Transcript I2b2 features leveraged for SHRINE

Harvard Catalyst SHRINE
October 13, 2010
Douglas MacFadden & Andrew McMurry
catalyst.harvard.edu
cbmi.med.harvard.edu
Created with the support of Harvard Catalyst | The Harvard Clinical and Translational
Science Center (NIH Grant #1 UL1 RR 025758-01 and financial contributions from
Harvard University and participating academic health care centers).
Foundational Work
• I2b2 - Clinical Data Repository
– Zak Kohane, Shawn Murphy et al.
– Turning everyday clinical encounters into huge research
cohorts
– Star-schema database with associated ontology
– JavaScript Web Client (Griffin Weber)
• SPIN - cross hospital query model
– Andy McMurry et al.
– Federated query of autonomous/independent hospitals
– Abstract away the differences of each data repository
enabling on the fly query translation
Harvard Catalyst SHRINE
Objective
• Query Clinical Data Across Multiple
Harvard Teaching Hospitals
– Increase Data Set Size
– Demonstrate Cooperation Across
Competing Institutions
– Develop Data Sharing Infrastructure
Architecture
I2b2 features leveraged
for SHRINE
Webclient, Project Management, Ontology, Data Repository
I2b2 features leveraged for
SHRINE:
Webclient
1. Webclient speaks to the broadcaster aggregator as if it were
another i2b2 Clinical Data Repository
2. Minor enhancements to support additional
auditing/monitoring of SHRINE queries
Griffin Weber, Nicholas Benik
I2b2 features leveraged for
SHRINE:
Project Management Cell
1. Authenticate local investigators
2. Pointers to “Cells in the Hive”
 Location for the Ontology
 Location of the Data Repository
 URLs for all i2b2 cells
I2b2 features leveraged for
SHRINE:
Ontology Cell
Handles deep “nested” hierarchies like
Diagnoses\Neoplasms\Cancer of breast
1. Demographics
• Age
• Gender
• Language
• Marital Status
• Religion
• Race and Ethnicity
2. Diagnoses
- HL7 Administrative Gender
- ISO 639-1
- HL7 Marital Status
- HL7 Religious Affiliation
- CDC Race & Ethnicity Code Sets
- ICD-9-CM and CCS hierarchy
3. Medications - RxNorm and NDF-RT hierarchy
4. Lab Tests (demo) - LOINC
I2b2 features leveraged for
SHRINE:
Data Repository Cell
Star Schema design concurrently supports multiple ontologies
(local ontology and SHRINE ontology)
SHRINE works with CRC v1.3 and v1.4
Use your existing i2b2 deployment, no code or data changes
required!
Shawn Murphy et al.
Challenges
• Organizational
• Informatics
• Usability
Challenges: Organizational
• Ground rules: contribute data to play, all users must
“belong” to participating institutions
• Regulatory Buy In
• Management Buy In
• Controls
– Query Topics
– User Agreement
– Audit Trails
• Consequences for Bad Behavior
Challenges: Informatics
• Implement Local Data Warehouse and ETL from
Operational Systems
• Server/Network security
• Design and Development of Core Ontology
• Perform Local Mapping to Core Ontology
• Implementation of Network and Systems at each Site
• Implement Required Controls
• Prevent Re-identification
Challenges: Usability
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Ease of Access
Easy Query Creation
Understanding of Query Results
Understanding the Limitations of Data
Coding from Operational Systems
Phase 1
6MPatients
1B Facts
4 Ontology Categories, 18K Terms
10K Potential Users
4 IRBs
4 major competing hospitals, 3 sites
Partners Health Care (BWH, MGH)
Children’s Hospital Boston
Beth Israel Deaconess Medical Center
SHRINE queries
(Actual Patient Counts)
• Comorbidity of Breast and Cervical Cancers
• Acute Myocardial Infarction with Gender Breakdown
• Pediatric Rhematoid Arthritis (rare)
• Countless more secondary uses of electronic medical records…
Where We Are Today
• Now:
– Second Round of Beta Test
– 1.7 + Saved Query
– Expanding to include Dana Farber
• Plan:
– SHRINE 2.0 – Limited Data Sets
• Opportunity:
– Regional and National Networks
Regional and National Networks
1. Agree to a common policy/understanding
for all sites
2. Implement i2b2 platform & SHRINE
technology
3. Develop local Ontology mappings
4. Implement network security
infrastructure
5. Join the network
The Team
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Zak Kohane
(SHRINE PI / HMS)
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Alexa McCray
(CBMI Director / HMS)
Andrew McMurry
(Architect / SPIN / HMS)
Bill Simon
(Informatics/ HMS)
Charles McGow
(Informatics / Children’s)
David Hardwick (Quality Assurance / HMS)
Doug MacFadden
(Informatics / CBMI Informatics Director / HMS)
Griffin Weber
(Informatics / HMS CTO / BIDMC)
Joanna Brownstein
(Project Manager /HMS)
John Orechia
(Informatics / DFCI)
Mike Mendis
(Informatics / i2b2 / Partners)
Nich Wattanasin
(Informatics / i2b2 / Partners)
Phillip Trevvett
(Ontology / HMS)
Shawn Murphy
(Informatics / i2b2 / Partners)
Susanne Churchill
(Regulatory / i2b2 Executive Director / Partners)