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i2b2 Clinical Research Chart
Shawn Murphy MD, Ph.D.Griffin Weber MD, Ph.D.
Michael MendisAndrew McMurryVivian Gainer MSLori Phillips MSRajesh Kuttan
Wensong Pan MSJanice Donahue
Susanne Churchill Ph.D.John Glaser Ph.D.
Isaac Kohane MD, Ph.D.
Enterprise-wide repurposing and distribution of medical record data for research
DataRepository
(CRC)
FileRepository
IdentityManagement
OntologyManagement
CorrelationAnalysis
De -Identification
Of data
NaturalLanguageProcessing
AnnotatingGenomicData #1
ProjectManagement
WorkflowFramework
PFTProcessing
AnnotatingGenomicData #2
AnnotatingImaging
Data
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
New Features in 1.4 to support Enterprise
Analysis viewsRole based access and auditingSecurity tokens and timeout of logonReplacement of Gridsphere with web services and AJAX clientMicrosoft Active Directory integrationServer-side plug-insPaging of PDOObfuscation of resultsOntology DB Totals1.6 – Distribution as Virtual Machines
Deep Dive – Identity Management Strategy
Encryption
Patient_num Patient_ide Pat_ide_source
1 Ftrlkggp[ MGH_E
2 Hl6800ol MGH_E
3 huigggiuj MGH_E
Patient_mapping table
Encounter_mapping table
DataImport
MappingEMPI
Services
Symmetric KeyHash
Deep Dive – CRC Server-side Plug-ins
QueryQueue Tables
PatientData
Patient SetEvent Set
XML Result Set
LocalPlug-inStorage
AnalysisPlug-inAnalysis
Plug-inCRCPlug-in
CRC
CRCEngine
In
Out
Analysis wrapped as a command-line or remotely executed programCan be started by trigger from clientCan be started as scheduled eventInput parameters are XML in Query Queue tablesOutput goes to Result tables, may have pointer to Local Plug-in Storage
Client
Use of CRC Server-side Plug-ins
Breakdowns of patient attributes
Two group comparisons
Increasingly complex types of analysesBreakdownSet up analysis Export
Analysis Title: Avandia vs. Pioglitazone Calculation for SNM0 on 3-04-2009
TimelineTreemap
Save File .. Open in ExcelOpen File ..
Deep Dive - Future of Virtual Machine Development
Support for self-configuring distributions - Auto configure cells URL with correct IP
- Don’t need to logon to get IP to access the web or java client
Built-in security for distributionAbility to deploy to enterprise ESX servers
DB’s on Local
Servers
i2b2 Virtual Machine
Workbench onLocal clients
Use of medical record data in clinical studies focused upon genomics and pharmacology
DataRepository
(CRC)
FileRepository
IdentityManagement
OntologyManagement
CorrelationAnalysis
De -Identification
Of data
NaturalLanguageProcessing
AnnotatingGenomicData #1
ProjectManagement
WorkflowFramework
PFTProcessing
AnnotatingGenomicData #2
AnnotatingImaging
Data
Repurpose medical record information for research studies I2b2 Workbench Natural language processing
Enable genomic studies Tissue/blood selection Genetic data integration
New Features in 1.4 to support Projects
Infrastructure to create projects from EnterpriseServer-side plug-insExport Tools – raw and patient orientedEclipse Plug-in distribution and install automation1.5 – import of derived concepts
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.
EDR
Selected patients
Data directly from EDR
Data from other sources
Data imported specifically for project
Automated Queries search for Patients and add Data
ProjectSpecific
Phenotypic Data
Approvals for user to create projectsSELECT APPROVALS
SELECT RESTRICTIONS
Restrictions for projects
Approval allows these people to be on the project
PICK USERS
Roles for people
Queries or sets of patients for whom to create Data MartIDENTIFY CASES
Queries or sets of patients to be excluded from Data MartEXCLUDE THESE PEOPLE FROM THE CASES
Queries or sets of patients from whom to include the controlsIDENTIFY CONTROLS
Queries or sets of patients whom should be excluded in controlsEXCLUDE THESE PEOPLE FROM THE CONTROLS
Data to be included from enterprise warehouse
Data to be excluded from enterprise warehouse
IDENTIFY DATA TO BE INCLUDED
EXCLUDE THIS DATA
REVIEW AND SIGN REQUEST
Approvals to be used
Restrictions to be usedPeople to be on the project
Initiate Process to Create Data Mart from Enterprise Repository
Outside of i2b2 core
Ontology management NCBO
Imaging Research BIRN / XNAT
Cross Site and Platform Integration SHRINE / caBIG
SHRINE (Shared Research Informatics Network)= Distributed Queries
Central “aggregator” broadcasts query to local hospital
“adaptors”, which return aggregate counts only
SHRINEadapter
SHRINEadapter
SHRINEadapter
QueryAggregator
i2b2
i2b2 caBIG
Community
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 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, WA
Georges Pompidous Hospital, Paris, France University of Goettingen, Goettingen, Germany University of Pavia, Pavia, Italy University of Seoul, Seoul, Korea
United States International