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.

Enterprise-wide repurposing and distribution of medical record data for research Data Repository (CRC) File Repository Identity Management Ontology Management Correlation Analysis De - Identification Of data Natural Language Processing Annotating Genomic Data #1 Project Management Workflow Framework PFT Processing Annotating Genomic Data #2 Annotating Imaging 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 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

Deep Dive – Identity Management Strategy Encryption Patient_numPatient_idePat_ide_source 1Ftrlkggp[MGH_E 2Hl6800olMGH_E 3huigggiujMGH_E Patient_mapping table Encounter_mapping table Data Import Mapping EMPI Services Symmetric Key Hash

Deep Dive – CRC Server-side Plug-ins Query Queue Tables Patient Data Patient Set Event Set XML Result Set Local Plug-in Storage Analysis Plug-in Analysis Plug-in CRC Plug-in CRC Engine In Out 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 Client

Use of CRC Server-side Plug-ins Breakdowns of patient attributes Two group comparisons Increasingly complex types of analyses

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 distribution Ability to deploy to enterprise ESX servers DB’s on Local Servers i2b2 Virtual Machine Workbench on Local clients

Use of medical record data in clinical studies focused upon genomics and pharmacology Data Repository (CRC) File Repository Identity Management Ontology Management Correlation Analysis De - Identification Of data Natural Language Processing Annotating Genomic Data #1 Project Management Workflow Framework PFT Processing Annotating Genomic Data #2 Annotating Imaging 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 Enterprise Server-side plug-ins Export Tools – raw and patient oriented Eclipse Plug-in distribution and install automation 1.5 – 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 Project Specific Phenotypic Data

Approvals for user to create projects SELECT 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 Mart IDENTIFY CASES Queries or sets of patients to be excluded from Data Mart EXCLUDE THESE PEOPLE FROM THE CASES Queries or sets of patients from whom to include the controls IDENTIFY CONTROLS Queries or sets of patients whom should be excluded in controls EXCLUDE 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 used People 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 Derived Codes

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 SHRINE adapter SHRINE adapter SHRINE adapter Query Aggregator 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 StatesInternational

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.