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Cancer Biomedical Informatics Grid™ (caBIG TM )

The Cancer Biomedical Informatics Grid™ (caBIG™) 2006 CODATA Conference Beijing, China Mary Jo Deering , Ph.D. Director, Informatics Dissemination NCI Center for Bioinformatics. Cancer Biomedical Informatics Grid™ (caBIG TM ).

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Cancer Biomedical Informatics Grid™ (caBIG TM )

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  1. The Cancer Biomedical Informatics Grid™ (caBIG™)2006 CODATA ConferenceBeijing, China Mary Jo Deering , Ph.D.Director, Informatics DisseminationNCI Center for Bioinformatics

  2. 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

  3. Cancer Biomedical Informatics Grid™ (caBIGTM) • caBIG™ infrastructure and tools are widely applicable outside cancer • caBIG™ components may be used by anyone

  4. caBIG™ principles • Open source • Open access • Open development • Federated

  5. caBIG™’s Informatics Core

  6. caBIG™ Operational Structure

  7. 2006 Clinical Trial Tools Development Activities • caAERS • Patient Study Calendar • Lab Data Hub • Making other CTMS systems caBIG compatible

  8. 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 Lifecycle Management ClinicalResearchInformation Exchange HL7 trans-actionaldatabase HL7/CAM SDK Adverse Events FDA Participant Registry SPONSOR EDC NCI Clinical Data Mgmt other PatientHealthRecord ResearchDataWarehouse De-identification Services

  9. Integrated Cancer Research • Microarray Repositories • Data Analysis & Statistics • Informatics for Proteomics • Genome Annotation • Pathways Tools • Translational Tools • Population Sciences and Cancer Control

  10. 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

  11. caTISSUE Core: Register Specimen Group

  12. 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).

  13. 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

  14. Interoperability ability of a system to and access use • the parts or equipment of another system Syntacticinteroperability Semanticinteroperability

  15. S E C U R I T Y Bioinformatics Objects Common Data Elements Enterprise Vocabulary caCORE

  16. Professional Documentation

  17. 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

  18. 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.

  19. Test bed Infrastructure caGrid 0.5 Test Bed

  20. Cancer Biomedical Informatics Grid™ (caBIGTM) • caBIG™ infrastructure and tools are widely applicable outside cancer • caBIG™ components may be used by anyone

  21. 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

  22. Additional Background and Detail • The following slides were not included in the presentation.

  23. 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

  24. 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

  25. Strategic Level Workspaces 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 tutorials, workshops, and training programs. Strategic Planning Assists in identifying strategic priorities for the development and evolution of the caBIGTM effort.

  26. REMBRANDT: Building a robust translational research framework for brain tumor studiesREpositoryof Molecular BRAin Neoplasia DaTa http://rembrandt.nci.nih.gov

  27. SNPArray data Proteomics data Rembrandt Knowledgebase caIntegrator -DataMart Expression array data Better understanding Better treatments Clinical data caBIG Analytic Tools

  28. 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

  29. SEMANTIC SEMANTIC SEMANTIC SYNTACTIC caBIG Compatibility Guidelines

  30. Common Data Elements • 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

  31. 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

  32. 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

  33. 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

  34. caCORE Architecture Clients Middleware Data HTTP Clients A P I Web Application Server Biomedical Data Interfaces Java SOAP XML A P I SOAP Clients Common Data Elements Domain Objects [Gene, Disease, etc.] Domain Objects [Gene, Disease, Agent, etc.] Data Access Objects A P I Perl Clients Enterprise Vocabulary Data Access Objects A P I Java Applications Authorization

  35. 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

  36. 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

  37. Mobius Globus BPEL GRAM Globus myProxy OGSA-DAI Globus Toolkit GSI CAS caCORE Globus caGrid Service-Oriented Architecture Functions Management Schema Management Metadata Management ID Resolution Workflow Security Resource Management Service Registry Service Service Description Grid Communication Protocol Transport OGSA Compliant - Service Oriented Architecture

  38. 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.

  39. 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

  40. 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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