The caBIG/HL7/CDISC Structured Protocol Representation

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The caBIG/HL7/CDISC Structured Protocol
Representation
Douglas B. Fridsma, MD, PhD Center for Biomedical
Informatics Center for Pathology and Oncology
Informatics University of Pittsburgh
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A Team Effort

• caBIG/HL7/caBIG SPR core modelers
• Christo Andonyadis
• Greg Anglin
• Lisa Chatterjee
• Julie Evans
• Douglas B Fridsma
• Smita Hastak
• Ray Heimbuch
• Charlie Mead
• Joyce Niland
• John Speakman
• Cara Willoughby
• Diane Wold

• Leadership and collaboration
• Sue Dubman, NCI
• Becky Kush, CDISC
• Linda Quade, HL7
• caPRI
• Mike Becich
• Doug Fridsma
• Linda Schmandt
• Mike Davis
• Xuegong Wang
• Becky Boes
• Brenda Crocker
• Rebecca Crowley
• Valerie Monaco
• Bill Gross
• John Milnes
• Denine Maglicco

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Vision of the SPR SIG (from July 2004 face to
face meeting)

• To define a computable protocol representation
  that supports the entire life-cycle of clinical
  trials protocol, and develop tools that use these
  protocol representations. These tools should be
  standards-based, caBIG compliant and assist users
  in creating, maintaining, and sharing clinical
  trials information.
• The clinical trials protocol representation will
  serve as a foundation for caBIG modules that
  support all phases of the clinical trials life
  cycle, (including protocol authoring) and be
  developed to meet user needs and requirements.
• At every stage, we will evaluate and test our work

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Vision of the SPR SIG (from July 2004 face to
face meeting)

• To define a computable protocol representation
  that supports the entire life-cycle of clinical
  trials protocol, and develop tools that use these
  protocol representations. These tools should be
  standards-based, caBIG compliant and assist users
  in creating, maintaining, and sharing clinical
  trials information.
• The clinical trials protocol representation will
  serve as a foundation for caBIG modules that
  support all phases of the clinical trials life
  cycle, (including protocol authoring) and be
  developed to meet user needs and requirements.
• At every stage, we will evaluate and test our work

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caSPR The comprehensive HL7/CDSIC/caBIG SPR
model
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Why caBIG/CDISC/HL7?

• We used the CDISC protocol representation element
  spreadsheet as a starting point for our model
  development efforts
• caBIG has been involved with both CDISC and HL7
• January 2005, HL7 adopted our model as the Domain
  Analysis model for the RCRIM committee (Regulated
  Clinical Research)
• Recognizes that this is a collaborative effort
• CDISC DSAM HL7 DAM caSPR

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The Communication Pyramid

Domain Experts
Technical Experts
Communication
Source Charlie Mead, MD, HL7
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The iterative process of creating the SPRStage
One
RIM
Domain elements (drawn from CDISC PR elements)
at this stage there are granular ideas that we
know we need to represent, but relationships not
clear
Business Inputs
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CDISC protocol elements
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The iterative process of creating the SPRStage
Three state at March 2005
RIM
reductionist model of structure of domain
elements
at this stage we analyze the model to boil it
down to its primitive data structure. It gets
close to RIM, but very abstract loses some
meaning to domain experts
Business Inputs
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Entities and Roles
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Entities and Roles
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The iterative process of creating the SPRStage
Two ? Stage Three ? Stage Four
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The iterative process of creating the SPRStage
Four
RIM
integrated model(s) of structure of domain
elements

• explode back to domain concepts, through
  instance diagrams, storyboards,vocabularies, and
  other tools
• Checking that the initial elements still hold in
  the model

Business Inputs
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ECOG 2190 Schema
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ECOG 2190 Protocol Activity
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Vision of the SPR SIG (from July 2004 face to
face meeting)

• To define a computable protocol representation
  that supports the entire life-cycle of clinical
  trials protocol, and develop tools that use these
  protocol representations. These tools should be
  standards-based, caBIG compliant and assist users
  in creating, maintaining, and sharing clinical
  trials information.
• The clinical trials protocol representation will
  serve as a foundation for caBIG modules that
  support all phases of the clinical trials life
  cycle, (including protocol authoring) and be
  developed to meet user needs and requirements.
• At every stage, we will evaluate and test our work

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caSPR forms the foundation for interoperable
module development
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Proposed caPRI System Description
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Portions currently implemented
EAV database
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Poster Session at the Annual Meeting

• caSPR
• caPRI
• Demonstration of the application

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Vision of the SPR SIG (from July 2004 face to
face meeting)

• To define a computable protocol representation
  that supports the entire life-cycle of clinical
  trials protocol, and develop tools that use these
  protocol representations. These tools should be
  standards-based, caBIG compliant and assist users
  in creating, maintaining, and sharing clinical
  trials information.
• The clinical trials protocol representation will
  serve as a foundation for caBIG modules that
  support all phases of the clinical trials life
  cycle, (including protocol authoring) and be
  developed to meet user needs and requirements.
• At every stage, we will evaluate and test our work

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The Importance of Process

• Processes to develop interoperable applications
• Derived from the HL7 Development Framework
• Processes to develop interchange standards
• Can use the HL7 Development framework
• Processes to maintain the SPR
• Developing methods of collaboration and
  versioning control, based on open-source
  architectures and methods
• Developing methods of model harmonization based
  on HL7 frameworks
• We need the coordination mechanisms to let us all
  work together toward a common goal!

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caSPR forms the foundation for interoperable
module development
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caSPR Domain Analysis Model
Module Development
CT Registry Module
Internal Tracking Module
AE Module
Eligibility Module
Statistical Module
Financial Module
Lab Module
Financial Module
Statistical Module
Eligibility Module
AE Module
CT Registry Module
Internal Tracking Module
Lab Module
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caSPR Domain Analysis Model
CT Registry Module
Internal Tracking Module
AE Module
Eligibility Module
Authoring Module
Lab Module
Financial Module
Authoring Module
Eligibility Module
AE Module
CT Registry Module
Internal Tracking Module
Lab Module
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A example development processcaPRI
Application Development
caSPR CDISC DSAM HL7 DAM
Interchange Specification
Increasing specificity and computability
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A example development processcaPRI
Application Development
caSPR module analysis model
caSPR CDE
caPRI input module (module specification)
Functional Requirements
caDSR candidate CDEs
Semantic connector UML loader
caSPR CDISC DSAM HL7 DAM
Interchange Specification
Increasing specificity and computability
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A example development processcaPRI
Application Development
caSPR module analysis model
caSPR CDE
caPRI input module (module specification)
Functional Requirements
caDSR candidate CDEs
Semantic connector UML loader
caSPR CDISC DSAM HL7 DAM
RCRIM DMIM
RMIM (interchange requirements)
HL7 XSD (Interchange specification)
Interchange Specification
Increasing specificity and computability
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A example development processcaPRI
Application Development
caSPR module analysis model
caSPR CDE
caPRI input module (module specification)
caPRI CT management framework
Functional Requirements
caDSR candidate CDEs
Semantic connector UML loader
caSPR CDISC DSAM HL7 DAM
RCRIM DMIM
RMIM (interchange requirements)
HL7 XSD (Interchange specification)
HL7 compliant framework
Interchange Specification
Increasing specificity and computability
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The Importance of Process

• Processes to develop interoperable applications
• Derived from the HL7 Development Framework
• Processes to develop interchange standards
• Can use the HL7 Development framework
• Processes to maintain the SPR
• Developing methods of collaboration and
  versioning control, based on open-source
  architectures and methods
• Developing methods of model harmonization based
  on HL7 frameworks

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The people processes

• Desiderata
• Open access for people to read and examine
• Open communication and discussion forums
• Mechanisms for proposing changes
• Mechanisms for harmonization
• Levels of access for readers, modelers, and
  stewards
• Tightly controlled versioning process with
  tracking
• Integration of model packages, application code,
  documentation, and user groups

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The People Processes
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Tools to Support the People Process

• Currently Piloting an installation of gForge
• Open source
• Used for projects like firefox and mozilla
• Bug and feature tracking
• Discussion forums
• Source control with CVS check-in/check-out
• Project administration
• Email and listservs with notification of code,
  discussion group, or document changes
• Ability to link and synchronize CVS repositories
  across sites

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Vision of the SPR SIG (from July 2004 face to
face meeting)

• To define a computable protocol representation
  that supports the entire life-cycle of clinical
  trials protocol, and develop tools that use these
  protocol representations. These tools should be
  standards-based, caBIG compliant and assist users
  in creating, maintaining, and sharing clinical
  trials information.
• The clinical trials protocol representation will
  serve as a foundation for caBIG modules that
  support all phases of the clinical trials life
  cycle, (including protocol authoring) and be
  developed to meet user needs and requirements.
• At every stage, we will evaluate and test our work

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What have we accomplished?

• caSPR
• Established excellent collaboration with CDISC,
  HL7 and other caBIG modelers
• Constructed the initial pieces of a comprehensive
  model still much to do
• Have established this model as the HL7 Domain
  analysis model
• Have established EA as the tool of choice, and
  moved the model from Rational Rose XDE into EA
• caPRI
• Demonstrated a caBIG compliant application that
  is modular, extensible, flexible, and driven off
  of the SPR model
• Set the stage for collaborative development of
  new modules and features
• Process
• Proposed a model development, collaboration, and
  version control process
• Currently piloting a website to support all
  aspects of model and application development
• caBIG and the SPR will be piloting the model
  maintenance and versioning processes

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The caFuture
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What we need

• Ask not what the structured protocol
  representation can do for you,
• Ask what you can do for the structured protocol
  representation

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Current caBIG/HL7/CDISC SPR needs

• Developing Instance diagrams, examples, and
  testing the model using the ECOG 2190 protocol as
  our initial test
• The model is static heavy
• Develop the behavioral portions of the model
• The people processes around clinical trials
• Calendars
• Activities
• Behaviors
• Study execution

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Priorities for the SPR (from last night)

• Storyboards (level 1 readers, story tellers)
• Determine eligibility
• Enroll a patient
• SIG involvement in 4-5 storyboards
• Others?
• Process descriptions, activity diagrams (level 2
  modelers, story writers)
• Activity and state diagrams
• Use cases
• Harmonization (level 3, story leaders)
• Integrate across SIGs and workspaces
• Development of people processes and technology

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Opportunities for collaborationcaSPR

• SIGs and projects
• Expand areas of the model with representations
  specific to the area of expertise
• AE
• Lab
• Reporting
• Individuals
• Assist in instance diagram development
• Develop behavioral models and business rules
• Assist in definition review and harmonization
• We ALL benefit from a SINGLE protocol
  representation for interoperability. This is it!
  Lets all work together to make it happen!

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Next steps in the SPR project our tasks

• caBIG/HL7/CDISC Structured Protocol
  Representation
• Dissemination and presentationroad show
• Presentation of the model to caBIG April 10th
• Presentation of the model to HL7 May 2nd
• Presentation of the model to CDISC middle/end of
  May
• Development and implementation of model
  versioning control and collaboration processes
• People and technical processes to be finalized
• gForge site beta to be moved to open access
• Need collaborators and testers of the site and
  model
• Incorporation of informal comments and correction
  of known model problems
• Next core modeling session end of May/early June

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Next steps in the SPR project

• Model development needs
• Review class and attribute definitions
• Assistance with instance diagrams and examples
• Requirements gathering for new functionality and
  subdomains
• New classes and attributes
• New areas around the life-cycle of the clinical
  trial protocol
• Application development needs
• Adopters of caPRI testing and improvement
• Development of business rules and enhanced
  functionality
• Evaluation of the architecture is the right
  approach?
• Developers of new modules
• Specification of UML classes, attributes and CDEs
• Early prototyping of applications and model
  extensions

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Next steps in the SPR project

• Integration within CTMS and across caBIG
• SIGs should be the leads in the requirements and
  testing of the parts of the model that they have
  expertise in
• AE
• Lab
• Reporting
• Financial
• Other workspaces activities will touch on the SPR
• Tissue banking and pathology tools
• Will need input from vocabulary, CDE, and
  architecture groups

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The Clinical Trial Lifecycle
ResearchDevelopment
Pre-Trial Setup
PatientEnrollment
New IdeaGeneration
PatientManagement
DataAnalysis
Reporting Administration
Financial Billing
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The Clinical Trial Life Cycle
Register protocol
1
Internal tracking (IRB,PRC, fiscal, etc)
2
PI protocol authoring
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CT registry to disseminate information
3
Custom report generation
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Data mining
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Pt eligibility determination
4
Trial results repository
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Pt registration
5
Statistical analysis
Patient Treatment calendar
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Custom case report forms
Financial and billing information
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Summary 4 reporting
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Budgeting calendar
CDUS reporting
Pt laboratory information
Adverse event reporting
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Lets Get Busy!Fridsma_at_cbmi.pitt.edu
caBIG.nci.nih.gov