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The cancer Biomedical Informatics Grid (caBIG): Enabling the patient-centric molecular medicine revolution

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The cancer Biomedical Informatics Grid (caBIG): Enabling the patient-centric molecular medicine revolution R. Mark Adams, Ph.D. Booz Allen Hamilton – PowerPoint PPT presentation

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Title: The cancer Biomedical Informatics Grid (caBIG): Enabling the patient-centric molecular medicine revolution


1
The cancer Biomedical Informatics Grid (caBIG)
Enabling the patient-centric molecular
medicine revolution
  • R. Mark Adams, Ph.D.
  • Booz Allen Hamilton
  • caBIG Project Manager

2
Talk Agenda
  • caBIG Overview
  • Development of the Program
  • Program Structure and Process

3
Talk Agenda
  • caBIG Overview
  • Development of the Program
  • Program Structure and Process

4
A Focus on Interaction
5
(No Transcript)
6
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.

7
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.

8
cancer Biomedical Informatics Grid
  • Common, widely distributed infrastructure permits
    cancer research community to focus on innovation
  • Shared vocabulary, data elements, data models
    facilitate information exchange
  • Collection of interoperable applications
    developed to common standard
  • Raw cancer research data is available for mining
    and integration

9
Talk Agenda
  • caBIG Overview
  • Development of the Program
  • Program Structure and Process

10
caBIG principles
  • Open source
  • Open access
  • Open development
  • Federated

11
Current caBIG community
  • NCI-designated Cancer Centers (50)
  • Academic Centers (integrated into broader
    biomedical infrastructure)
  • Stand-alone (community leaders)
  • Community outreach
  • Government
  • Industry
  • International Groups
  • gt700 active participants

12
caBIG action plan
  • Establish pilot network of NCI Cancer Center
  • Groups agreeing to caBIG principles
  • Mixture of capabilities
  • Mixture of contributions
  • Expanding collection of participants
  • Establish consortium development process
  • Collecting and sharing expertise
  • Identifying and prioritizing community needs
  • Expanding development efforts
  • Moving at the speed of the internet

13
Common needs helped shape priority areas for the
caBIG pilot activities
Database Datasets
Imaging Tools Databases
Integration
High Performance Computing
Clinical Trial Management Systems
Pathways
Licensing Issues
LIMS
Meeting
Microarray Gene Expression Tools
Tissue Banks Pathology
Proteomics
Remote/Bandwidth
Visualization Front-End Tools
Statistical Data Analysis Tools
Vocabulary Ontology Tools Databases
Integrative Cancer Research
Meta-Project
Common Data Elements Architecture
Center Integration Management
Tissue Pathology Tools
Access to Data
Translational Research Tools
Distributed Data Sharing/Analysis Tools
Staff Resources
Clinical Data Management Tools
0
5
10
15
20
25
30
35
Number of Needs Reported
14
(No Transcript)
15
Four Domain Workspaces and two Cross Cutting
Workspaces have been launched
DOMAIN WORKSPACE 1 Clinical Trial Management
Systems
addresses the need for consistent, open and
comprehensive tools for clinical trials
management.
DOMAIN WORKSPACE 2 Integrative Cancer Research
provides tools and systems to enable integration
and sharing of information.
DOMAIN WORKSPACE 3 Tissue Banks Pathology Tools
provides for the integration, development, and
implementation of tissue and pathology tools.
DOMAIN WORKSPACE 4 Imaging
provides for the sharing and analysis of in vivo
imaging data.
responsible for evaluating, developing, and
integrating systems for vocabulary and ontology
content, standards, and software systems for
content delivery
CROSS CUTTING WORKSPACE 1 Vocabularies Common
Data Elements
developing architectural standards and
architecture necessary for other workspaces.
CROSS CUTTING WORKSPACE 2 Architecture
16
Strategic Level Planning Groups
Data Sharing and Intellectual Capital
Addresses issues related to the sharing of data,
applications and infrastructure both within the
consortium and in the larger cancer research
community.
Training
Developing strategies for providing training in
the use of the caBIG developed resources
including on-line turtorials, workshops, training
programs.
caBIG Strategic Planning
Assists in identifying strategic priorities for
the development and evolution of the caBIG effort.
17
Data Description Infrastructure Overview
  • Client and service APIs are object oriented, and
    operate over well-defined and curated data types
  • Objects are defined in UML and converted into
    ISO/IEC 11179 Administered Components, which are
    in turn registered in the Cancer Data Standards
    Repository (caDSR)
  • Object definitions draw from vocabulary
    registered in the Enterprise Vocabulary Services
    (EVS), and their relationships are thus
    semantically described
  • XML serialization of objects adhere to XML
    schemas registered in the Global Model Exchange
    (GME)

18
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

19
caBIG Compatibility Guidelines
20
(No Transcript)
21
caBIG Deliverables Clinical Trials Management
Systems
  • Componentized, interoperable and standards-based
    Clinical Trials Management Systems, both
    purpose-built and commercial off-the-shelf to
    handle, in an automated fashion, many aspects of
    developing, managing, conducting, and reporting
    Clinical Trials
  • Biomedical Research Integrated Domain Group Model
    (BRIDG)
  • Adverse Events Reporting Tool
  • C3D
  • C3PR
  • caBIG Compatibility evaluation for existing
    commercial tools
  • Harmonization of UML Representations
  • Ontological Representations and Data Elements for
    Clinical Trials
  • Metadata Harmonization

22
caBIG Communications Tools
  • A variety of communications mechanisms are
    available to get informed on and stay up-to-date
    on the program
  • Regular teleconferences- more than 50 a month
  • Face to face meetings
  • LISTSERVs
  • Program Updates
  • Center Directors Letter
  • Virtual Town Hall Meetings
  • and Whats BIG this Week
  • For all of these, see the caBIG Website
    http//caBIG.nci.nih.gov

23
caBIG Interactions with Outside Groups
  • caBIG has representation at a number of
    important outside groups including
  • FDA
  • HL7
  • CDISC
  • Global Grid Consortium
  • W3C
  • etc

24
Talk Agenda
  • caBIG Overview
  • Development of the Program
  • Program Structure and Process

25
caBIG a new way of doing business
  • Coordinated development
  • Active management
  • Community directed
  • Common services

26
The NCIs General Contractor
  • Responsible for coordination of Workspace
    activities
  • Provides funding through contracts to
    participating centers
  • Provides a channel for communication of guidance
    and priorities
  • Provides a measure of participant progress (e.g.,
    contract milestones)
  • Fosters accountability and provides mechanisms
    for conflict resolution

The NCI is investing resources for administration
and support of the caBIG project, decreasing the
burden on the participating community
27
How does caBIG work?
28
How can my Center Participate?
  • Participation in Workspaces
  • Development of Tools
  • Sharing of Data
  • Adoption of Tools
  • etc.
  • The main mechanism is through RFPs issued by the
    Project on relevant topics- Workspace
    participation is a key way to stay abreast of
    relevant opportunities..

29
How can my Center get Funding?
  • Your Center may be already funded- as are 50
    Designated Cancer Centers nationwide
  • The caBIG Point of Contact for your organization
    is a key resource
  • Those with projects that may be of interest to
    the program are encouraged to participate in the
    Workspaces, and be on the project mailing lists
    where RFPs for project activities are distributed

30
How can my Center benefit from caBIG Tools?
  • Everything developed by the program is open
    source and freely available
  • The latest versions of all the software developed
    as part of the project can be obtained from the
    caBIG CVS site
  • http//cabigcvs.nci.nih.gov/viewcvs/viewcvs.cgi/
  • Commercial-grade documentation is provided as
    part of the project, which will be located at the
    project gforge site
  • http//gforge.nci.nih.gov

31
How can I get support for these tools?
  • NCICB Applications Support will coordinate
    support for caBIG tools
  • Live Support Monday Friday 8 am 8 pm Eastern
    Time
  • Telephone support is available Monday to Friday,
    8 am 8 pm Eastern Time, excluding government
    holidays.
  • You may leave a message, send an email or submit
    a support request via the Web at any time.
  • Email ncicb_at_pop.nci.nih.gov
  • Phone 301-451-4384
  • Toll-free 888-478-4423
  • Web http//ncicbsupport.nci.nih.gov

32
A Sample of the caBIG Participant Community
Ohio State University-Arthur G. James/Richard
Solove Oregon Health and Science
University Roswell Park Cancer Institute St Jude
Children's Research Hospital Thomas Jefferson
University-Kimmel Translational Genomics Research
Institute Tulane University School of
Medicine University of Alabama at
Birmingham University of Arizona University of
California Irvine-Chao Family University of
California, San Francisco University of
California-Davis University of Chicago University
of Colorado University of Hawaii University of
Iowa-Holden University of Michigan University of
Minnesota University of Nebraska University of
North Carolina-Lineberger University of
Pennsylvania-Abramson University of
Pittsburgh University of South Florida-H. Lee
Moffitt University of Southern
California-Norris University of
Vermont University of Wisconsin Vanderbilt
University-Ingram Velos Virginia Commonwealth
University-Massey Virginia Tech Wake Forest
University Washington University-Siteman Wistar Ya
le UniversityNorthwestern University-Robert H.
Lurie
9Star Research Albert Einstein Ardais Argonne
National Laboratory Burnham Institute California
Institute of Technology-JPL City of Hope
Clinical Trial Information Service (CTIS) Cold
Spring Harbor Columbia University-Herbert
Irving Consumer Advocates in Research and
Related Activities (CARRA) Dartmouth-Norris
Cotton Data Works Development Department of
Veterans Affairs Drexel University Duke
University EMMES Corporation First Genetic
Trust Food and Drug Administration Fox Chase
Fred Hutchinson GE Global Research
Center Georgetown University-Lombardi IBM Indiana
University Internet 2 Jackson Laboratory Johns
Hopkins-Sidney Kimmel Lawrence Berkeley
National Laboratory Massachusetts Institute of
Technology Mayo Clinic Memorial Sloan
Kettering Meyer L. Prentis-Karmanos New York
University
33
The NCI 2015 challenge goal eliminate
suffering and death due to cancer
When I look into the eyes of a patient losing
the battle with cancer, I say to myself, It
doesnt have to be this way.Dr. A.C. von
Eschenbach, M.D.Director, National Cancer
Institute The Nations Investment in Cancer
Research (2003)
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