Yes, KUMC's data shows artifacts from date shifting. It was approved in this form.
What was approved for research was our locked CDM from Apr 7; that's what we use to service popmednet queries. We're adding labs and meds and such, but that's in separate storage. I expect to learn how this new CDM build gets used for research in the Obesity Demonstration Projects: Wave 1 Data Characterization Query Description meeting Aug 12 (ticket:510#comment:5<https://informatics.gpcnetwork.org/trac/Project/ticket/510#comment:5>). The corresponding section of KUMC's C4UK_DCDREP is: We would like to understand more about your processes for refreshing your DataMart and creating a locked/static version of each DataMart refresh. Can you please describe your processes for us? When you refresh your DataMart, do you perform a complete update or a partial update (e.g. updating new or changed information)? We start from scratch every month; no incremental updates. We have a monthly ETL process to go from Epic etc. into i2b2. On demand, we use the SCILHS i2p-transform approach (roughly) to go from i2b2 to CDM. details are in https://github.com/kumc-bmi/i2p-transform . We have a cdm_freeze job that makes a compressed offline backup. Given the time necessary to refresh your data, what is the latest data that will be available in the DataMart relative to the date of query receipt? For example, if we send you a DC query on July 1, what is the date of the latest information you expect to be captured in the DataMart? Supposing a query arrives July 1, the latest data from source systems would be from about May 31. That data would be collected from clinical partners, run through our ETL process, and released to the HERON customer base in mid June. So far we build our CDM datamart on demand, but we could run it every month as part of our ETL process, making the latency 2 to 6 weeks. To date, we have only reported results from our de-identified (and hence date-shifted) CDM. So the event on May 30 would be shifted back up to 365 days. We have the technical capacity to build a CDM with real dates, but we have not used it to send results as regulatory aspects are unclear. For reference/redundancy: 9dec55490dc2e063a7ef17bd0ac8eaf5 /home/jenkins/oracle_export//cdmv3_CONDITION_20160407_160654.dmp 7283c370b7cd5f407c2c5bfd2e2f2032 /home/jenkins/oracle_export//cdmv3_DEATH_20160407_160654.dmp 6bc82d1670b5a2be4dbedcea6b8d6299 /home/jenkins/oracle_export//cdmv3_DEATH_CAUSE_20160407_160654.dmp 7a3bbd3e44eff86b32ef41183c4635ab /home/jenkins/oracle_export//cdmv3_DEMOGRAPHIC_20160407_160654.dmp 1a9bd5ec9a1a58dfe2eb6395051f5e50 /home/jenkins/oracle_export//cdmv3_DIAGNOSIS_20160407_160654.dmp f374dcb1d1f089330a12f3ec49f71513 /home/jenkins/oracle_export//cdmv3_DISPENSING_20160407_160654.dmp b773582aad45a3370e39959d2ab5b14f /home/jenkins/oracle_export//cdmv3_ENCOUNTER_20160407_160654.dmp 08256fac496087b9802f9d6a928a027b /home/jenkins/oracle_export//cdmv3_ENROLLMENT_20160407_160654.dmp aa33dbd9662d250065da75ce1a98d212 /home/jenkins/oracle_export//cdmv3_HARVEST_20160407_160654.dmp f97a4592704f53aaf0ae36d296ec9fbd /home/jenkins/oracle_export//cdmv3_LAB_RESULT_CM_20160407_160654.dmp bc9347f39d70239b0e76c44bad706642 /home/jenkins/oracle_export//cdmv3_PCORNET_TRIAL_20160407_160654.dmp a633952123b4faff7d3e53252ced4785 /home/jenkins/oracle_export//cdmv3_PRESCRIBING_20160407_160654.dmp 835d62f656e669ee8eec1d0f8fd8c363 /home/jenkins/oracle_export//cdmv3_PROCEDURES_20160407_160654.dmp 20452f2ead3af1f4124b1589fe86a4aa /home/jenkins/oracle_export//cdmv3_PRO_CM_20160407_160654.dmp 95f5df676e2ba29b58cd394b54956f61 /home/jenkins/oracle_export//cdmv3_VITAL_20160407_160654.dmp -- Dan ________________________________ From: Phillip Reeder [[email protected]] Sent: Monday, August 01, 2016 1:46 PM To: Dan Connolly; <[email protected]> Subject: Re: gpc-dev 2 Aug agenda and meeting notes We received feedback/questions from PCORI. I have some questions for everyone regarding how refreshes/archiving should be done for it. Here are the questions from PCORI: 1)We would like to understand more about your processes for refreshing your DataMart and creating a locked/static version of each DataMart refresh. Can you please describe your processes for us? When you refresh your DataMart, do you perform a complete update or a partial update (e.g. updating new or changed information)? 2)Given the time necessary to refresh your data, what is the latest data that will be available in the DataMart relative to the date of query receipt? For example, if we send you a DC query on July 1, what is the date of the latest information you expect to be captured in the DataMart? For UTSW, I currently have the data in Oracle and we can do a complete update every month when we update our i2b2. But, when we do so, it will wipe out and re-load all of the data. What are others doing to create a “locked/static” version? We’re also still creating our CDM from the de-identified, date shifted version of i2b2. Are other GPC sites doing the same? Or have you eliminated date shifting on the CDM? I could fairly easily use our pre-shifted version of i2b2 but want to be consistent with other sites with regards to the process. I’m also wondering if the date shifting may be causing our vitals data to look like it’s spiking around 1 year ago. I haven’t created a non-date shifted version to compare to through. Thanks, Phillip From: <[email protected]<redir.aspx?REF=tZCoKgWqVilUbQ5noDP8WO4xzAKsNHEZlp6JWJssJJNtzn1NPLrTCAFtYWlsdG86Z3BjLWRldi1ib3VuY2VzQGxpc3RzZXJ2Lmt1bWMuZWR1>> on behalf of Dan Connolly <[email protected]<redir.aspx?REF=gjzjv8PystS7y70uVkkDpxY_AwQ7l5cIhzDNDWcLV-9tzn1NPLrTCAFtYWlsdG86ZGNvbm5vbGx5QGt1bWMuZWR1>> Date: Monday, August 1, 2016 at 1:32 PM To: "<[email protected]<redir.aspx?REF=0YnNj8O0cDaD9rrjiFK-T9g3JWT66M8BsfsN_MmUFKhtzn1NPLrTCAFtYWlsdG86Z3BjLWRldkBsaXN0c2Vydi5rdW1jLmVkdQ..>>" <[email protected]<redir.aspx?REF=0YnNj8O0cDaD9rrjiFK-T9g3JWT66M8BsfsN_MmUFKhtzn1NPLrTCAFtYWlsdG86Z3BjLWRldkBsaXN0c2Vydi5rdW1jLmVkdQ..>> Subject: gpc-dev 2 Aug agenda and meeting notes What else for tomorrow? * gpc-dev 2 Aug shared notes<redir.aspx?REF=OX4hYyehSAhNotMER9tOAXUmR3bDInaK3cT3ogRoscltzn1NPLrTCAFodHRwczovL2RvY3MuZ29vZ2xlLmNvbS9kb2N1bWVudC9kLzFkSElRTVZSV1I4eTZCcFhvWDNCUEQ4ZkdYTDAxaHc5bnJqVlNyYjc2RExBL2VkaXQ.>; scribe: MU ________________________________ 1. Convene, take roll, review records and plan next meeting * Meeting ID and access code: 817-393-381<redir.aspx?REF=wysTjPuiqo-n103TKPl6I-7b1dTnvxj18S8eQXxYTe1tzn1NPLrTCAFodHRwczovL2dsb2JhbC5nb3RvbWVldGluZy5jb20vbWVldGluZy9qb2luLzgxNzM5MzM4MQ..>; call +1 (571) 317-3131 * roll: all 12DevTeams<redir.aspx?REF=W3H0AWlJNwQXJQDoubc2T6kTC9rI-j8s5bOLJR5srFVtzn1NPLrTCAFodHRwczovL2luZm9ybWF0aWNzLmdwY25ldHdvcmsub3JnL3RyYWMvUHJvamVjdC93aWtpL0RldlRlYW1z> represented? KUMC, CMH, UIOWA, WISC, MCW, MCRF, UMN, UNMC, UTHSCSA, UTSW, MU, IU Reminder - put institution after your name in GoToMeeting preferences * today's scribe: MU * comments on the agenda? on last week’s notes (#12<redir.aspx?REF=RBaa-839AkQq54kR7-RxYqvGkPcP1fbwRjP4QxLgSY9tzn1NPLrTCAFodHRwczovL2luZm9ybWF0aWNzLmdwY25ldHdvcmsub3JnL3RyYWMvUHJvamVjdC90aWNrZXQvMTI.>)? Recent tickets opened/closed<redir.aspx?REF=widhbfV1rwBCKcdKK2ujtqlbQnTElIep0ZrbVgwiyKdtzn1NPLrTCAFodHRwczovL2luZm9ybWF0aWNzLmdwY25ldHdvcmsub3JnL3RyYWMvUHJvamVjdC90aW1lbGluZQ..> - FYI * ... * #520 (DataBuilder limited to one terms / concepts table) created<redir.aspx?REF=ImF_6wff0eWyJyh46oQQFdYpQOZ2tBpLQZG6LKEYqNJtzn1NPLrTCAFodHRwczovL2luZm9ybWF0aWNzLmdwY25ldHdvcmsub3JnL3RyYWMvUHJvamVjdC90aWNrZXQvNTIw> minor * #409 (submit year 1 sustainability plan (milestone 2.7.1)) closed<redir.aspx?REF=rkwj-S7JOt3Fhj31VTgZB7xiqkBXKrS9_C1awQyphtFtzn1NPLrTCAFodHRwczovL2luZm9ybWF0aWNzLmdwY25ldHdvcmsub3JnL3RyYWMvUHJvamVjdC90aWNrZXQvNDA5I2NvbW1lbnQ6Ng..> * Next Meeting: 9 Aug - scribe? Note LRU schedule<redir.aspx?REF=udlwrHKHfJD9CpBRjjzc-u1xhDFJGfa6CzCyDjyBiXZtzn1NPLrTCAFodHRwczovL2luZm9ybWF0aWNzLmdwY25ldHdvcmsub3JnL3RyYWMvUHJvamVjdC90aWNrZXQvMTIjY29tbWVudDo5Mg..>, which nominates MCW, MCRF, … 2. Feasibility Query: National Diabetes Amputation Prevention Study (NDAMPS)<redir.aspx?REF=m8vh6rky8kbAeCCJtPc1lVaRr2CBXavD78K58ltyQ7dtzn1NPLrTCAFodHRwOi8vbGlzdHNlcnYua3VtYy5lZHUvcGlwZXJtYWlsL2dwYy1kZXYvMjAxNnEzLzAwMzA2NS5odG1s> Mei Liu: “Some learning points from the experience: …” 3. Milestone:tapir-trial-1 <redir.aspx?REF=ttpiy-8DgnpJL3kEQctGy-oK98zOKjLlQ3HdQ34vKQFtzn1NPLrTCAFodHRwczovL2luZm9ybWF0aWNzLmdwY25ldHdvcmsub3JnL3RyYWMvUHJvamVjdC9taWxlc3RvbmUvdGFwaXItdHJpYWwtMQ..>#521<redir.aspx?REF=RfNc50045Mf0tDySj73hHbZOJtoIAUpYpZJho8mXH0Ftzn1NPLrTCAFodHRwczovL2luZm9ybWF0aWNzLmdwY25ldHdvcmsub3JnL3RyYWMvUHJvamVjdC90aWNrZXQvNTIx>identify providers in TAPIR trial<redir.aspx?REF=RfNc50045Mf0tDySj73hHbZOJtoIAUpYpZJho8mXH0Ftzn1NPLrTCAFodHRwczovL2luZm9ybWF0aWNzLmdwY25ldHdvcmsub3JnL3RyYWMvUHJvamVjdC90aWNrZXQvNTIx>: “KUMC is going first; MCW and UTSW to follow.” 4. Next-d geocoding #508<redir.aspx?REF=-vKsGap-dUyMzx6s54ZkWP-4Uc1dnWCGcbL1Yw_veXRtzn1NPLrTCAFodHRwczovL2luZm9ybWF0aWNzLmdwY25ldHdvcmsub3JnL3RyYWMvUHJvamVjdC90aWNrZXQvNTA4>Handling small geographic areas in geocoded data for Next-D<redir.aspx?REF=-vKsGap-dUyMzx6s54ZkWP-4Uc1dnWCGcbL1Yw_veXRtzn1NPLrTCAFodHRwczovL2luZm9ybWF0aWNzLmdwY25ldHdvcmsub3JnL3RyYWMvUHJvamVjdC90aWNrZXQvNTA4> closed fixed: “... using a non-derived/randomly generated id for the Geo-ID to link up the tables would satisfy safe harbor ...” 5. #402<redir.aspx?REF=1QOMNIgylRB_xks3RstWWT8lhAGXAJ1cuon0lhys-RZtzn1NPLrTCAFodHRwczovL2luZm9ybWF0aWNzLmdwY25ldHdvcmsub3JnL3RyYWMvUHJvamVjdC90aWNrZXQvNDAy> enhanced data resource from GPC Cohort Characterization study with CMS data: “the [RESDac] project was approved” * CompleteData<redir.aspx?REF=aKEviSvlMZedPtQ8nauwz6wEL7FujiD_8_BAwjjLbTfOL4BNPLrTCAFodHRwczovL2luZm9ybWF0aWNzLmdwY25ldHdvcmsub3JnL3RyYWMvUHJvamVjdC93aWtpL0NvbXBsZXRlRGF0YQ..> -> GROUSE 6. #459<redir.aspx?REF=_h9VTjk2k7pNQXBjisd2iIJn06tE5E4u926LSwA5chXOL4BNPLrTCAFodHRwczovL2luZm9ybWF0aWNzLmdwY25ldHdvcmsub3JnL3RyYWMvUHJvamVjdC90aWNrZXQvNDU5>How to add GPC sites to SNOW SHRINE network? <redir.aspx?REF=_h9VTjk2k7pNQXBjisd2iIJn06tE5E4u926LSwA5chXOL4BNPLrTCAFodHRwczovL2luZm9ybWF0aWNzLmdwY25ldHdvcmsub3JnL3RyYWMvUHJvamVjdC90aWNrZXQvNDU5>“In discussion of the health systems payor demonstration project, Russ learned that SCILHS is willing to host a SHRINE network for PCORNet.” 7. Milestone:bc-dx-px<redir.aspx?REF=HSr_2W70a7QFsD3T9yqxgyc0tkuYL73HHtEIJIJgbIzOL4BNPLrTCAFodHRwczovL2luZm9ybWF0aWNzLmdwY25ldHdvcmsub3JnL3RyYWMvUHJvamVjdC9taWxlc3RvbmUvYmMtZHgtcHg.> - #448 done! Yay! How many hours of effort did it take? I have estimates from MCW, UMN. I'd appreciate estimates from UIOWA, MCRF, WISC, UNMC, UTSW. 8. Milestone:cohort-char-bc-db <redir.aspx?REF=C-3aDF5_gT8DCDdUioKnIygWPncT6n7vfzqqQ7w-WRLOL4BNPLrTCAFodHRwczovL2luZm9ybWF0aWNzLmdwY25ldHdvcmsub3JnL3RyYWMvUHJvamVjdC9taWxlc3RvbmUvY29ob3J0LWNoYXItYmMtZGI.>#358<redir.aspx?REF=VBIdH9LLrS0i4hadlh6S-NXifw98krqlCCp8zoRI46_OL4BNPLrTCAFodHRwczovL2luZm9ybWF0aWNzLmdwY25ldHdvcmsub3JnL3RyYWMvUHJvamVjdC90aWNrZXQvMzU4>NAACCR ETL: update all [8 participating] sites to include summary of treatment etc.<redir.aspx?REF=VBIdH9LLrS0i4hadlh6S-NXifw98krqlCCp8zoRI46_OL4BNPLrTCAFodHRwczovL2luZm9ybWF0aWNzLmdwY25ldHdvcmsub3JnL3RyYWMvUHJvamVjdC90aWNrZXQvMzU4> * Participating sites * KUMC - ETL done locally; need to update babel * UIOWA * WISC * MCW * MCRF * UMN * UNMC * UTSW - full marks! * Other sites * CMH * IU * MU * UTHSCSA ________________________________ -- Dan ________________________________ UT Southwestern Medical Center The future of medicine, today.
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