UC-CSC Rex 20140804 Final

Report
UC-Rex:
A model for cross-campus
collaboration and data sharing
UC-CSC Meeting
San Francisco
August 4, 2014
Doug Berman UCSF and Ayan Patel UCLA
ucrex.org
Today’s discussion:
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What is UC-ReX?
Who is involved and what did we do?
What technology was involved?
How we worked together:
• Project structure
• Sponsorship, leadership, governance, workgroups and
coordination
• Results and outcomes
• Results
• What we learned about working together
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UC- Research Exchange (UC-ReX)
Background
• During the past few years UC Medical
Campuses have made significant
investment in Electronic Health Records
• Research is a key mission at each campus
• We recognize the power in working
together in research
• Medical campuses may share data in
order to achieve a large population for our
work
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UC-ReX Goals
• Five-Year Goal:
Enable researchers and quality improvement specialists
to query and analyze clinical data collected at the point
of care at all UC medical campuses for research or
quality improvement purposes under a common crossinstitutional IRB approval process (Trust/Rely) and in a
manner that preserves privacy.
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UC-ReX Sponsors
• UC Office of the President Funding for Cross-UC
Data Sharing $5 million/5 years (July 2011- 2016)
• UC - BRAID Biomedical Research Acceleration,
Integration & Development
• Local CTSA’s (Clinical Translational Science Awards)
• Campus CIO’s
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Demonstration :
UCReX Data Explorer (SHRINE)
https://ucrexi2b2.ucsf.edu/
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Governance Structure
Working Groups
Technology
Strategy
(Lisa Dahm, UCI)
UC BRAID
PI from each UC
CTSA
Budgetary oversight
Review quarterly
status reports
UC ReX
Steering
1 voting + 1 nonvoting member
from each UC
Simple majority
Rotating Chair
http://www.ucbraid.org/informaticsmdashuc-rex.html
Technical
Implementation
(Lisa Dahm, UCI)
Data
Harmonization
(DaveraGabriel, UCD)
User Support
(Mini Kahlon, UCSF)
Data Quality
(Doug Bell, UCLA)
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Working Groups
Technology
Strategy
Technical
Implementation
Data
Harmonization
User Support
Data Quality
• Specify use cases
• Provide functional gap analysis
• Propose technology roadmap
• Ensure that infrastructure & critical software are
deployed & maintained
• Ensure semantic interoperability
• Oversee data quality
• Define processes, create SOPs
• Coordinate user training & support
• Design UCReX Website, roll-out pilot
• Review completeness and consistency of data
across campuses
• Identify opportunities to improve data quality
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Technology Strategy
• Identify use cases
• Review and select technologies and
partners
• Sets technical direction
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UC-ReX Use Cases
Support Clinical Trials and Recruitment
• Clinical studies are challenging
• It is difficult to identify and recruit appropriate research
subjects.
• Clinical studies may take years to recruit sufficient populations
to support conclusions; many fail for lack of patients
Performing studies in larger populations may make many studies
possible.
Quality comparisons among sites to identify best practices
Research Questions on Retrospective data
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Technical Implementation
• Open source software developed at Harvard
• i2b2 – Informatics for Integrating Biology and the Bedside
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Scalable informatics framework that enables clinical researchers to use existing clinical data for
discovery research
https://www.i2b2.org/
• SHRINE - Shared Health Research Information Network
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System for enabling clinical researchers to query across distributed hospital electronic medical
record systems
https://open.med.harvard.edu/wiki/display/SHRINE/SHRINE++Basics
• 1 Proxy Server, 2 Application Servers, 1 Database Server
• Proxy Server – Apache
• i2b2 Application Server – jBoss
• SHRINE Application Server – Tomcat
• Database Server – Oracle/SQL Server
• UCSF, UCLA, UCD – Oracle
• UCI, UCSD – SQL Server
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What’s at each site
• Unique ETL - Moves data to harmonized
dataset
• i2b2 database
• Web-site for queries
• Management agent
• Local provisioning for access
• Local support for users
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UCReX Network Topology
Central Node (located at UC Davis-MC)
Data remain at each UC
• The Central
Management Node
(CMN) is a webapp
deployed to
complement SHRINE –
as agent or manager
• Provides a central point
for monitoring nodes
and gathering
information
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UC-Rex Architecture
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Data Harmonization
• Develop/determine ontology to reference source data from each site
• In order to query all sites, we all must speak the same language
• 5 different EMR implementations (4 sites with Epic EMR – Not much help)
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Clinical workflows implemented differently
Different modules at different stages of deployment
What about legacy data?
• Types of Medical Data
• Demographics – Local source data mapped to various standards from CDC,
WHO, ISO, HL7
• Diagnoses and Procedures – ICD9 Standard Terminology used consistently
across all sites for billing/finance
• Lab Results
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Different laboratories with different equipment
Different reference ranges and units for the same lab
• Medications
• Maintaining Consistent Ontology
• GitHub repository set up to ensure each site has the same ontology
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User Support
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Communicate with local users
Develop websites, documentation
Provide training and support
Develop support protocols and communication
among site-based support groups
• Implement processes for sharing identified data
(IRB approvals, data sharing agreements, request
process and secure delivery of results)
• Receive feedback from use community
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Data Quality
• Discovery data anomalies by querying the i2b2 databases
• Look at trends of counts of data types by year from each site
• View distribution of demographics
• One site had a unreasonably high percentage of a certain
race, upon investigation it was discovered that that race was
used as a default value
• Lab Results
• Look at medians and means for each lab type
• Discovered some lab units were not converted to the
appropriate unit agreed upon in Data Harmonization
• Continue to slice and dice data and look at it from different
perspectives
• Investigate potential issues - feedback discoveries to Technical
Implementation and Data Harmonization
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Lessons learned
• Balance Project Goals
• Research project versus IT project to support
research
• Focus on delivery
• Expect institutional differences
• Infrastructure, organization, approval and
change processes will differ at each institution
• Time lines needed to adapt to diversity among
institutions
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Lessons learned (continued)
• Project management was key
• Program management - central coordination and
decision making
• Site level – planning resources and deliverables
• Virtual work – Conference calls and screen
shares are effective
• Team members from each site work together
directly
• ‘Perfect is the enemy of good’
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UCReX –Team
UCD Kent Anderson
UCSD Elizabeth Bell
Nicholas Anderson
UCI
Davera Gabriel
Samuel Morley
Hyeon-eui Kim
Lucila Ohno-Machado
Travis Nagler
Paulina Paul
Yi-Cheng (Andrea )Hwang
UCSF Douglas Berman
Lisa Dahm
Robert Hink
Ray Pablo
Bhuwan Karki
Dana Ludwig
UCLA Douglas Bell
Vijay Rayanaker
Robert Follett
Kimberly Romero
Leslie Yuan
Ayan Patel
Marianne Zachariah
Program Manager Lattice Armstead
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Questions
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