caBIG, an Open Platform for Interoperable Biomedical Informatics

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caBIG, an Open Platform for Interoperable
Biomedical Informatics

• R. Mark Adams, Ph.D.caBIG Program Manager
• Booz Allen Hamilton

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Molecular Medicine Personalized Approaches
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Challenges Biologic Complexity

• Cancers biological complexity requires a
  multi-dimensional study of its pathways and
  mechanisms.

Source Muller Scherle, Nature Reviews Cancer
6613 (2006).
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Challenges Researcher Isolation

• Traditional incentives for researchers discourage
  collaboration.

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Challenges Technology Disconnect

• IT systems were either not connected, ill
  equipped or non-existent.

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Scientific Information Exchange
17th Century

• Royal Society of London
• Oldest learned society (1660)
• Oldest scientific journal (1665)

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caBIGNCIs Platform for Molecular Medicine
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caBIG Vision

• A virtual web of interconnected data,
  individuals, and organizations redefines how
  research is conducted, care is provided, and
  patients / participants interact with the
  biomedical research enterprise

Next generation World Wide Webof biomedical
research
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caBIG Mission

• Connect the cancer research community through a
  shareable, interoperable infrastructure
• Deploy and Extend standard rules and a common
  language to more easily share information
• Build or adapt tools for collecting, analyzing,
  integrating and disseminating information
  associated with cancer research and care

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caBIG Principles

• The principles driving caBIG are
• Open Source
• Open Access
• Open Development
• Federated Model

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caBIG Imperatives
Integrate the biological and clinical silos
Integrate IT infrastructure, software and data
Integrate institutions and people
Address the complexity of cancer
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caBIG Connects the Cancer Community
Researchers, Clinicians, Patients
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caBIG From Concept to Reality

• Expanding the Network
• More caBIG compatible systems and tools
• Resources for adoption and support
• New partners from IT and biomedicine
• Extension to other health categories

2007
2006

• Delivering Software Tools and caGrid
• 40 software products delivered
• caGrid 1.0 launched December 18th
• 900 active participants at 80 institutions
• New partnerships private sector, regions,
  Federal agencies

• Establishing Connectivity
• Connectivity achieved between pilot nodes of
  caGrid
• Pre-existing software retrofitted for caBIG
  compatibility
• caBIG compatibility embedded into NCI Advanced
  Technology programs, Cancer Centers, and external
  product development activities

2005
2004

• Building Community
• caBIG pilot launched - February 2004
• Project plans developed and Working Groups
  established
• Standards conventions determined
• First generation software tools developed

2003

• NCI studies the IT challenges and develops
  strategic plan for a large-scale bioinformatics
  network

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The caBIG Pilot Phase

• An unprecedented effort to connect people,
  organizations, and data throughout the cancer
  research community
• 190 participating organizations
• 300 software components
• 40 end-user applications in discovery, clinical
  trials management, biospecimen management, etc.
• caGrid providing data transmission network that
  connects everyone
• 43 Cancer Centers actively participating in
  caBIG deployment program
• 45 peer-reviewed publications about caBIG

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caBIG into the Future
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How to Leverage caBIG for Your Organization

• Organizations can leverage the NCIs major
  investment in caBIG through the following
• Access the full capabilities of caBIG, including
  software, data standards, training,
  documentation, and support
• Apply caBIG to achieve bench-to-bedside-to-bench
  molecular medicine
• Apply caBIG beyond cancer to other diseases

By applying caBIG technology, you can accelerate
the adoption of personalized medicine and improve
patient outcomes
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Grid of Grids
Bilateral Negotiations
caGrid
NCRI ONIX
NHLBI Grid (CVRG)
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Addressing real world issues
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• caBIG In Action

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Molecular Medicine as a Complex Continuum
Molecular Medicine
Imaging
Clinical Research
Pathology
Molecular Biology
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The People
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The People
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The People
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The People
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The Software Tools
Clinical TrialManagement

• Patient Study Calendar (PSC)
• Cancer Central Clinical Patient Registry (C3PR)
• Cancer Central Clinical Database (C3D)

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The Software Tools
Imaging

• National Cancer Imaging Archive (NCIA)

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The Software Tools
Tissue Banking

• caTissue
• caTIEs
• Clinical annotations

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The Software Tools
Molecular Profiling

• caARRAY/geWorkbench
• caIntegrator
• Cancer Translational Informatics Research
  Platform (caTRIP)

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Deploy Three Bundles
1. Clinical Trials Management Systems (CTMS)
3. Security / Data Sharing Framework
2. Biomedical Informatics and caGrid

• Decision framework for evaluating sensitivity of
  data and appropriate access terms
• Model provisions for IRB applications, data use
  agreements, MTAs, etc.
• Security policies and procedures for caGrid-wide
  authentication and authorization
• Web-based information products for various
  institutional constituencies

• Center deploys a functional caGrid node
• Center uses a caGrid software application
• Center has an accessible caGrid node

• Electronic Management of Clinical Trials
• Uses of Common Data Elements (CDEs)
• Specified subset of clinical data electronically
  available

Deployment Supported through a Range of
Programmatic Services
CBIIT SupportActivities
Knowledge Centers
Designated Support Contractors
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caBIG and Clinical Trials

• Sample capabilities and tools
• Adverse event management (caAERS)
• Clinical data exchange (caXchange)
• Study participant calendar (PSC)
• Study participant registry (C3PR)
• Virtual clinical data warehouse (CTODS)
• caBIG-compatible systems architecture (caGrid)
• Integration with caBIG-compatible data
  management systems

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caBIG and Life Sciences

• Sample capabilities and tools
• Biobanking management systems (caTissue
  Core)
• Virtual clinical data warehouse (CTODS)
• Genome-wide data management system(caGWAS)
• In vivo image repository (NCIA)
• Microarray data management system (caArray)
• Microarray gene expression and sequence data
  management (geWorkbench)
• caBIG-compatible systems architecture (caGrid)

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Data Sharing and Security

• Sample resources
• caBIG Policies
• Processes and Best Practices
• Model Documents

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caBIG Support Resources
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Goal

• Fifty percent of the Cancer Centers using caBIG
  within the next year

all Cancer Centers on pathway
to caBIG compatibility within 3 years.
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caBIG Into the Future

• caBIG the Early Days
• The caBIG Community
• Standards, Tools and Infrastructure

• caBIG Today and Tomorrow
• Expand Community of Stakeholders
• Drive the development and adoption of
  interoperable tools, standards and infrastructure
  to facilitate data sharing
• and integration
• Enable Personalized Molecular Medicine

• Expanding caBIG Needs
• Facilitate the widespread adoption of caBIG
  standards, tools and infrastructure
• Expand the support structure for end users
  beyond the Workspaces, caBIG Program Staff and
  NCI

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Defining the Enterprise Support Network (ESN)
A collection of diverse organizations that, with
guidance from the NCI, caBIG Program staff, and
caBIG workspaces, will expand and support the
caBIG community by providing appropriate
services, mentoring and expertise
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caBIG Enterprise Support Activities
Knowledge Centers
Designated Support Contractors
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A Look At caBIG Knowledge Centers

• Established at institutions with demonstrated
  expertise in a specific area of focus or domain
• Web-based environment for education, outreach,
  training, and deployment needs to the caBIG and
  broader cancer enterprise
• Key services include
• Domain Expertise
• Community Outreach
• Web-Based Support
• Repository of domain-specific tools,
  documentation, policies, standards

caGrid Clinical Trials Management Systems Data
Sharing and Intellectual Capital Molecular
Analysis Tools Tissue/Biospecimen Banking and
Technology Tools Vocabulary
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A Look At caBIG Support Service Providers

• Successful applicants will be granted a limited
  license to NCIs caBIG program trademarks,
  adequate to
• Identify the applicant as a caBIG Support
  Service Provider
• Market and communicate the caBIG Support Service
  Providers support services.
• NCI has full discretion to determine the number
  of providers selected to enter into negotiations
  to secure a license to use the caBIG trademarks.

Help Desk Support Adaptation and Enhancement of
caBIG-Compatible Software Applications Deployment
Support for caBIG Software Applications Document
ation and Training Materials and Services
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• caBIG Tomorrow

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Future of caBIG
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Make no little plans, they have no magic to stir
mens blood and probably themselves will not be
realizedD.H. Burnham, architect (Chicago) 1901
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Keeping our Priorities in Order
My friends, you and I are tasked with answering
the call of every patient, every survivor, every
caregiver, every friend, and every loved one. We
are privileged to be their beacons of honesty,
support, and hope. Dr. John Niederhuber,
M.D.Director, National Cancer Institute 2006
meeting American Association of Cancer Research
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caBIG Power of Connection
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caBIG in ActionThe Cancer Genome Atlas Project
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The Cancer Genome Atlas (TCGA) A 3-year pilot
project of the National Cancer Institute (NCI)
and the National Human Genome Research Institute
(NHGRI)to increase our comprehensive
understanding of the genetic basis of cancer
It is anticipated that TCGAsintegrated database
of molecular and clinical informationwill
provide scientists unprecedented opportunities to
discover and develop a new generation of targeted
diagnostics, therapies, and preventives for
cancer.
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Challenge One Connecting multiple sources,
experiments, and data types
Three forms of cancer glioblastoma
multiforme(brain) squamous carcinoma(lung) s
erouscystadenocarcinoma(ovarian)
12 Organizations Biospecimen CoreResource 7
Cancer GenomicCharacterization Centers 3
GenomeSequencingCenters Data Coordinating Center
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Challenge Two Empowering researchers to query
increasingly complexlayers of cancer biology,
from gene to clinical phenotype, as a whole
ClinicalOutcomes
Gene
Genome
Genomes
Pathways
All from their computer
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A Single Web-Based Portal for All Analyses
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A Single Web-Based Portal for All Analyses
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A Single Web-Based Portal for All Analyses
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A Single Web-Based Portal for All Analyses
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Task Gene Expression and Clinical Outcomes

• From TCGA Specific Needs Mapping possible
  connections between expression, sequence, and/or
  clinical data patterns
• Through the CMA Portal, users can conduct a wide
  range of analyses that link clinical outcomes to
  gene expression, genetic variation and copy
  number alteration

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Gene View
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Gene Expression Analyses
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Gene Expression Analyses Related to Clinical
Outcome
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Gene Variation Analyses
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Gene Variation Analyses
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Task Gene Expression and Clinical Outcomes

• From TCGA Specific Needs Identify non-serial
  linkage and/or networks between groups of genes,
  pathways or genomic regions based on partition
  clustering of clinical and genomic level data
• Through the CMA Portal, users can analyze groups
  of genes in the context of their genomic context,
  and make genome-clinical outcome correlations

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Genome Analyses
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Genome Analyses
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Genome-Clinical Outcome Correlation
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Task Gene Expression and Clinical Outcomes

• From TCGA Specific Needs Finding correlations
  between specific expression patterns (and/or
  other genomic level data) and distinct clinical
  stages or aspects of a cancer
• Through the CMA Portal, users can carry out a
  range of high-level analysis, making use of
  existing workflows that integrate a range of
  informatics tools and outside data resources.
  These workflows can be stored, recalled and
  potentially shared with colleagues.

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High Order Analyses
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High Order Analyses GenePattern
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High Order Analyses GenePattern
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High Order Analyses Pathways
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High Order Analyses Pathways
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High Order Analyses Pathways