KUMC Biomedical Informatics Resources for your Research: a focus on HERON

1. KUMC Biomedical Informatics Resources for your Research: a focus on HERON This project is supported in part by NIH grant UL1TR000001 and NSF Award CNS-1258315

2. Biomedical Informatics Can Help Your Research • We have tools and expertise to manage data and convert it into information • REDCap and CRIS – enter and manage data • HERON – fish for data from the hospital/clinic • Biweekly Frontiers Clinical Informatics Clinics • Tuesday 4-5 pm in 1028 Dykes Library. • Next session April 30, 2013.

3. You’re that fisherman: wanting to land data to answer your research hypothesis Bennett Spring Trout Park, Lebanon Missouri http://mdc.mo.gov/regions/southwest/bennett-spring

4. The Fish: Diagnoses, Demographics, Observations, Treatments

5. Why so many fish? Current Goal: Build Hatchery, Manage the Fishery

6. Second Goal: If you need help fishing, get a guide Photo Credit: HuntFishGuide.com http://www.flickr.com/photos/huntfishguide/5883317106/

7. Prepare and Analyze Data Photo Credit: S. Klathill http://www.flickr.com/photos/sklathill/505464990/

8. Our shared goal: a tasty publication Photo Credit: Steve Velo http://www.flickr.com/photos/juniorvelo/259888572/

9. Nightmare: looks like a nice river, but can’t catch fish • I’ll just enter everything in Excel…. • What if I lose or accidentally sort my spreadsheet? • How to I let students only review de-identified data? • Hospital/Clinic is making me use this Electronic Medical Record and I get nothing in return... Little White Salmon River, Washington State, last Summer in July

10. Sometimes, You’re willing to enter data/buy fish: REDCap: ResearchElectronicDataCapture • https://redcap.kumc.edu • It uses the same username and password as your KUMC email. • Non-KUMC researchers can request an affiliate account through Frontiers CTSA office • Check out the training materials under videos • Case Report Forms and Surveys • For consultation and to move project to production: Register your project with us so we can keep track of your request. • http://biostatistics.kumc.edu/projectReg.aspx • After you register your project, a CRIS team member, likely Kahlia Ford will get in touch with you. • Check out other institutions using REDCap and possibly borrow from the master library. • http://www.project-redcap.org/

11. REDCapCase Report Form Example

12. REDCapSurvey: Think SurveyMonkey

13. Option Two: CRISREDCapDisclaimer • For clinical trials, CRIS (Velos) may be a better fit • Multiple years of experience • CRIS team builds for you with biostatistics review • Budget for CRIS team and biostatistics explicitly • “Investigator driven” REDCap only works if you, the Principal Investigator, takes responsibility for your data • Scalability: informatics provides consultation and responsibility for technical integrity; not your dictionary or data entry. • Underwritten by CTSA, but you “feed and talk to your fish” • Middle model where informatics can build for you in REDCap. • Again, you budget for our team’s time

14. REDCap: think Fish Tank you manage http://www.flickr.com/photos/wiccked/185270913/lightbox/

15. I want to go fishing, not fill a fish tank (REDCap) • Use HERON: a managed fishery Bonneville Hatchery: Trout, Salmon, Sturgeon, Columbia River, Oregon

16. Central CTSA Informatics Aim: Create a data “fishing” platform: HERON, https://heron.kumc.edu • Get a License: Develop business agreements, policies, data use agreements and oversight. • Get a Fishing Rod and Bass Boat: Implement open source NIH funded (i.e. i2b2 https://www.i2b2.org/) initiatives for accessing data. • Know what your catching: Transform data into information using the NLM UMLS Metathesaurus as our vocabulary source. • Stock Different Tasty Fish: link clinical data sources to enhance their research utility.

17. HERON: Getting a Fishing License Single sign-on using your email username Real-time check for current human subjects training • Fill out System Access Agreements to sponsor students/staff • Fill out Data Use Agreement to request data export • No Limit!!! IRB Protocol Not Required to view or pull de-identified data • Must be on campus or use VPN or https://access.kumed.com • Check http://frontiersresearch.org/frontiers/HERON-Introduction for more information, status, and training videos

18. The i2b2 “Fishing Rod”: build Diabetes cohort Types of “fish” in folders Drag concepts from upper left into panels on the right

19. i2b2 : ANDin Frontiers Research Registry Dragging over the second condition

20. i2b2: ANDa high Hemoglobin A1C When you add a numeric concept, i2b2 asks if you want to set a constraint

21. i2b2 Result: 497patients in Cohort Run the Query Query took 4 seconds 497 patient in cohort

22. I2b2: Explore Cohort, Visualize

23. The dream: landing the big one Catch the data for JAMA, NEJM publication http://www.oregon.com/columbia_gorge_attractions/bonneville_hatchery

24. Without getting bit

26. How the team works: HERON Evolves Every Month • Goal: stable monthly process, minimal downtime • Complete rebuild of the repository, not HL7 messaging update based. • Two databases: create new DB while old DB is in use. • When the new DB is ready, switch over i2b2 to serve customers fresh data. • Initial Files from Clinical Organizations • Export KUH Epic Clarity relational database instead of Cache/MUMPS. • Monthly file from UKP clinic billing system (GE IDX). UHC CDB, NAACCR • Demographics, services, diagnoses, procedures, and Frontiers research participant flag. • Extract Transform Load (ELT) processes largely SQL (some Oracle PL/SQL) • Wrapped in python scripts. • Goals for a monthly release (20 months in a row so far): • Fresh data. Example: another month of visits = millions of facts • New types of data. Example: family history • New functionality: Example: link data by encounter across clinical and financial sources; distinguish medication administration from prescription

27. Monthly Release • Blog highlights: • Features • Size • Dates of sources https://informatics.kumc.edu/work/blog

28. HERON’s Data Sources, Types of Data https://informatics.kumc.edu/work/wiki/HeronProjectTimeline#Sep2012Planning - contains current plan for next several monthly releases

29. “Who’s Using HERON” and collaboration approaches • Find a colleague • Talk with hospital, clinic to understand workflow • Attend bi-weekly clinics • Watch the videos: http://frontiersresearch.org/frontiers/informatics-training-videos • Request a consult http://frontiersresearch.org/frontiers/biomedical-informatics If you don’t see what you want, or you really like things, let us know: https://redcap.kumc.edu/surveys/?s=3SBkPg&tool=1

30. HERON De-identification: Remove HIPAA 18 identifiers -> non human subjects research • HIPAA Safe Harbor De-identification • Remove 18 identifiers and randomly date shifting by up to 365 days back in time • Downside: can’t do seasonal studies without IRB approval to go back and get actual dates • In general, tack on 7 months when wanting volume for the last year. • Resulting in non-human subjects research data but treated as a limited data set from a system access perspective. System users and data recipients agree to treat as a limited data set (acknowledging re-identification risk) • To be addressed: • For now, we won’t add free text such as progress notes with text scrubbers (DeID, MITRE Identification Scrubber toolkit) • Date Shift example: • Patient was bornAugust 13, 1968, had their blood pressure measured on November 28, 2012. • Each month dates shifted, ex: to -15 for January release: Newbirthday is July 29, 1968 and the blood pressure measurement occurred on November 13, 2012. • For another patient, their offset might be -278. Next month the Aug 13th patient’s offset might be -192.

31. Research Context: Medical Informatics Hypotheses Hypothesis #2: Computer + Clinical Process-> Better Health? Hypothesis #1: Admin + Clinical -> Better Knowledge?

32. Emerging Functionality: From Data Aggregation to Hospital Quality Preliminary Analysis • Motivation: Build a way to go beyond counting and obtain insight before you need a Data Use Agreement and release patient data. • Grows out Dan Connolly’s survival analysis tool for NCI site visit • Intermediate step of a multi-cohort generalized survival plugin • R Data Builder plugin in i2b2 and integration with RStudio Server • (http://www.rstudio.com/ide/docs/server/getting_started) • Test Case: Antibiotic Administration for Septic patients in the Emergency Room • Past publication to bring in flowsheet data an important foundation • University HealthSystem Consortium CDB “gold” standard for KU Hospital • What can you solve in i2b2 “same financial encounter” versus send to R?

33. Repurposing i2b2 Clinical Research Infrastructure for Inpatient Quality Improvement • i2b2 “largely” ambulatory or population/genomics focused • Is i2b2 version 1.6 with same financial encounter and modifiers now useful for inpatient research? • Goal: understand medication timing and antibiotic selection • Suspect vancomycin preferred • Validate HERON medications • Especially administration timing

34. Systems Architecture

35. R Data Builder Plugin and RStudio Server Web based for user. Just another tab in the browser All data stays on the server so there’s no data release and risk of re-identification due to a lost file i2b2 Plugin invokes a program that creates a Rda file in their directory on the server

36. UHC, Flowsheets, Medications data sources: what i2b2 could answer versus R analysis i2b2 could define cohort cohort refinement with R

37. Density Plots: Time from Arrival to First Antibiotic Broad Spectrum versus Vancomycin Lag when given outside Emergency Room Lag in Broad Spectrum after Vancomycin Administration relative to RN Sepsis Screen

38. Aligning Clinical Research Informatics for Quality: Registry Abstraction and Data Delivery • REDCap registries into i2b2 allows intuitive exploration • Researchers may need less abstraction as data is extracted from the EMR. • i2b2 into REDCap: inherit security model, graphical/export tools

39. Next Steps • Informatics Research and Systems for Hypothesis #1 • Administrative plus Clinical/Biomedical providers better knowledge • Current UHC models of administrative data based on linear regression • Want to reproduce UHC models with for our datain HERON • Then develop systematic method to evaluate utility of clinical data • Perhaps applicability of newer machine learning and statistical methods and methods for validation (ex: bootstrapping) • Engage with Clinical Researchers and Hospital Quality • Continue to harvest valuable data: microbiology discrete pathology results • Advance streamlined methods for self service • Recognize though that data driven research is non-trivial and sometime the effort is underestimated by investigators • Harvest Epic alerts (best practice, drug interaction), Orderset Utilization to evaluate Hypothesis #2 • Computer + Clinical Process -> Improved Decisions and Better Health

40. Questions?