caBIG

1
caBIG Industry Partners MeetingCancer Center
Perspective

• J. Robert Beck, M.D.
• Fox Chase Cancer Center
• Strategic Level Strategic Planning Working Group
  of the Cancer Biomedical Informatics Grid

2
The Knowledge Explosion Challenges to Research

• Small group research -gt Lab notebooks
• Clinical trials individual investigators or
  cooperative groups
• Ad hoc collection of biomedical samples
• All of these are changing!

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What is the caBIG Community?

• A Community of Communities
• Sharing Common Interests
• Data Standards
• Sharable and Interoperable Architectures
• Informatics Tools
• Cancer Research
• To the Ultimate Benefit of Patients

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caBIGs Five Year Mission

• Develop Standards, Tools, and Prototypes
• Bias Toward Action and Interaction
• Easy Methods of Dissemination
• Open Source
• Open Access
• Open Development
• Federation

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A Focus on Interaction
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Scenario, 2008
Cell Type
Small Molecules

• A researcher involved in a phase II clinical
  trial of a new molecularly targeted therapeutic
  for brain tumors observes that cancers derived
  from one specific tissue progenitor appear to be
  strongly affected. The trial has been generating
  proteomic and microarray data. The researcher
  would like to identify potential biochemical and
  signaling pathways that might be different
  between this cell type and other potential
  progenitors in cancer, deduce whether anything
  similar has been observed in other clinical
  trials involving agents known to affect these
  specific pathways, and identify any studies in
  model organisms involving tissues with similar
  pathway activity.

Pathways
Clinical Trials
Animal Models
Therapeutics
Homologous Proteins
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Today vs 2008?

• In 2005 such a study would involve immense
  manual work getting information locally and from
  other sites, precluding the possibility of
  identifying the required data and thus being
  unable to deduce the likely significance of the
  trial observation.

However, with caBIG compliant components now
under development, the researcher would be able
to perform the analysis routinely, with data
flowing through systems and analysis being
automatic. This analysis will yield biomarkers
and potential drug targets gathered from multiple
workspaces and make it possible to develop
treatment modalities faster, less expensively,
and more effective for patients.
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Discovery utilizing caBIG Integrated Cancer
Research Tools
CTMS Workspace
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Overall Goals for caBIGThree-year (mid-2008)

• Develop sufficient research tools and standards
  to have a positive impact on the cancer research
  community, as measured by adoption of relevant
  caBIG principles in project proposals.
• Ensure widespread adoption of developer standards
  so that funded developer projects are operating
  under the Gold standard of compatibility.
• Adopt and use caBIG interoperable tools and
  data sets within the caBIG community.
• Develop mechanisms for engaging and promoting
  caBIG compliant technologies and established
  datasets within the oncology research community.

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Overall Goals for caBIGFive-year (mid-2010)

• Ensure widespread adoption, dissemination, and
  use of caBIG interoperable tools, standards,
  and data sets within the larger cancer community,
  to include the biopharmaceutical industry,
  non-NCI cancer centers, and the national cancer
  research enterprise.
• Begin to see results of caBIG -compliant
  interdisciplinary and inter-institutional
  research affecting clinical oncology care.

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What does caBIG mean to the Cancer Centers?

• Productin CTMS, ICR, Tissue Banking
• Support for large scale collaborative research
• No need to go it alone with bioinformatics or
  other quantitative support tools

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The Workspaces Meet Centers Needs
ICR data sharing
caTIES info extract
caTissue tissue bank
Clinical trials tools are Cancer Centers
caBIGs TOP Priority
All Development activities
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Clinical Trials Management

• Inventory of Tools
• Available now C3D Cancer Central Clinical
  Database
• Available 4th Qtr 2005 Data Mapping Foundation
• Available 1st Qtr 2006 Adverse Events Reporting,
  Protocol Submission Tools and Data Export tools
  for commercial systems
• Pathway for Cancer Centers to implement tools at
  their sites
• Adopters and Working Group roles
• Funded and Volunteer roles and pathway to get
  there
• Developer roles for future projects

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Clinical Trials Management Three Levels of
Interaction Based on Institutional Readiness
Additional Functionality
C3D Adoption
No Existing System
exchange data
New caBIG modules
caBIG Open Source Core Functionality
Existing System Change Imminent
Interoperable caBIG Community
Additional Functionality
Existing System No Change
caBIG compatibility efforts with vendor
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What does caBIG offer the Cancer Center for
Clinical Trials Management?

• Cancer Center Clinical Database or C3D
  available today
• Data Mapping Foundation or caDMF caBIG
  compliant data sharing between centers
  available 4th Qtr 2005
• Adverse Event Reporting or caAERS available 1st
  Qtr 2006
• Clinical Trial Structured Protocol Authoring or
  caSPR available 1st Qtr 2006
• Key is to understand the workflows to support
  clinical trials and choose a starting point for
  use of caBIG tools

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Tools for Translational Research

• caBIG Compatibility Guidelines
• 3 year plan all tool development at Gold level
• Successful Developer-adopter relationships
• Extension to other research areas
• Imaging
• Population Science

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ICR Software Maturity Table
Maturity Level Description
1 Basic research/Design The key concepts for the system have been defined, algorithms outlined, use cases documented, requirements and specification document(s) prepared.
2 Prototype/Proof of Principle A semi-functional system has been implemented for the purpose of getting feedback from potential end-users on the execution of the design.
3 First working implementation (beta) System has gone through at least one round of testing by end users and some feedback has been incorporated. System is in trial use by a limited number of users. Only intended for limited distribution by users in close contact with the development team.
4 Deployed and in use System has gone though a thorough beta test and is deployed and in use at at least one site. Additional sites may deploy the software with possible assistance from the development team. Initial user and developer guides are available. Known defects are documented.
5 Post deployment and maintenance System is readily deployed by any interested party with no assistance from the development team. Known defects are documented. Mature user and developer guides are available as well as training materials.
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Project Name Maturity Level at the end of caBIG Year 1 Project Development caBIG Compatibility Level at the end of caBIG Year 1 Project Developement
Cancer Molecular Pages GUI 4 API 3 Silver Level
FunctionExpress 5 Designed to be Silver Level
GoMiner 4 Silver Level
PIR 3 Silver Level
SEED Analysis 3/4 Readout 2/3 Silver Level Silver Level
TrAPSS 4 Silver Level
Magellan 4
Distance-Weighted Discrimination 3/4 Silver Level
GenePattern Year 1 caBIG mods 3/4 Silver Level
VISDA 4 Silver Level
caWorkbench 3/4 Silver Level
Pathways Tools 4 overall Silver Level
QPACA 3/4 Silver Level
caArray 4 (current release) pre-Silver (current release)
RProteomics 2/3 Gold
Proteomics LIMS 3 Silver

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Data Sharing and Intellectual Capital
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Training Working Group
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Cancer Center Roles in caBIG

• Developer (20 of centers)
• Key is to create an environment for sharing tools
  with other centers
• One of the most important issues is not to ignore
  the need for common data elements and vocabulary
  services
• Adopter (20 of centers)
• Key is to understand the needs at local center
  (and be vocal)
• Dont abandon other development efforts think
  modular
• When adopting tools make sure they talk to
  legacy systems
• Working Group Strategic Planning (60 of
  centers)
• These are not soft roles
• Critical to the success of the program
• White paper development will guide caBIG
  successes
• Make sure to communicate internally to all parts
  of the Cancer Center

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caBIG Compatibility

• What does caBIG compatibility mean to CC
• caBIG is all about Interoperability
• Key is to create tools for sharing info with
  other centers
• Not an easy task due to silo mentality
• CDEs and EVS enable common language and data
  values
• Software design principles ensure cross
  compatibility of developed software
• Extensible infrastructure
• Expandable and modular software to plug in to
  existing systems so current development efforts
  are not wasted
• Scalable so that efficiency is gained by software
  engineering
• Ensures partnerships
• Built on commercial software development
  principles
• Encourages relationships between academia,
  government and industry
• Scalable so that commercial partners can utilize
  open source

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Industry Partners with Cancer Centers

• Plug and Play with caBIG architecture
  requirement for new tool or system adoption
• Take caBIG developed tools at Silver or Gold
  level of compliance, create commercially
  supportable versions thereof and take to market
• Evaluate intellectual property in grid context