-SjJKVwwntFL9bvGvKZpsX-4j1sIPaTqQFBJxj7M&s=B3SrslBepuIX-gYXylNplKA3xS__8U6uQYG8dvIO09M&e=> (#12<https://urldefense.proofpoint.com/v2/url?u=https-3A__informatics.gpcnetwork.org_trac_Project_ticket_12&d=DwMGaQ&c=II16XUCNF0uj2WHDMBdftpHZzyfqZU4E6o4J8m7Yfh-XF5deecOtjPXuMFvj1uWy&r=MwmdyHUR1MNPWZBi1oQ_Ksh4XI39nGu45nleZO875iA&m=MGu-SjJKVwwntFL9bvGvKZpsX-4j1sIPaTqQFBJxj7M&s=kx93yKivi8EZQYfo_dQgZE5XcPzPQDppJ0KpVm8v05M&e=>) Recent tickets opened/closed<https://urldefense.proofpoint.com/v2/url?u=https-3A__informatics.gpcnetwork.org_trac_Project_timeline&d=DwMGaQ&c=II16XUCNF0uj2WHDMBdftpHZzyfqZU4E6o4J8m7Yfh-XF5deecOtjPXuMFvj1uWy&r=MwmdyHUR1MNPWZBi1oQ_Ksh4XI39nGu45nleZO875iA&m=MGu-SjJKVwwntFL9bvGvKZpsX-4j1sIPaTqQFBJxj7M&s=HBIACkwITz9s0MoYyvxFIVdz3XV7D20TFvQdUX6StVY&e=> - FYI (i.e. not intended for discussion) * None this week * Next meeting(s): Jul 28; scribe: UTSW?, IU? * Note scribe rotation<https://urldefense.proofpoint.com/v2/url?u=https-3A__docs.google.com_document_d_1fPoDn0pdVvC-2DMct58X7wkGD2rNiId8aNZ9JG-5FWCbcf4_edit-23heading-3Dh.zbjzupqx0rh7&d=DwMGaQ&c=II16XUCNF0uj2WHDMBdftpHZzyfqZU4E6o4J8m7Yfh-XF5deecOtjPXuMFvj1uWy&r=MwmdyHUR1MNPWZBi1oQ_Ksh4XI39nGu45nleZO875iA&m=MGu-SjJKVwwntFL9bvGvKZpsX-4j1sIPaTqQFBJxj7M&s=RaNr94XsGOJNlktH5ITN0JnNjWQ3s2dTLvdiFvUmA5E&e=> appendix * #759<https://urldefense.proofpoint.com/v2/url?u=https-3A__informatics.gpcnetwork.org_trac_Project_ticket_759&d=DwMGaQ&c=II16XUCNF0uj2WHDMBdftpHZzyfqZU4E6o4J8m7Yfh-XF5deecOtjPXuMFvj1uWy&r=MwmdyHUR1MNPWZBi1oQ_Ksh4XI39nGu45nleZO875iA&m=MGu-SjJKVwwntFL9bvGvKZpsX-4j1sIPaTqQFBJxj7M&s=MRxvi70P1--4oJ_raSR_vLOa7qnJCI06RY5jKtVEqjs&e=> covid19 PCORNet datamarts<https://urldefense.proofpoint.com/v2/url?u=https-3A__informatics.gpcnetwork.org_trac_Project_ticket_759&d=DwMGaQ&c=II16XUCNF0uj2WHDMBdftpHZzyfqZU4E6o4J8m7Yfh-XF5deecOtjPXuMFvj1uWy&r=MwmdyHUR1MNPWZBi1oQ_Ksh4XI39nGu45nleZO875iA&m=MGu-SjJKVwwntFL9bvGvKZpsX-4j1sIPaTqQFBJxj7M&s=MRxvi70P1--4oJ_raSR_vLOa7qnJCI06RY5jKtVEqjs&e=> 28 May “pause additional ETL development” until PCORI completes its review… Russ standing by for more info * Dan/KUMC to get more info about volume / quality issues where the line was divided (not immediately) * Marshfield will submit Bardet-Biedl Syndrome request through DROC 1. PCORnet CDM refresh with PPRL<https://urldefense.proofpoint.com/v2/url?u=https-3A__informatics.gpcnetwork.org_trac_Project_wiki_PPRL&d=DwMGaQ&c=II16XUCNF0uj2WHDMBdftpHZzyfqZU4E6o4J8m7Yfh-XF5deecOtjPXuMFvj1uWy&r=MwmdyHUR1MNPWZBi1oQ_Ksh4XI39nGu45nleZO875iA&m=MGu-SjJKVwwntFL9bvGvKZpsX-4j1sIPaTqQFBJxj7M&s=X6QSJ3cZyhkMdLWytchewzksxR0AnHUUC8Ne5oiDiyY&e=> - due July 27 * C4UI r024 Approved<https://urldefense.proofpoint.com/v2/url?u=http-3A__listserv.kumc.edu_pipermail_gpc-2Ddev_2020q3_011015.html&d=DwMGaQ&c=II16XUCNF0uj2WHDMBdftpHZzyfqZU4E6o4J8m7Yfh-XF5deecOtjPXuMFvj1uWy&r=MwmdyHUR1MNPWZBi1oQ_Ksh4XI39nGu45nleZO875iA&m=MGu-SjJKVwwntFL9bvGvKZpsX-4j1sIPaTqQFBJxj7M&s=BXxEDqWx6AzL36Vn3iIuIPOG1AsHgCl850sVmfLcMhc&e=> gold star! 1. Milestone:tumor-reg-18<https://urldefense.proofpoint.com/v2/url?u=https-3A__informatics.gpcnetwork.org_trac_Project_milestone_tumor-2Dreg-2D18&d=DwMGaQ&c=II16XUCNF0uj2WHDMBdftpHZzyfqZU4E6o4J8m7Yfh-XF5deecOtjPXuMFvj1uWy&r=MwmdyHUR1MNPWZBi1oQ_Ksh4XI39nGu45nleZO875iA&m=MGu-SjJKVwwntFL9bvGvKZpsX-4j1sIPaTqQFBJxj7M&s=8EpQE0ZU8BBvcVGp9hgtXVShocJcoDVdTCcs6WIgxDM&e=> aiming for Jul 10 * #749<https://urldefense.proofpoint.com/v2/url?u=https-3A__informatics.gpcnetwork.org_trac_Project_ticket_749&d=DwMGaQ&c=II16XUCNF0uj2WHDMBdftpHZzyfqZU4E6o4J8m7Yfh-XF5deecOtjPXuMFvj1uWy&r=MwmdyHUR1MNPWZBi1oQ_Ksh4XI39nGu45nleZO875iA&m=MGu-SjJKVwwntFL9bvGvKZpsX-4j1sIPaTqQFBJxj7M&s=5DHyEZ1UJVKg9_NE9fpqrWkBuDYH9dapeFDP9Aj4W58&e=> PCORNet style TUMOR table<https://urldefense.proofpoint.com/v2/url?u=https-3A__informatics.gpcnetwork.org_trac_Project_ticket_749&d=DwMGaQ&c=II16XUCNF0uj2WHDMBdftpHZzyfqZU4E6o4J8m7Yfh-XF5deecOtjPXuMFvj1uWy&r=MwmdyHUR1MNPWZBi1oQ_Ksh4XI39nGu45nleZO875iA&m=MGu-SjJKVwwntFL9bvGvKZpsX-4j1sIPaTqQFBJxj7M&s=5DHyEZ1UJVKg9_NE9fpqrWkBuDYH9dapeFDP9Aj4W58&e=> * Brian to update gpc-dev w.r.t. DROC request * #739<https://urldefense.proofpoint.com/v2/url?u=https-3A__informatics.gpcnetwork.org_trac_Project_ticket_739&d=DwMGaQ&c=II16XUCNF0uj2WHDMBdftpHZzyfqZU4E6o4J8m7Yfh-XF5deecOtjPXuMFvj1uWy&r=MwmdyHUR1MNPWZBi1oQ_Ksh4XI39nGu45nleZO875iA&m=MGu-SjJKVwwntFL9bvGvKZpsX-4j1sIPaTqQFBJxj7M&s=bURAS024FnxLAZ3CIK2PYgpef17xoVaOvyeMOlxszOA&e=> HERON NAACCR ETL outdated by v18<https://urldefense.proofpoint.com/v2/url?u=https-3A__informatics.gpcnetwork.org_trac_Project_ticket_739&d=DwMGaQ&c=II16XUCNF0uj2WHDMBdftpHZzyfqZU4E6o4J8m7Yfh-XF5deecOtjPXuMFvj1uWy&r=MwmdyHUR1MNPWZBi1oQ_Ksh4XI39nGu45nleZO875iA&m=MGu-SjJKVwwntFL9bvGvKZpsX-4j1sIPaTqQFBJxj7M&s=bURAS024FnxLAZ3CIK2PYgpef17xoVaOvyeMOlxszOA&e=> kumc-bmi/naaccr-tumor-data<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_kumc-2Dbmi_naaccr-2Dtumor-2Ddata&d=DwMGaQ&c=II16XUCNF0uj2WHDMBdftpHZzyfqZU4E6o4J8m7Yfh-XF5deecOtjPXuMFvj1uWy&r=MwmdyHUR1MNPWZBi1oQ_Ksh4XI39nGu45nleZO875iA&m=MGu-SjJKVwwntFL9bvGvKZpsX-4j1sIPaTqQFBJxj7M&s=VmiHtkQDPqCOg42A25okyA3IaFdPm5yRKoxF0qaQq7M&e=> * DC to look into patient_mapping using item 2300 MRN 1. 1228 covid query due July 21 PR: what’s expected, given May 28 “pause additional ETL development”? Steph to ask DRNOC to clarify. DC to confirm Russ is attending today’s PCORnet steering committee meeting and suggest that he seek clarification. Done: 1228 covid query due July 21? <https://urldefense.proofpoint.com/v2/url?u=http-3A__listserv.kumc.edu_pipermail_gpc-2Ddev_2020q3_011014.html&d=DwMGaQ&c=II16XUCNF0uj2WHDMBdftpHZzyfqZU4E6o4J8m7Yfh-XF5deecOtjPXuMFvj1uWy&r=MwmdyHUR1MNPWZBi1oQ_Ksh4XI39nGu45nleZO875iA&m=MGu-SjJKVwwntFL9bvGvKZpsX-4j1sIPaTqQFBJxj7M&s=kx_HUjy2eRT_t-LaTnwkL26FMEb_bRHOdlpuppZe9l8&e=> Block, Jason Perry,M.D. wash your hands ...<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.cdc.gov_coronavirus_2019-2Dncov_prepare_prevention.html&d=DwMGaQ&c=II16XUCNF0uj2WHDMBdftpHZzyfqZU4E6o4J8m7Yfh-XF5deecOtjPXuMFvj1uWy&r=MwmdyHUR1MNPWZBi1oQ_Ksh4XI39nGu45nleZO875iA&m=MGu-SjJKVwwntFL9bvGvKZpsX-4j1sIPaTqQFBJxj7M&s=EI0a8zIyZyfq2KxQfvYOMM80ZWwNiyEIemRpVKN7Vhk&e=> -- Dan NOTICE: This e-mail is for the sole use of the intended recipient and may contain confidential and privileged information. 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