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

Deep Dive - Eclipse plug-in distribution with automated upload and install

Deep Dive - Support for entering derived data

NLP Specialists

Export Notes

Import DerivedCodes

Outside of i2b2 core

Ontology management NCBO

Imaging Research BIRN / XNAT

Cross Site and Platform Integration SHRINE / caBIG

Extensible Neuroimaging Archive Toolkit (XNAT) used to integrate image management into i2b2

i2b2

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

i2b2 Clinical Research Chart

Shawn Murphy MD, Ph.D.Griffin Weber MD, Ph.D.

Michael MendisAndrew McMurryVivian Gainer MSLori Phillips MSRajesh Kuttan

Wensong Pan MSHenry Chueh MD

Susanne Churchill Ph.D.John Glaser Ph.D.

Isaac Kohane MD, Ph.D.