1. Medical Imaging Informatics Bench to Bedside (mi2b2)
Shawn Murphy MD, Ph.D.

2. PRINCIPAL AIM FOR CTSC-BIRN PROPOSAL
The purpose of this Administrative Supplement project is to develop and disseminate additions to the Informatics for Integrating Biology and the Bedside (i2b2)-based projects to hospitals that will allow clinical imaging data from sophisticated medical imaging modalities such as MRI, PET, ultrasound and high-speed CT to be used for secondary research purposes.

3. Enable i2b2 to be used for Image Analysis in CTSC by connecting BIRN/XNAT
Query is done
To find patients
Derive new
data from images
i2b2
BIRN/XNAT
Request
Images with
Accession #’s
Study
Images
PACS
DICOM
CFIND
DICOM
CGET
DICOM
CSTORE

4. What is the “Informatics for Integrating Biology and the Bedside” (i2b2) project?
One of 7 roadmap projects funded by the National Center for Biomedical Computing
Open source software for the collection, querying, and analysis of clinical data, trials data, genotypic data, and imaging annotations
Software supports large enterprise repositories and specific-purpose project repositories

5. i2b2 software is used across the country
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
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
Tufts New England Medical Center, Boston, MA
University of California Davis, Davis, CA
University of California San Francisco, SF, CA
University of Massachusetts Medical School, Worcester, MA
University of Michigan Medical Center, Ann Arbor, MI
University of Pennsylvania School of Medicine, Philadelphia, PA
University of Rochester Medical Center, Rochester, NY
University of Texas Health Sciences Center Houston, Houston, TX
University of Texas Health Sciences Center San Antonio, SA, TX
University of Texas Health Sciences Center Southwestern,
Utah Health Science Center, Salt Lake City, UT
University of Washington, Seattle, WI
Georges Pompidous Hospital, Paris, France
University of Goettingen, Goettingen, Germany
University of Pavia, Pavia, Italy
University of Seoul, Seoul, Korea

6. i2b2 Hive allows queries to return various types of patientsC
local
shared / central
“Hive” of software services and core CRC cells
However, it is relatively decoupled from other cells, such that various cells that it depends upon may be replaced by locally built cells. For example, loading occurs through the Identity management cell, and the Ontology management cell is necessary to check codes as they put into the repository.
remote
Clinical Research Chart

7. “Hive” of software services and core CRC cells Clinical Research Chart
Project Task: Enable queries to find patients associated with medical images using i2b2
i2b2 project portal B A C
local
shared / central
“Hive” of software services and core CRC cells
However, it is relatively decoupled from other cells, such that various cells that it depends upon may be replaced by locally built cells. For example, loading occurs through the Identity management cell, and the Ontology management cell is necessary to check codes as they put into the repository.
Billing Codes
remote
HL7
Clinical Research Chart

8. Human Subject Privacy Plan
Follow common plan as for other clinical data types
All patients at a site are added to enterprise repository with HIPAA notification that their data may be used for research upon registration.
General queries produce only aggregated numbers that are obfuscated to prevent identification of individuals
Submit IRB proposal for specific hypothesis & detailed data request for specific set of patients
PI of approved study given identifiable data in secure transfer
IRB can audit all data transfers

9. Queries can be is performed to return sets of patients with images

10. Project Task : Enable automated requests for medical images to PACS and copy to XNAT
Query is done
To find patients
Derive new
data from images
i2b2
XNAT
Request
Images with
Accession #’s
Study
Images
PACS
DICOM
CFIND
DICOM
CGET
DICOM
CSTORE

11. What is BIRN/XNAT? An open source BIRN imaging informatics platform.
Core features:
DICOM workflow
Web interface
Extensible data model
RESTful web services API
Pipeline processing
Built on various open source Java (Jakarta Turbine, Maven, Restlets, dcm4che) and Javascript (YUI) technologies.

15. XNAT Connects multiple applications throughout BIRN
BIRN Mediator (BIRN-CC)
LONI Pipeline (UCLA)
3D Slicer (NAMIC)

16. Project Task: enable progressive annotations to images in i2b2

17. Resulting i2b2-XNAT-PACS Integration
Dr Y
Desktop Alzheimer
Dr Z
Desktop Chronic pain management
Dr X Desktop Pediatric rare disease
Dr W
Desktop Quantitative cancer biomarkers
XNAT
Enterprise
Slicer:
Data visualization analysis
PACS
PACS
Project
Management
Annotating
Genomic
Data #2
File
Repository
De -
Identification
Of data
Ontology
Management
Identity
Management
Natural
Language
Processing
Data
Repository
(CRC)
Workflow
Framework
Annotating
Genomic
Data #1
Correlation
Analysis 17
i2b2 HIVE

18. Annotated imaging data can be added back to i2b2 Enterprise Repository
i2b2 DB
Project 1
[ Enterprise
Shared
Data ]
i2b2 DB
Project 2
Shared data
of Project 1
Ontology
Consent/Tracking
of Project 2
i2b2 DB
Project 3
Security
Since during their creation and management they shared a common architecture, they can be joined together at any point to created a large shared CRC.
of Project 3

19. Allowing queries for imaging data to be made across i2b2 distributed “Shared Health Research Information Network”
SHRINE
adapter
Hospital 1
i2b2
Hospital 3
caBIG
I2b2 Query
Aggregator
SHRINE
adapter
SHRINE
adapter
Hospital 2
i2b2
Central “aggregator” broadcasts query to local hospital “adaptors”, which return aggregate counts 19

20. i2b2 & Catalyst leadership: Shawn Murphy & Randy Gollub
mi2b2: Implementation
i2b2 & Catalyst leadership: Shawn Murphy & Randy Gollub
Project lead architect: Chris Herrick
Project lead scientist: Steve Pieper
Hospital Departments of Radiology IT leaders:
Ramin Khorasani / Kathy Andriole (BWH)
Keith Dreyer / Darren Sack (MGH)
Robert Lenkinski / Jesse Wei (BIDMC)
Daniel Nigrin / Richard Robertson / Bill Tellier /
Paul Lamonica (CHB)
Programmers: Wensong Pan, Yong Gao
Dissemination: Valerie Humblet
XNAT team: Dan Marcus, Tim Olson, John Paulett
Wiki page: Posting of all Meeting minutes, agendas, etc