Translational Research Session Facilitating Translational Research using the caGrid

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Translational Research Session Facilitating
Translational Research using the caGrid

• Rakesh Nagarajan
• Washington University/Siteman Cancer Center
• Smita Hastak
• ScenPro, Inc.

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Current Status of caBIGTM Tools
Proteomics LIMS
GOMiner
SEED
Q5
caTissue CAE
TrAPSS
caFE
DWD
GenePattern
RProteomics
PIR
caArray
Cancer Molecular Pages
caTIES
caTissue Core
VISDA
geWorkBench
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Current Status of caBIGTM Tools
Proteomics LIMS
caGrid
GOMiner
SEED
Q5
caTissue CAE
TrAPSS
caFE
DWD
GenePattern
RProteomics
PIR
caArray
Cancer Molecular Pages
caTIES
caTissue Core
VISDA
geWorkBench
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Current Status of caBIGTM Tools
?
Proteomics LIMS
caGrid
GOMiner
SEED
Q5
caTissue CAE
TrAPSS
caFE
DWD
GenePattern
RProteomics
PIR
caArray
Cancer Molecular Pages
caTIES
caTissue Core
VISDA
geWorkBench
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Barriers to Usability of caBIGTM Tools

• There are no user interfaces that can leverage
  and orchestrate these tools on the caGrid
• caB2B
• caTRIP
• The MAJORITY of CDEs created by the information
  models of these tools are distinct and are not
  shared. Thus, the MAJORITY of applications are
  NOT currently semantically interoperable

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Barriers to Usability of caBIGTM Tools
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Addressing the Semantic INOPERABILITY Barrier

• CTMS
• Harmonizing application specific models to BRIDG

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CTMS Progress to Date

• CTMS Models
• 1. BRIDG Model
• 2. Project Specific Models
• Lab Model
• PSC
• Relationship between BRIDG and project models

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Models from CTMS WS BRIDG Model

• BRIDG a Biomedical Research Integrated Domain
  Group Model
• An analysis model of the shared semantics of
  regulated clinical trials research
• The goal is to provide the foundation to achieve
  semantic interoperability for application and
  message development in HL7, caBIG, and CDISC
• A common domain model for the caBIG CTMS
  workspace projects modeling efforts
• BRIDG Status
• The model is not complete, and harmonization and
  adoption requires participation and contribution
  to BRIDG from others
• The model is new and is changing, so
  harmonization and adoption requires flexibility
  and change
• It is work in progress and is developed by the
  stakeholders of the BRIDG model

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Models from CTMS WS BRIDG Model

• Model has a HL7 like basic four skeleton
  concepts
• Entity (green classes)
• Role (yellow classes)
• Participation (blue classes)
• Activity (red classes)

A physical thing, group of physical things or an
organization capable of participating in Acts,
while in a role.
A record of something that is being done, has
been done, can be done, or is intended or
requested to be done.
A competency of the Entity playing the Role as
identified, defined, guaranteed, or acknowledged
by the Entity that Scopes the Role.
An association between an Act and a Role with an
Entity playing that Role. Each Entity (in a
Role) involved in an Act in a certain way is
linked to the act by one Participation-instance.
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Framework of BRIDG Model
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Example of the framework concepts
Example 1 A Person in a Role of an Investigator
Participating as a StudyInvestigator in a
Study Example 2 A Person in a role of a
Participant participating as a ResearchSubject
in a Study
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Models from CTMS WS Project Specific Models

• Lab Domain Model (caXchange) -- The overall goal
  of this project is to build a hub system that can
  be adapted and extended to multiple data formats.
  It also involves building a model to represent
  the patient lab data that could be exchanged
  between cancer centers via the HL7 v3 CT Lab
  message
• Patient Study Calendar Model (PSC) --The purpose
  of this project is to develop a well defined and
  automated Patient Study Calendar that can be
  implemented in multiple clinical trial sites
• Adverse Event Reporting Model (AERS) -- The
  purpose of this project will be to develop and to
  deploy an Adverse Events Reporting system that is
  nationally scalable with a robust architecture to
  meet the needs of the caBIG community. 
• Cancer Clinical Central Patient Registry Model
  (C3PR) The purpose of this project will be to
  develop, deploy and adopt the next release of the
  Cancer Clinical Central Patient Registry (C3PR)
  application. 

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Patient Study Calendar Model

• Objective The purpose of this project is to
  develop a well defined and automated Patient
  Study Calendar that can be implemented in
  multiple clinical trial sites 
• PSC model was built by leveraging some core BRIDG
  concepts
• Model recently went through BRIDG harmonization
  process
• The model added many new concepts to the BRIDG
  model (planned and scheduled activities,
  calendars, etc.)
• Currently in semantic integration process of
  caBIG
• Scheduled for completion Mid-December 2006

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Relationship of BRIDG modelto CTMS Project models

• PSC and Lab models were built by leveraging some
  of the core concepts of BRIDG model
• caAERS model in phase 1 was also built from HL7
  and BRIDG core classes
• C3PR will also be built by using BRIDG classes,
  when appropriate
• BRIDG Harmonization Process
• Processes in place on how to build BRIDG based
  models and generate BRIDG harmonizable artifacts
  (artifacts include both, static and dynamic
  models)
• When complete the project models are harmonized
  with BRIDG. Very often this results in changes
  and enhancements to the BRIDG model as well as to
  the project model
• During harmonization the focus is on harmonizing
  the semantics of the common concepts and
  developing consensus around them
• BRIDG model is use case driven, the project
  models bring the use cases or new areas for
  further development of the BRIDG model (e.g., PSC
  introduced the concepts of planned and scheduled
  activities Lab and CTOM introduced performed
  activities, etc.)

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Model building in BRIDG environment
New classes, attr. associations
Develop project model Annotate, refine
concepts, etc.
Complete model and take to BRIDG harmonization
Borrow Core BRIDG Concepts as beginner classes
BRIDG an analysis model
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BRIDG - Domain Analysis Model
Implementation Specific Models
Patient Study Calendar
Lab Model/caXchange
CTOM
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Implementation Independent Domain Analysis Model
--BRIDG
Implementation Specific Models
Patient Study Calendar
Lab Model/caXchange
CTOM
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BRIDG - Domain Analysis Model
Implementation Specific Models
Patient Study Calendar
Lab Model/caXchange
CTOM
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Addressing the Semantic INOPERABILITY Barrier

• CTMS
• Harmonizing application specific models to BRIDG
• ICR
• Genomic Identifier CDEs
• TBPT

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TBPT Applications

• caTissue Core
• Biospecimen banking informatics system
• caTIES
• Concept coding pathology reports
• caTissue CAE
• Annotating biospecimens using AP LIS, CP LIS,
  tumor registry, etc.

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Addressing the Semantic INOPERABILITY Barrier

• CTMS
• Harmonizing application specific models to BRIDG
• ICR
• Genomic Identifier CDEs
• TBPT
• Participant -gt Accession -gt Specimen backbone
• VCDE
• Large Scale Harmonization SIG- Backbone Model

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Backbone Model
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Backbone Model
ICR
ICR-TBPT Links
TBPT
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Backbone Model ICR
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Backbone Model TBPT
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Conclusions and Questions

• A basic level of interoperability has been
  proposed for applications within the ICR, TBPT,
  and CTMS workspaces.
• The Backbone Model proposes SOME interlinks
  between ICR and TBPT models
• How will TBPT and ICR models interoperate with
  CTMS models?
• What are the common classes or touch points?

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Touch Points

• Participant/Patient
• Biospecimen
• Protocol
• Study Calendar
• Consent
• Annotations
• Discrete clinical trials data
• Lab Values
• Treatment