i2b2 National Center for Biomedical i2b2 National Center for Biomedical Computing Computing i2b2 i2b2 Clinical Research Chart Clinical Research Chart and Hive Architecture and Hive Architecture Henry Chueh Henry Chueh Shawn Murphy Shawn Murphy Isaac Kohane, PI Isaac Kohane, PI
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I2b2 National Center for Biomedical Computing i2b2 Clinical Research Chart and Hive Architecture Henry Chueh Shawn Murphy Isaac Kohane, PI.
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i2b2 National Center for Biomedical Computingi2b2 National Center for Biomedical Computing
i2b2i2b2Clinical Research ChartClinical Research Chartand Hive Architecture and Hive Architecture
Henry ChuehHenry ChuehShawn MurphyShawn Murphy
Isaac Kohane, PIIsaac Kohane, PI
i2b2 National Center for Biomedical Computingi2b2 National Center for Biomedical Computing
SummarySummary
• Background
• Intro to the Clinical Research Chart (CRC)
• Hive / Cell Software Architecture
• More details on establishing and using the CRC
i2b2 National Center for Biomedical Computingi2b2 National Center for Biomedical Computing
BackgroundBackground
• Clinical documentation is…clinical
• Lack of systematic approach for organizing clinical data for research
• Ownership issues are unique
• Consent issues are a challenge
i2b2 National Center for Biomedical Computingi2b2 National Center for Biomedical Computing
• Leverage existing workflow standards and software
• Use Web services as basic form of interaction
• Assume unlimited choreography, but…
• Provide tools to distill complexity into basic automation for clinical investigators
i2b2 National Center for Biomedical Computingi2b2 National Center for Biomedical Computing
SW Licensing and DistributionSW Licensing and Distribution
• Commit to Open Source software
• Use GNU Lesser General Public License
• Establish local i2b2 repository exposed through i2b2 website
• Contribute to a more global NCBC SourceForge style repository if it emerges ?NIH Forge
• Keep i2b2 protocols fully open
i2b2 National Center for Biomedical Computingi2b2 National Center for Biomedical Computing
Interoperability across NCBCInteroperability across NCBC
• Strongly consider Web services as basic protocol for generic shared interactions
• Consider sharing datasets
• Promote diversity of approach and use of shared software (don’t impose uniformity)
• Facilitate/promote NCBC Open Source project teams
i2b2 National Center for Biomedical Computingi2b2 National Center for Biomedical Computing
Pre-CRC Data Pre-CRC Data Pipeline/WorkflowPipeline/Workflow
Populating the Clinical Research Populating the Clinical Research Chart (CRC)Chart (CRC)
i2b2 National Center for Biomedical Computingi2b2 National Center for Biomedical Computing
Pre-CRC Data Pipeline/WorkflowPre-CRC Data Pipeline/Workflow
• Use workflow framework to choreograph applications services in specific sequences
• Used to extract, transform, conform, and load data and metadata into the CRC
i2b2 National Center for Biomedical Computingi2b2 National Center for Biomedical Computing
Pre-CRC Data Pipeline/WorkflowPre-CRC Data Pipeline/Workflow
Ontology Consent/Tracking Application Pool Management
Services:
Data flowing
Custom Interfaces
Soap/Http interfaces
OutputInput
A program
increasingly useful
Local or through SOAP service
i2b2 National Center for Biomedical Computingi2b2 National Center for Biomedical Computing
Ontology ServiceOntology Service
Ontology Consent/Tracking Application Pool Management
• Manages mappings of terms to common vocabularies• Provides lists of acceptable (enumerated) values for
various attribute and value slots.• Allows for management of hierarchies, groupings, and
relationships between terms
Ontology
i2b2 National Center for Biomedical Computingi2b2 National Center for Biomedical Computing
Person Consent/Tracking ServicePerson Consent/Tracking Service
Ontology Consent/Tracking Application Pool Management
• Provides mappings between patient/subject identifiers• Tracks patient/subject consent information• Allows identification of the patient/subject based upon
fuzzy demographic matches
Consent/Tracking
i2b2 National Center for Biomedical Computingi2b2 National Center for Biomedical Computing
Application Pool (CVS) ServiceApplication Pool (CVS) Service
Ontology Consent/Tracking Application Pool Management
• Stores programs/scripts used in pipeline• Provides applications to be downloaded when needed• Manages versioning of software• Provides documentation
Application Pool
i2b2 National Center for Biomedical Computingi2b2 National Center for Biomedical Computing
Management ServiceManagement Service
Ontology Consent/Tracking Application Pool Management
• Stores workflow execution plan• Starts and controls workflow execution• Schedules workflow execution• Monitors workflow execution and data locations• Controls permissions associated with workflow
execution
Management
i2b2 National Center for Biomedical Computingi2b2 National Center for Biomedical Computing
Data Pipeline/Workflow ApplicationData Pipeline/Workflow ApplicationUse Case for Asthma DataUse Case for Asthma Data
Ontology Consent/Tracking Application Pool Management
Services:
Data flowing
Custom Interfaces
Soap/Http interfaces
OutputInput
A program
RPDR
CRC DB
AsthmaMartData retrieval
Data de-identification
Language processing
Vocabulary matching
Load Data into Mart
i2b2 National Center for Biomedical Computingi2b2 National Center for Biomedical Computing
Data Pipeline/WorkflowData Pipeline/WorkflowImplementationImplementation
• Define standard XML representation for workflow - MoML
• Define standards for SOAP services and resource discovery
• Adopt and extend open source workflow package (Kepler)
• Prototypes by July timeframe
• BIRN -> NAMIC and LONI collaboration
• Can follow construction details at http://diagon/i2b2