i2b2 Clinical Research Chart

1
i2b2 Clinical Research Chart

• Shawn Murphy MD, Ph.D.
• Griffin Weber MD, Ph.D.
• Michael Mendis
• Andrew McMurry
• Vivian Gainer MS
• Lori Phillips MS
• Rajesh Kuttan
• Wensong Pan MS
• Janice Donahue
• Susanne Churchill Ph.D.
• John Glaser Ph.D.
• Isaac Kohane MD, Ph.D.

2
Enterprise-wide repurposing and distribution of
medical record data for research

• Enable high performance collection of medical
  record data for querying and distribution
• Enterprise web client
• Create patient cohorts for further investigation
• Enable discovery within data on enterprise wide
  scale
• Relevance networks
• Pharmacovigilance

3
New Features in 1.4 to support Enterprise

• Analysis views
• Role based access and auditing
• Security tokens and timeout of logon
• Replacement of Gridsphere with web services and
  AJAX client
• Microsoft Active Directory integration
• Server-side plug-ins
• Paging of PDO
• Obfuscation of results
• Ontology DB Totals
• 1.6 Distribution as Virtual Machines

4
Deep Dive Identity Management Strategy

• Encryption

Hash
Symmetric Key
Data Import
Mapping
EMPI Services
Patient_mapping table
Patient_num Patient_ide Pat_ide_source
1 Ftrlkggp MGH_E
2 Hl6800ol MGH_E
3 huigggiuj MGH_E
Encounter_mapping table
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Deep Dive CRC Server-side Plug-ins
Query Queue Tables
CRC
Client
In
CRC Engine
Local Plug-in Storage
Analysis Plug-in
Analysis Plug-in
CRC Plug-in
Patient Data
Out
Patient Set Event Set XML Result Set
Analysis wrapped as a command-line or remotely
executed program Can be started by trigger from
client Can be started as scheduled event Input
parameters are XML in Query Queue tables Output
goes to Result tables, may have pointer to Local
Plug-in Storage
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Use of CRC Server-side Plug-ins

• Breakdowns of patient attributes
• Two group comparisons
• Increasingly complex types of analyses

7
Deep Dive - Future of Virtual Machine Development

• Support for self-configuring distributions
•     - Auto configure cells URL with correct
  IP    - Dont need to logon to get IP to access
  the web or java client
• Built-in security for distribution
• Ability to deploy to enterprise ESX servers

DBs on Local Servers
Workbench on Local clients
i2b2 Virtual Machine
8

• Repurpose medical record information for research
  studies
• I2b2 Workbench
• Natural language processing
• Enable genomic studies
• Tissue/blood selection
• Genetic data integration

Use of medical record data in clinical studies
focused upon genomics and pharmacology
9
New Features in 1.4 to support Projects

• Infrastructure to create projects from Enterprise
• Server-side plug-ins
• Export Tools raw and patient oriented
• Eclipse Plug-in distribution and install
  automation
• 1.5 import of derived concepts

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I2b2 allows a set of patients to be selected from
the Enterprise Repository and be gathered into a
project data set associating scientific and
medical record data.
Project Specific Phenotypic Data
Selected patients
EDR
Data directly from EDR
Data from other sources
Data imported specifically for project
Automated Queries search for Patients and add Data
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Initiate Process to Create Data Mart from
Enterprise Repository
SELECT APPROVALS
Approvals for user to create projects
Approvals to be used
SELECT RESTRICTIONS
Restrictions to be used
Restrictions for projects
People to be on the project
PICK USERS
Roles for people
Approval allows these people to be on the project
IDENTIFY CASES
Queries or sets of patients for whom to create
Data Mart
EXCLUDE THESE PEOPLE FROM THE CASES
Queries or sets of patients to be excluded from
Data Mart
IDENTIFY CONTROLS
Queries or sets of patients from whom to include
the controls
EXCLUDE THESE PEOPLE FROM THE CONTROLS
Queries or sets of patients whom should be
excluded in controls
IDENTIFY DATA TO BE INCLUDED
Data to be included from enterprise warehouse
EXCLUDE THIS DATA
Data to be excluded from enterprise warehouse
REVIEW AND SIGN REQUEST
12
Deep Dive - Eclipse plug-in distribution with
automated upload and install
13
Deep Dive - Support for entering derived data
Export Notes
Import Derived Codes
NLP Specialists
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Outside of i2b2 core

• Ontology management
• NCBO
• Imaging Research
• BIRN / XNAT
• Cross Site and Platform Integration
• SHRINE / caBIG

15
Extensible Neuroimaging Archive Toolkit (XNAT)
used to integrate image management into i2b2
i2b2
16
SHRINE (Shared Research Informatics Network)
Distributed Queries
SHRINE adapter
i2b2
Query Aggregator
SHRINE adapter
SHRINE adapter
caBIG
i2b2
Central aggregator broadcasts query to local
hospital adaptors, which return aggregate
counts only
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Community
United States
International

• Beth Israel Deaconness Hospital, Boston, MA
• Boston University School of Medicine, Boston, MA
• Brigham and Women's Hospital, Boston, MA
• Children's Hospital, Boston, MA
• Denver Children's Hospital, Denver, CO
• Cincinnati Children's Hospital, Cincinnati, OH
• Cleveland Clinic, Cleveland, OH
• Weil Medical College of Cornell, NYC, NY
• Group Health Cooperative
• Harvard Medical School, Boston, MA
• Massachusetts General Hospital, Boston, MA
• Maine Medical Center, Portland, ME
• Marshfield Clinic, Wisconsin
• Morehouse School of Medicine, Atlanta, GA
• Oregon Health Science University, Portland, OR
• Ohio State University Medical Center, Columbus,
  OH
• Philadelphia Children's Hospital, Philadelphia,
  PA
• Renaissance Computing Institute, Chapel Hill, NC

• Georges Pompidous Hospital, Paris, France
• University of Goettingen, Goettingen, Germany
• University of Pavia, Pavia, Italy
• University of Seoul, Seoul, Korea

18
i2b2 Clinical Research Chart

• Shawn Murphy MD, Ph.D.
• Griffin Weber MD, Ph.D.
• Michael Mendis
• Andrew McMurry
• Vivian Gainer MS
• Lori Phillips MS
• Rajesh Kuttan
• Wensong Pan MS
• Henry Chueh MD
• Susanne Churchill Ph.D.
• John Glaser Ph.D.
• Isaac Kohane MD, Ph.D.