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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. Biomedical Informatics Can Help Your Research. We have tools and expertise to manage data and convert it into information

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Kumc biomedical informatics resources for your research a focus on heron
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

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.

Bennett Spring Trout Park, Lebanon Missouri


  • Second Goal: research hypothesisIf you need help fishing, get a guide

Photo Credit: HuntFishGuide.com


Photo Credit: S. Klathill


Photo Credit: Steve Velo


  • 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

  • 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/

  • REDCap research hypothesisCase Report Form Example

  • REDCap research hypothesisSurvey: Think SurveyMonkey

  • 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 research hypothesis: think Fish Tank you manage


Bonneville Hatchery: Trout, Salmon, Sturgeon, Columbia River, Oregon

  • 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.

  • HERON platform: : 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

Types of “fish” in folders

Drag concepts from upper left

into panels on the right

  • i2b2 : platform: ANDin Frontiers Research Registry

Dragging over the second condition

  • i2b2: platform: ANDa high Hemoglobin A1C

When you add a numeric concept,

i2b2 asks if you want to set a constraint

Run the Query

Query took 4 seconds

497 patient in cohort

Catch the data




How the team works: platform: 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


  • HERON platform: ’s Data Sources, Types of Data


- contains current plan for next several monthly releases

  • Find a colleague

  • Talk with hospital, clinic to understand workflow

  • Attend bi-weekly clinics

  • Watch the 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:


HERON De-identification: Remove HIPAA 18 platform: 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.

Research Context: Medical Informatics Hypotheses platform:

Hypothesis #2: Computer + Clinical Process-> Better Health?

Hypothesis #1:

Admin + Clinical

-> Better Knowledge?

Emerging Functionality platform: : 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?

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

Systems Architecture Inpatient Quality Improvement

R Data Builder Inpatient Quality ImprovementPlugin 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

UHC, Inpatient Quality ImprovementFlowsheets, Medications data sources:

what i2b2 could answer versus R analysis

i2b2 could define cohort

cohort refinement with R

Density Plots: Time from Arrival to First Antibiotic Inpatient Quality Improvement

Broad Spectrum versus Vancomycin

Lag when given outside Emergency Room

Lag in Broad Spectrum after Vancomycin

Administration relative to RN Sepsis Screen

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

Next Steps Abstraction and

  • 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

Questions? Abstraction and