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.
UC Davis School of Medicine Travis H. NaglerHealth Informatics Program Master’s Thesis December 11, 2013
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.
UC Davis School of Medicine Travis H. NaglerHealth Informatics Program Master’s Thesis December 11, 2013
What We’ll Talk About
Introduction to Observational Studies Data Delivery Method Data Dictionary/Data Import (DDDI) Project Demonstration Limitations and Future Work
UC Davis School of Medicine Travis H. NaglerHealth Informatics Program Master’s Thesis December 11, 2013
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.
UC Davis School of Medicine Travis H. NaglerHealth Informatics Program Master’s Thesis December 11, 2013
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.
UC Davis School of Medicine Travis H. NaglerHealth Informatics Program Master’s Thesis December 11, 2013
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
UC Davis School of Medicine Travis H. NaglerHealth Informatics Program Master’s Thesis December 11, 2013
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).
UC Davis School of Medicine Travis H. NaglerHealth Informatics Program Master’s Thesis December 11, 2013
What We’ll Talk About
Introduction to Observational Studies Data Delivery Method Data Dictionary/Data Import (DDDI) Project Demonstration Limitations and Future Work
UC Davis School of Medicine Travis H. NaglerHealth Informatics Program Master’s Thesis December 11, 2013
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)
UC Davis School of Medicine Travis H. NaglerHealth Informatics Program Master’s Thesis December 11, 2013
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”
UC Davis School of Medicine Travis H. NaglerHealth Informatics Program Master’s Thesis December 11, 2013
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
UC Davis School of Medicine Travis H. NaglerHealth Informatics Program Master’s Thesis December 11, 2013
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.
UC Davis School of Medicine Travis H. NaglerHealth Informatics Program Master’s Thesis December 11, 2013
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.
UC Davis School of Medicine Travis H. NaglerHealth Informatics Program Master’s Thesis December 11, 2013
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
UC Davis School of Medicine Travis H. NaglerHealth Informatics Program Master’s Thesis December 11, 2013
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
UC Davis School of Medicine Travis H. NaglerHealth Informatics Program Master’s Thesis December 11, 2013
Data Delivery MethodREDCap™ Data Dictionary
UC Davis School of Medicine Travis H. NaglerHealth Informatics Program Master’s Thesis December 11, 2013
Data Delivery MethodREDCap™ Data Import Tool
UC Davis School of Medicine Travis H. NaglerHealth Informatics Program Master’s Thesis December 11, 2013
Data Delivery MethodREDCap™ Data Entry Page
UC Davis School of Medicine Travis H. NaglerHealth Informatics Program Master’s Thesis December 11, 2013
What We’ll Talk About
Introduction to Observational Studies Data Delivery Method Data Dictionary/Data Import (DDDI) Project Demonstration Limitations and Future Work
UC Davis School of Medicine Travis H. NaglerHealth Informatics Program Master’s Thesis December 11, 2013
Data Dictionary/Data Import (DDDI) Project
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
UC Davis School of Medicine Travis H. NaglerHealth Informatics Program Master’s Thesis December 11, 2013
OneFunction!
Data Dictionary/Data Import (DDDI) Project
DDDI Project Sample EMR Query Result CSV File
UC Davis School of Medicine Travis H. NaglerHealth Informatics Program Master’s Thesis December 11, 2013
Data Dictionary/Data Import (DDDI) Project
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
UC Davis School of Medicine Travis H. NaglerHealth Informatics Program Master’s Thesis December 11, 2013
What We’ll Talk About
Introduction to Observational Studies Data Delivery Method Data Dictionary/Data Import (DDDI) Project Demonstration Limitations and Future Work
UC Davis School of Medicine Travis H. NaglerHealth Informatics Program Master’s Thesis December 11, 2013
Demonstration
What We’ll Talk About
Introduction to Observational Studies Data Delivery Method Data Dictionary/Data Import (DDDI) Project Demonstration Limitations and Future Work
UC Davis School of Medicine Travis H. NaglerHealth Informatics Program Master’s Thesis December 11, 2013
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™
UC Davis School of Medicine Travis H. NaglerHealth Informatics Program Master’s Thesis December 11, 2013
Limitations and Future WorkFuture Work• Update code to create longitudinal dataset imports• Field Labels to be human-readable
UC Davis School of Medicine Travis H. NaglerHealth Informatics Program Master’s Thesis December 11, 2013
What We’ll Talk About
Introduction to Observational Studies Data Delivery Method Data Dictionary/Data Import (DDDI) Project Demonstration Limitations and Future Work
UC Davis School of Medicine Travis H. NaglerHealth Informatics Program Master’s Thesis December 11, 2013
Hypothesis Recap
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.
UC Davis School of Medicine Travis H. NaglerHealth Informatics Program Master’s Thesis December 11, 2013
Hypothesis Recap
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.
SUCCESS!!!
UC Davis School of Medicine Travis H. NaglerHealth Informatics Program Master’s Thesis December 11, 2013
Additional AcknowledgementsHealth Informatics ProgramDr. Peter YellowleesMark Carroll, MPHJennifer BannisterKrystal CardenasDr. Este GeraghtyDr. Sean PeisertDr. Mike HogarthDr. Tina PalmieriDr. Jim Greene
UC Davis School of Medicine Travis H. NaglerHealth Informatics Program Master’s Thesis December 11, 2013
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
UC Davis School of Medicine Travis H. NaglerHealth Informatics Program Master’s Thesis December 11, 2013
My wonderful wife, Lori!
Thank You!
UC Davis School of Medicine Travis H. NaglerHealth Informatics Program Master’s Thesis December 11, 2013
Questions?
UC Davis School of Medicine Travis H. NaglerHealth Informatics Program Master’s Thesis December 11, 2013
REDCap Database Creation
UC Davis School of Medicine Travis H. NaglerHealth Informatics Program Master’s Thesis December 11, 2013
REDCap Database Creation
UC Davis School of Medicine Travis H. NaglerHealth Informatics Program Master’s Thesis December 11, 2013
REDCap Database Creation
UC Davis School of Medicine Travis H. NaglerHealth Informatics Program Master’s Thesis December 11, 2013
REDCap Database Creation
UC Davis School of Medicine Travis H. NaglerHealth Informatics Program Master’s Thesis December 11, 2013
REDCap Database Creation
UC Davis School of Medicine Travis H. NaglerHealth Informatics Program Master’s Thesis December 11, 2013
REDCap Database Creation
UC Davis School of Medicine Travis H. NaglerHealth Informatics Program Master’s Thesis December 11, 2013
REDCap Database Creation
UC Davis School of Medicine Travis H. NaglerHealth Informatics Program Master’s Thesis December 11, 2013
REDCap Database Creation
UC Davis School of Medicine Travis H. NaglerHealth Informatics Program Master’s Thesis December 11, 2013
REDCap Database Creation
UC Davis School of Medicine Travis H. NaglerHealth Informatics Program Master’s Thesis December 11, 2013