cancer biomedical informatics grid™ (cabig tm )
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The Cancer Biomedical Informatics Grid™ (caBIG™)
2006 CODATA ConferenceBeijing, China
Mary Jo Deering , Ph.D.Director, Informatics DisseminationNCI Center for Bioinformatics
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Cancer Biomedical Informatics Grid™ (caBIGTM)
• Common, widely distributed infrastructure permits research community to focus on innovation
• Shared vocabulary, data elements, data models facilitate information exchange
• Collection of interoperable applications developed to common standards
• Raw published cancer research data is available for mining and integration
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Cancer Biomedical Informatics Grid™ (caBIGTM)
• caBIG™ infrastructure
and tools are widely
applicable outside cancer
• caBIG™ components may be used by anyone
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caBIG™ principles
• Open source
• Open access
• Open development
• Federated
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caBIG™’s Informatics Core
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caBIG™caBIG™
caBIGTM Architecture WorkspacecaBIGTM Architecture Workspace
caBIGTM Vocabularies and Common Data Elements WorkspacecaBIGTM Vocabularies and Common Data Elements Workspace
Strategic Planning
Workspace
Strategic Planning
Workspace
Training Workspace
Training Workspace
Integrative Cancer
Research Workspace
Integrative Cancer
Research Workspace
In VivoImaging
Workspace
In VivoImaging
Workspace
Tissue Banks &
Pathology Tools
Workspace
Tissue Banks &
Pathology Tools
Workspace
Data Sharing & Intellectual
Capital Workspace
Data Sharing & Intellectual
Capital Workspace
Clinical Trials Mgmt
Systems Workspace
Clinical Trials Mgmt
Systems Workspace
caBIG™ Operational Structure
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2006 Clinical Trial Tools Development Activities
• caAERS
• Patient Study Calendar
• Lab Data Hub
• Making other CTMS systems caBIG compatible
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Clinical Research IT Infrastructure
Clinical Systems
De-identificationServices
Labs,EMR,
Tissue,etc.
ClinicalTrials
ExternalReporting
HL7/CAM
SDK
HL7- v3
HL7-v3,Janus
ClinicalData Mgmt
EDC
Adverse Events
Participant Registry
etc.
TranslationService
FDA
SPONSOR
NCI
other
HL7 trans-
actionaldatabase
ClinicalResearch
InformationExchange
HL7- v2.x,other
ResearchData
Warehouse
HL7-v3,Janus
PatientHealthRecord
Lifecycle Management
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Integrated Cancer Research
• Microarray Repositories
• Data Analysis & Statistics
• Informatics for Proteomics
• Genome Annotation
• Pathways Tools
• Translational Tools
• Population Sciences and Cancer Control
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Tissue Banks and Pathology Tools
• caTISSUE Core (WU) – Core specimen handling and tracking functions
• caTISSUE Clinical Annotation Engine (UPMC) - Annotation of specimens with clinical data
• caTIES (UPMC) - Text extraction and de-identification of surgical pathology reports
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caTISSUE Core:
Register Specimen Group
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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).
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caBIG™ Compatibility
• caBIG™ is all about Interoperability– Key is to create tools for sharing information
• Extensible infrastructure – Expandable and modular software to plug into existing
systems so current development efforts are not wasted
• Ensures partnerships– Encourages relationships between academic, government and
industry
• Evolving– Compatibility guidelines are being translated into certification
procedures
• Compatibility Guidelines at https://cabig.nci.nih.gov/guidelines_documentation
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use access
SemanticSemanticinteroperabilityinteroperability
SyntacticSyntacticinteroperabilityinteroperability
Interoperability
ability of a system to
and
the parts or equipment of another system
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caCORE
Bioinformatics Objects
Enterprise Vocabulary
Common Data Elements
SECURITY
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Professional Documentation
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caCORE Software Development Kit Components
• UML Modeling Tool (any with XMI export)
• Semantic Connector (concept binding utility)
• UML Loader (model registration in caDSR)
• Codegen (middleware code generator)
• Security Adaptor (Common Security Module)
• caCORE SDK generates a caBIG-Silver compliant system
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Grid Technology in caBIGTM
• What is a ‘Grid’
– “A Grid is a system that coordinates resources that are not subject to centralized control using standard, open, general-purpose protocols and interfaces to deliver nontrivial qualities of service.” - Ian Foster Grid Today, July 20, 2002
• Grid Technology supplies two useful components to a network of computers:
– Advertising: Inform the network about the capabilities of new systems
– Discovery: Allow users to find resources that meet their needs.
• The caGrid project is the ‘Grid in caBIGTM’; the actual infrastructure that data and analytical services will use to interoperate.
• The current caGrid is version 0.5; caGrid 1.0 in December.
• The combination of data and analytical service nodes in caBIGTM produced a design that utilizes a variety of standard Grid technologies including the Globus Toolkit and OGSA-DAI, DQP, GRAM, etc.
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Test bed Infrastructure
caGrid 0.5 Test Bed
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Cancer Biomedical Informatics Grid™ (caBIGTM)
• caBIG™ infrastructure
and tools are widely
applicable outside cancer
• caBIG™ components may be used by anyone
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Contact Information
Mary Jo Deering, Ph.D
Director for Informatics Dissemination
NCI Center for Bioinformatics
National Cancer Institute
National Institutes of Health, USDHHS
6116 Executive Blvd. - #403
Rockville, MD 20852
(o) 301-496-3458
(f) 301-480-4222
deeringm@mail.nih.gov
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Additional Background and Detail
• The following slides were not included in the presentation.
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Current caBIG™ community• NCI-designated Cancer Centers (50)
– Academic Centers (integrated into broader biomedical infrastructure)
– Stand-alone (community leaders)
– Community outreach
• NCI Divisions and Programs
• National Institutes of Health
• Other Government Agencies
• Industry
• International Groups – Standards development organizations
– U.K.’s National Cancer Research Institute
• ~900 active participants
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Four Domain Workspaces and two Cross Cutting Workspaces have been launched
DOMAIN WORKSPACE 3Tissue Banks & Pathology ToolsDOMAIN WORKSPACE 3Tissue Banks & Pathology Tools
Provides for the integration, development, and implementation of tissue and pathology tools.
DOMAIN WORKSPACE 2Integrative Cancer ResearchDOMAIN WORKSPACE 2Integrative Cancer Research
Provides tools and systems to enable integration and sharing of information.
DOMAIN WORKSPACE 1Clinical Trial Management SystemsDOMAIN WORKSPACE 1Clinical Trial Management Systems
Addresses the need for consistent, open and comprehensive tools for clinical trials management.
CROSS CUTTING WORKSPACE 2Architecture
CROSS CUTTING WORKSPACE 2Architecture
Developing architectural standards and architecture necessary for other workspaces.
CROSS CUTTING WORKSPACE 1Vocabularies & Common
Data Elements
CROSS CUTTING WORKSPACE 1Vocabularies & Common
Data Elements
Responsible for evaluating, developing, and integrating systems for vocabulary and ontology content, standards, and software systems for content delivery.
DOMAIN WORKSPACE 4ImagingDOMAIN WORKSPACE 4Imaging
Provides for the sharing and analysis of in vivo imaging data.
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Strategic Level Workspaces
Strategic PlanningStrategic PlanningAssists in identifying strategic priorities for the development and evolution of the caBIGTM effort.
TrainingTrainingDeveloping strategies for providing training in the use of the caBIG developed resources including on-line tutorials, workshops, and training programs.
Data Sharing and Intellectual CapitalData 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.
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http://rembrandt.nci.nih.gov
REMBRANDT: Building a robust translational research framework for brain tumor studies
REpository of Molecular BRAin Neoplasia DaTa
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Rembrandt Knowledgebase
Better understanding
Better treatments
Expression array data
Clinical data
SNPArray data
Proteomics data
caIntegrator -DataMart
caBIG Analytic Tools
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caBIGTM Compatibility Guidelines
• The caBIGTM compatibility guidelines are designed to insure that systems designed in a Federated environment are still interoperable on the caBIGTM Grid, both syntactically and semantically
• Since achieving interoperability is a process, caBIGTM recognizes four levels of compatibility, starting from Legacy (not interoperable) through Bronze, Silver and Gold (fully interoperable)
• caBIGTM compatibility is all about interfaces rather than the scientific content of the system
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SYNTACTIC
SEMANTIC
SEMANTIC
SEMANTIC
caBIG Compatibility Guidelines
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• What do all those data classes and attributes actually mean, anyway?
• Data descriptors or “semantic metadata” required
• Computable, commonly structured, reusable units of metadata are “Common Data Elements” or CDEs.
• NCI uses the ISO/IEC 11179 standard for metadata structure and registration
• Semantics all drawn from Enterprise Vocabulary Service resources
Common Data Elements
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Cancer Data Standards Repository (caDSR)
• Basic caDSR unit of metadata information to describe a datum is a Common Data Element or CDE
• Enterprise-class system for storing metadata, with APIs that give runtime access to both metadata and semantics
• Implements the ISO 11179 standard, a flexible model for describing arbitrary metadata
• Used to describe metadata associated with clinical case report forms and UML Models
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Enterprise Vocabulary Services
• Controlled vocabulary resources for caCORE and the cancer research community
• Vocabulary Products and Services
– NCI Thesaurus
– NCI Metathesaurus
– External vocabularies
• NCI Thesaurus - controlled vocabulary source for metadata
– Has excellent coverage of cancer terminology
– Expands based on needs for additional terminology
– Based on concepts rather than terms
– Each concept has a unique identifier or CUI with definitions and synonym
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Data Standards in caBIG™ • The V/CDE workspace is responsible for facilitating the
development and ratification of Data Standards for caBIG™
• Data Standards can be Vocabularies or Common Data Elements (CDEs) with their associated controlled terminology
• A caBIG™ Data Standard is, in effect, a ‘pre-approved’ mechanism for semantically modeling an attribute or series of attributes in a data object. Ideally, having a standard available shortens development time for other projects that need to present such data
• Whenever possible, caBIG™ adopts standards that are derived from other standards bodies (HL7, ISO, USPS, UPU, W3C, etc.) and in general use within our community
• In the last year, the V/CDE workspace has developed a consensus driven mechanism for approving Data Standards and applied it to an increasing number of CDEs
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Java Applications
Data AccessObjects
Web Application Server
Interfaces
Java
SOAP
XML
HTTP Clients
SOAP Clients
DataDataClientsClients
Perl Clients
EnterpriseVocabulary
CommonData
Elements
MiddlewareMiddleware
API
API
API
API
Data AccessObjects
DomainObjects[Gene,
Disease, etc.]
DomainObjects[Gene,
Disease, Agent,etc.]
caCORE Architecture
BiomedicalData
Authorization
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Use cases for caGrid• Advertisement
– Service Provider composes service metadata describing the service and publishes it to grid.
• Discovery– Researcher (or application developer) specifies search criteria
describing a service of interest
– The research submits the discovery request to a discovery service, which identifies a list of services matching the criteria, and returns the list.
• Invocation– Researcher (or application developer) instantiates the grid
service and access its resources
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caGrid 0.5 Services• Data Services
– caBIO: Gene-centric bioinformatics objects
• NCICB-Rockville, MD
– caArray: MAGE-OM compliant microarray repository
• NCICB-Rockville, MD
• Lombardi Cancer Center-Georgetown, DC
– gridPIR: Protein Information Resource
• Lombardi Cancer Center-Georgetown, DC
– caTIES: Text Information Extraction System for pathology reports
• UPMC-Pittsburgh, PA
– SNP500: Polymorphism database with population frequencies
• NCI Core Genotyping Facility-Gaithersburg, MD
– caMOD II: Cancer Model Organism Database
• NCI Mouse Models of Human Cancer Consortium (MMHCC)
• Analytical Service– RProteomics: Statistical analysis of proteomics data
• Duke-Durham, NC
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Grid Communication Protocol
Service Description
Service
Workflow
Service R
egistry
Secu
rity
Metad
ata Man
agem
ent
Reso
urce M
anag
emen
t
Functions Management
ID R
esolu
tion
OGSA Compliant - Service Oriented Architecture
Transport
caGrid Service-Oriented Architecture
Sch
ema M
anag
emen
t GSI
CAS
myProxy
Globus
OGSA-DAIGlobusGRAM
Globus Toolkit
GlobusBPEL
Mobius
caCORE
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Enabling Technology
• The NCI provides freely available enabling technology for caBIGTM compatibility
• These technologies are distributed under a ‘non-viral’ open source license.
• caCORE
– Enterprise Vocabulary Services (EVS)
– Cancer Data Standards Repository (caDSR)
• caCORE Software Development Kit
– When complete process is followed, the outcome is a caBIG ‘Silver’ compliant data system.
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How can my research benefit from caBIG™ Tools?
• Everything developed by the program is open source and freely available
• Training is available at https://cabig.nci.nih.gov/training
• The latest versions of all the software developed as part of the project can be obtained from the caBIG™ project gforge site:
– http://gforge.nci.nih.gov
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caBIG™: Getting Involved
• To get involved with caBIG™:
– Track caBIG™ activities on the NCI’s caBIG™ website, https://cabig.nci.nih.gov/
– Attend caBIG™ Annual Meeting, February 5-7, 2007, Wardman Park Marriott, Washington, DC
– Learn about the existing bioinformatics infrastructure, caCORE, at https://ncicb.nci.nih.gov/core
– Download currently available caBIG™ tools from the caBIG™ website at https://cabig.nci.nih.gov/inventory
– Sign up for the caBIG™ mailing list at http://list.nih.gov/archives/cabig_announce.html
• Please visit the main caBIG™ website for more information: https://cabig.nci.nih.gov/
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