ucrex.org

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.org2

Today’s discussion:

• 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

ucrex.org3

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

ucrex.org4

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 cross-institutional IRB approval process (Trust/Rely) and in a manner that preserves privacy.

ucrex.org5

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

ucrex.org

Demonstration :UCReX Data Explorer (SHRINE)

https://ucrexi2b2.ucsf.edu/

ucrex.org

Governance Structure

UC BRAID UC ReX Steering

Technology Strategy

(Lisa Dahm, UCI)

Technical Implementation

(Lisa Dahm, UCI)

Data Harmonization

(Davera Gabriel, UCD)

User Support

(Mini Kahlon, UCSF)

Data Quality (Doug Bell, UCLA)

Working Groups

1 voting + 1 non-voting member from each UCSimple majorityRotating Chair

PI from each UC CTSABudgetary oversightReview quarterly status reports

http://www.ucbraid.org/informaticsmdashuc-rex.html

ucrex.org

Working Groups• Specify use cases• Provide functional gap analysis• Propose technology roadmap

Technology Strategy

• Ensure that infrastructure & critical software are deployed & maintained

Technical Implementation

• Ensure semantic interoperability• Oversee data quality

Data Harmonization

• Define processes, create SOPs• Coordinate user training & support• Design UCReX Website, roll-out pilot

User Support

• Review completeness and consistency of data across campuses

• Identify opportunities to improve data qualityData Quality

ucrex.org9

Technology Strategy

• Identify use cases• Review and select technologies and

partners• Sets technical direction

ucrex.org10

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

ucrex.org11

Technical Implementation• Open source software developed at Harvard

• i2b2 – Informatics for Integrating Biology and the Bedside• 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• 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

ucrex.org12

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

ucrex.org

Central Node (located at UC Davis-MC)

Data remain at each UC

UCReX Network Topology

• 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

ucrex.org14

UC-Rex Architecture

ucrex.org15

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)

• 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

• 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

ucrex.org16

User Support

• 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

16

ucrex.org17

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

ucrex.org18

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

ucrex.org19

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’

ucrex.org20

UCReX –Team

UCD Kent Anderson

Nicholas Anderson UCSD Elizabeth Bell

Davera Gabriel Hyeon-eui Kim Samuel Morley Lucila Ohno-Machado

Travis Nagler Paulina Paul

UCI 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

Ayan Patel Leslie Yuan

Marianne Zachariah

Program Manager Lattice Armstead

ucrex.org21

Questions