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The cancer Biomedical Informatics Grid caBIG: Enabling the patientcentric molecular medicine revolut

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Title: The cancer Biomedical Informatics Grid caBIG: Enabling the patientcentric molecular medicine revolut


1
The cancer Biomedical Informatics Grid (caBIG)
Enabling the patient-centric molecular
medicine revolution
  • Ken Buetow
  • NCICB/NCI/NIH/DHHS

2
NCI biomedical informatics
  • Goal A virtual web of interconnected data,
    individuals, and organizations redefines how
  • research is conducted
  • care is provided
  • patients/participants interact with the
    biomedical research enterprise

3
cancer Biomedical Informatics Grid (caBIG)goals
  • 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

4
caBIG a new way of doing business
  • Coordinated development
  • Active management
  • Community directed
  • Common services

5
Boundaries and Interfaces
  • focus on boundaries, interfaces, how things fit
    together,
  • not on the internal details of how theyre built
    assume that will be diverse changing

6
cancer Common Ontologic Representation
Environment (caCORE)
  • Information integration
  • Cross-discipline reasoning

biomedical objects
common data elements
controlled vocabulary
7
caBIG infrastructure joins diverse data within
an organization
8
caBIG will facilitate sharing of infrastructure,
applications, and data
9
caBIG networks the componentsof the cancer
enterprise
Local network
10
caBIG deliverables
  • Componentized, standards-based Clinical Trials
    Management System
  • e-IND filing/regulatory reporting with FDA
  • Electronic management of trials
  • Integration of diverse trials
  • Tissue Management System
  • Systematic description and characterization of
    tissue resources
  • Ability to link tissue resources to clinical and
    molecular correlative descriptions
  • Plug and Play analytic tool set
  • microarray
  • proteomics
  • pathways
  • data analysis and statistical methods
  • gene annotation
  • Diverse library of raw, structured data

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
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
13
caBIG Products and Data
  • caArray Cancer microarray management system
  • C3D - Trials data capture application
  • Structured Protocol Representation Prototype -
    Standardized clinical trial protocol model
  • caWorkbench - Microarray analysis suite
  • caTIES - Automated free-text pathology data
    extraction tool

Q1
  • caCore Curriculum - Essential training on caBIG
    infrastructure
  • Gene Ontology Miner (GOMiner) - Tool for
    aggregate analysis of gene sets
  • caTISSUE Core Prototype - Database and specimen
    tracking system
  • caTISSUE Prototype - Biological annotation and
    mapping system for specimens
  • C3PR - Clinical trial participant registry tool

Q2
  • RProteomics - MALDI-TOF proteomics analysis tool
  • caGRID Architecture Prototype

Q3
  • Distance Weighted Discrimination - Microarray
    data analysis integrator
  • Cancer Molecular Pages Prototype - Cancer gene
    annotation with web-based visualization
  • Magellan - Tool for the analysis of heterogeneous
    data types (e.g., microarray)
  • Visual and Statistical Data Analyzer (VISDA) -
    Multivariate statistical visualization tool for
    the analysis of complex data
  • FunctionExpress - Tool for integrated analysis
    and visualization of Microarray data
  • Quantitative Pathway Analysis in Cancer (QPACA) -
    Pathway modeling and analysis tool
  • TrAPSS - Disease gene mutation discovery and
    analysis tool
  • Proteomics Laboratory Information Management
    System Prototype
  • Pathways Tool Project - Pathway visualization
    tools
  • HapMap - caBIG accessible map of haplotypes in
    human genome
  • Promoter Database

Q4
Products
  • Zebrafish Microarray Data Microarray data from
    Zebrafish model system for human development
  • Q5 - Proteomics analysis tools
  • Reactome (GKB) Data - Metabolic interactions
    database
  • Under development
  • CTMS/CDUS Reporting Tool
  • Trials Financial Billing Tool
  • Trials Laboratory Interface
  • Gene Pattern Bioinformatics Analysis Workflow

2005
2006
Q1
Q2
Q3
Q4
Data
Q4
  • Curated Cancer Pathways Data - Data sets
    generated from 60 human cancer cell lines
  • Ovarian Tumor Gene Expression Data
  • SEED - Genome annotation
  • NCI-60 Data - Data sets generated from 60 human
    cancer cell lines

Q3
Q1
  • Clnical Trials
  • Cancer microarray data sets
  • Protein Information Resources (PIR) - Protein
    sequence and annotation database
  • Additional Human Cancer and Non-cancer Data Sets

14
Clinical Research IT Infrastructure
External Reporting
Clinical Systems
Clinical Trials
TranslationService
etc.
HL7-v3, Janus
HL7-v3, Janus
HL7- v2.x,other
Labs, EMR, Tissue, etc.
HL7- v3
Adverse Events
ClinicalResearchInformation Exchange
HL7 trans-actionaldatabase
HL7/CAM SDK
Protocol Authoring
FDA
Participant Registry
SPONSOR
RDC
NCI
Clinical Data Mgmt
other
PatientHealthRecord
ResearchDataWarehouse
De-identification Services
15
C3PR Participant Registration
16
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17
Clinical Research Information Exchange (CRIX)
  • Electronic submissions
  • Investigator Registry
  • eIND
  • eNDA
  • eBLA
  • Controlled Data Sharing

18
caIMAGE Cancer Images Database
  • caIMAGE allows researchers to submit and retrieve
    images and annotations.
  • Images are streamed for efficient access.
  • Researchers can search images based on tissue and
    diagnosis and experiment information.
  • Use of common terminology originating from the
    NCI Enterprise Vocabulary Server (EVS).

19
caTISSUE Core Register Specimen Group
20
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21
Pathway Database
  • Enhance value of imperfect, but available,
    pathway knowledge
  • Make biological assumptions explicit
  • Combine sources of data (e.g. KEGG, BioCarta,
    ...)
  • Merge data from separate pathways
  • Build a causal framework to support (future)
    quantitative simulation/analysis

22
repositories
Gene Expression Data
Tissue Bank
Research Center
caCORE - caBIO - caDSR - EVS
NCICB
Data Mart
Clinical Data
Gene Expression Data
  • Data Services
  • Analytical Services
  • Annotation Services
  • Service Advertisement
  • Service Discovery
  • Service Query
  • Semantic mapping
  • Security Services

Clinical Data
Proteomics Data
Analysis Tools
Research Center
Genomics Data
23
REMBRANDT Building a robust translational
research framework for brain tumor
studiesREpository of Molecular BRAin Neoplasia
DaTa
http//rembrandt.nci.nih.gov
24
Rembrandt Knowledgebase
caIntegrator -DataMart
Expression array data
Better understanding Better treatments
Clinical data
caBIG Analytic Tools
25
Rembrandt Application - Homepage
  • Highlights
  • Web-based application
  • Secure login

26
Gene Expression Query page
  • Searchable Fields
  • Gene symbol
  • Differential Fold Change (between tumor group
    and Normal group)
  • Chromosomal Region (Cytoband or bp position)
  • Clone ID/Probe Set ID
  • GO Classification
  • Pathways
  • Array platform
  • (Oligo vs cDNA arrays)
  • Clone Location
  • (for cDNA arrays)

27
Group Multiple Queries
  • Combine different queries
  • Gene expression queries can be grouped with
    Clinical and Comparative Genomic queries
  • Queries are validated before submission

28
Survival plot
29
Gene Expression plot
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NCRI Strategic Framework for Developing Cancer
Informatics in the UK
  • Approach to creating UK Cancer Informatics
    Platform allowing data flow from all areas of
    cancer research
  • The NCRI Strategic Framework
  • Sets out a national vision for cancer informatics
  • Maps out ongoing activity
  • Provides a focus for future funding
  • Develop coherent approaches to ethics,
    data-sharing etc

43
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44
Sample NCRI and caBIG synergies
DOMAIN WORKSPACE 1 Clinical Trial Management
Systems
CancerGRID, eRDC
DOMAIN WORKSPACE 2 Integrative Cancer Research
MyGrid
DOMAIN WORKSPACE 3 Tissue Banks Pathology Tools
Imaging and Pathology Project
DOMAIN WORKSPACE 4 Imaging
E-DiaMoND projects
CROSS CUTTING WORKSPACE 1 Vocabularies Common
Data Elements
CLEF Services
CROSS CUTTING WORKSPACE 2 Architecture
Platform Reference Model
45
acknowledgements
  • NCICB
  • Peter Covitz
  • Sue Dubman
  • Leslie Derr
  • Mary Jo Deering
  • Carl Schaefer
  • Mervi Heiskanen
  • Denise Hise
  • Kotien Wu
  • Frank Hartel
  • LPG/CCR
  • Michael Edmundson
  • Bob Clifford
  • Cu Nguyen

http//ncicb.nci.nih.gov http//cmap.nci.nih.gov h
ttp//caBIG.nci.nih.gov
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