novel research data delivery system using redcap 20131211

Novel Research Data Delivery System Using REDCap™ Data

Dictionary/Data Import Functionality

Master’s Thesis

Travis H. NaglerHealth Informatics Program

Advisor: Dr. Peter YellowleesUC Davis School of Medicine

December 11, 2013

Acknowledgment

I would very much like to thank the knowledgeable members of my committee for their generous help and encouragement in completing my thesis. Without their unwavering support this would not have been possible.

Dr. Alberto OdorDr. Wasyl MalyjDeborah Lee, MBA

UC Davis School of Medicine Travis H. NaglerHealth Informatics Program Master’s Thesis December 11, 2013

Disclaimer

I have no financial interest, arrangement or affiliation in any company or product mentioned in this presentation.

Hypothesis

Functionality can be developed which automates the creation and uploading of a REDCap™ data dictionary and the importation of IRB-approved EMR query results using a minimum number of manual steps and man-hours.

What We’ll Talk About

Introduction to Observational Studies Data Delivery Method Data Dictionary/Data Import (DDDI) Project Demonstration Limitations and Future Work

Introduction to Observational Studies

Introduction to Observational StudiesObservational Studies• Three Types

– Cross-sectional• Observe all of a population at one specific point in time

– Case-control• Compare “case” group (w/disease) to “control” group (w/o disease

but otherwise similar)– Cohort

• Prospective– Collect research data from study start point forward– Framingham Heart Study

• Retrospective– Patient research data is collected from past records

-- Yang, W., et al., Observational studies: going beyond the boundaries of randomized controlled trials. Diabetes Res Clin Pract, 2010. 88 Suppl 1: p. S3-9.-- Carlson, M.D. and R.S. Morrison, Study design, precision, and validity in observational studies. J Palliat Med, 2009. 12(1): p. 77-82.

Introduction to Observational StudiesRetrospective Cohort Studies• Medical studies based on the results of clinical practice• Differ from Clinical Trials (CT)– Little/no direct intervention in medical care

• Drawbacks– Confounding variables

• Ice cream vs. drowning– Bias

• In control group selection• Misclassified information regarding the factor being assessed• Reliance on the record-keeping of others for the data

-- Yang, W., et al., Observational studies: going beyond the boundaries of randomized controlled trials. Diabetes Res Clin Pract, 2010. 88 Suppl 1: p. S3-9.-- Carlson, M.D. and R.S. Morrison, Study design, precision, and validity in observational studies. J Palliat Med, 2009. 12(1): p. 77-82.

Introduction to Observational StudiesRetrospective Cohort Studies• Advantages– Less time

• Data is already in EMR, time limited to EMR data pull– Less resources

• Need minimum of staff to analyze data– Less expensive

• Little to no researcher/physician/nurse man-hours needed to interact with patients

– Good assessment of rare diseases• Cohort of patients is already identified

Introduction to Observational StudiesRetrospective Cohort Studies• Basic Result– “Odds-Ratio”

• Relative odds that the studied variable is the cause of the effect• No evidence of definitive causation• To calculate the odds-ratio, need data that is reliably retrieved,

compiled, and stored

A good store of retrospective patient data is the hospital’s Electronic Medical Record (EMR).

Data Delivery Method

Data Delivery MethodData Retrieval Process• Steps– IRB-approved research study requires retrospective EMR

data– Principle Investigator (PI) submits request for EMR data

retrieval to Biomedical Informatics (BI) group – BI programmer meets with the PI to go over which

patients need to be pulled and what is being pulled about them

– BI programmer puts together database query to pull requested data

– BI programmer gives data to PI using Microsoft Excel© spreadsheet (Excel)

Data Delivery MethodData Breaches• Section 13402(e)(4) of the HITECH Act• In California alone, from September 2009 through June 2013,

57 breaches of unsecured PHI– 500 or more individuals– “Loss” or “Theft” of a laptop, desktop, or other portable electronic

device– Not including “Hacking/IT incident”, “Unauthorized

Access/Disclosure”, “Unknown”, “Other”

Health Information Privacy: Breaches Affecting 500 or More Individuals. 2013 October 21, 2013]; A list of entities who breached HIPAA laws with groups of 500 and more patients.]. Available from: http://www.hhs.gov/ocr/privacy/hipaa/administrative/breachnotificationrule/breachtool.html.

Data Delivery MethodBI Concerns With Excel*• Not Health Insurance Portability and Accountability Act of

1996 (HIPAA) compliant• Lack of automated backups for disaster, computer theft or

computer loss situations• Ease of accidental corruption of data• Limited change history logging for auditing purposes• No built-in user authentication and authorization features• No built-in or automated storage for study metadata• Cumbersome data validation

* Twenty-five references in thesis pertaining to this section

Data Delivery MethodData Management Tool• Three Basic Requirements– Create a database– Input/import the data– Export the data

For this project, only concerned with first two requirements.

Data Delivery MethodREDCap™ Data Management Tool• Developed by Vanderbilt University – Dr. Paul Harris• “software solution designed for the rapid development and

deployment of electronic data capture tools to support clinical and translational research.”

• Allows a researcher to create secure, online databases and surveys that support the collection, storage, and extraction of study datasets

• Installed at UC Davis Health System in December 2011• Version 4.7.1

--Harris, P.A., et al., Research electronic data capture (REDCap)--a metadata-driven methodology and workflow process for providing translational research informatics support. J Biomed Inform, 2009. 42(2): p. 377-81.--Obeid, J.S., et al., Procurement of shared data instruments for Research Electronic Data Capture (REDCap). J Biomed Inform, 2013. 46(2): p. 259-65.

Data Delivery MethodREDCap™ Data Management Tool• Create a Database– Need “super user” access– Create New Project wizard– Add User Rights– Define and Upload Data Dictionary

• Input/import the Data– For manual data entry, use REDCap™ data entry forms– For automated data import, use Data Import Tool

Data Delivery MethodREDCap™ Data Dictionary• Manually created, no automation• CSV file• Four mandatory fields out of 15 total– Variable/Field Name

• How the database tells one field apart from another– Form Name– Field Type

• Examples: text, dropdown, radio, descriptive, notes, checkbox– Field Label

• User-viewed text on the data entry form

Data Delivery MethodREDCap™ Data Dictionary

Data Delivery MethodREDCap™ Data Import Tool

Data Delivery MethodREDCap™ Data Entry Page

Data Dictionary/Data Import (DDDI) Project

DDDI Project• Basic Principle– Automate data dictionary creation– Include data import functionality

• Why?– Data Dictionary creation is time-consuming– More secure and accessible method for data delivery– EMR Data Retrievals contain both headers and data

OneFunction!

DDDI Project Sample EMR Query Result CSV File

DDDI Project• How?– Create new functionality based on current automated

methods• Data Dictionary Upload and Data Import Tool already exist

– Update web PHP code to read and properly format an imported EMR query result CSV file• Add study_id

– Mesh Data Import Tool code into new Data Dictionary creation code

– Update user interface code to add button and tab for DDDI functionality

Demonstration

Limitations and Future Work

Limitations and Future WorkLimitations• “Classic” datasets only• All fields types are “text”• All fields on one data entry form• Field Label is not human-readable• New code might be damaged in REDCap version upgrades• Do not use API or DTS functions in REDCap™

Limitations and Future WorkFuture Work• Update code to create longitudinal dataset imports• Field Labels to be human-readable

Hypothesis Recap

SUCCESS!!!

Additional AcknowledgementsHealth Informatics ProgramDr. Peter YellowleesMark Carroll, MPHJennifer BannisterKrystal CardenasDr. Este GeraghtyDr. Sean PeisertDr. Mike HogarthDr. Tina PalmieriDr. Jim Greene

Biomedical InformaticsSamuel Morley, MSDr. Brian ChanShawn Wei, MSMomeena Ali

All my HIP classmates!

Dr. Paul Harris and the REDCap™ Team – Vanderbilt University

And…

Additional Acknowledgements

My wonderful wife, Lori!

Thank You!

Questions?

REDCap Database Creation

novel research data delivery system using redcap 20131211

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