KUMC Biomedical Informatics Resources for your Research a

KUMC Biomedical Informatics Resources for your Research: a focus on HERON Russ Waitman, Ph. D Director of Medical Informatics, Associate Professor, Department of Biostatistics Director, Frontiers Biomedical Informatics Assistant Vice Chancellor, Enterprise Analytics University of Kansas Medical Center Kansas City, Kansas This project is supported in part by NIH grant UL 1 TR 000001 and NSF Award CNS-1258315

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.

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

The Fish: Diagnoses, Demographics, Observations, Treatments

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

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

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

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

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 deidentified 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

Sometimes, You’re willing to enter data/buy fish: REDCap: Research Electronic Data Capture • 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/project. Reg. 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/

REDCap Case Report Form Example

REDCap Survey: Think Survey. Monkey

Option Two: CRIS REDCap Disclaimer • 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

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

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

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. i 2 b 2 https: //www. i 2 b 2. 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.

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 deidentified 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

The i 2 b 2 “Fishing Rod”: build Diabetes cohort Types of “fish” in folders Drag concepts from upper left into panels on the right

i 2 b 2 : AND in Frontiers Research Registry Dragging over the secondition

i 2 b 2: AND a high Hemoglobin A 1 C When you add a numeric concept, i 2 b 2 asks if you want to set a constraint

i 2 b 2 Result: 497 patients in Cohort Run the Query took 4 seconds 497 patient in cohort

I 2 b 2: Explore Cohort, Visualize

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

Without getting bit

How the team works: HERON Evolves Every Month • Goal: stable monthly process, minimal downtime • Complete rebuild of the repository, not HL 7 messaging update based. • Two databases: create new DB while old DB is in use. • When the new DB is ready, switch over i 2 b 2 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

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

HERON’s Data Sources, Types of Data https: //informatics. kumc. edu/work/wiki/Heron. Project. Timeline#Sep 2012 Planning - contains current plan for next several monthly releases

“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/frontie rs/informatics-training-videos • Request a consult http: //frontiersresearch. org /frontiers/biomedicalinformatics If you don’t see what you want, or you really like things, let us know: https: //redcap. kumc. edu/surveys/? s=3 S Bk. Pg&tool=1

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 (De. ID, MITRE Identification Scrubber toolkit) • Date Shift example: – Patient was born August 13, 1968, had their blood pressure measured on November 28, 2012. – Each month dates shifted, ex: to -15 for January release: New birthday 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 13 th patient’s offset might be -192.

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

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 i 2 b 2 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 Health. System Consortium CDB “gold” standard for KU Hospital – What can you solve in i 2 b 2 “same financial encounter” versus send to R?

Repurposing i 2 b 2 Clinical Research Infrastructure for Inpatient Quality Improvement • i 2 b 2 “largely” ambulatory or population/genomics focused • Is i 2 b 2 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

Systems Architecture

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 i 2 b 2 Plugin invokes a program that creates a Rda file in their directory on the server

UHC, Flowsheets, Medications data sources: what i 2 b 2 could answer versus R analysis i 2 b 2 could define cohort refinement with R

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

Aligning Clinical Research Informatics for Quality: Registry Abstraction and Data Delivery • REDCap registries into i 2 b 2 allows intuitive exploration – Researchers may need less abstraction as data is extracted from the EMR. • i 2 b 2 into REDCap: inherit security model, graphical/export tools

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 data in 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

Questions?