The Cancer Biomedical Informatics Grid™ (caBIG™) 2006 CODATA ...

National Cancer Institute The Cancer Biomedical Informatics Grid™ (caBIG™) 2006 CODATA Conference Beijing, China Mary Jo Deering , Ph.D. Director, Informatics Dissemination NCI Center for Bioinformatics National Cancer Institute 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 National Cancer Institute Cancer Biomedical Informatics Grid™ (caBIGTM) • caBIG™ infrastructure and tools are widely applicable outside cancer • caBIG™ components may be used by anyone National Cancer Institute caBIG™ principles • Open source • Open access • Open development • Federated National Cancer Institute caBIG™‟s Informatics Core National Cancer Institute caBIG™ Operational Structure cc a B IG ™ a B IG ™ SS tra te g ic tra te g ic PP la n n in g la n n in g W oo rk s p a c e W rk s p a c e C lin ic aa l C lin ic l TT ria lsM gg m t ria ls M m t SS ys te m s ys te m s W oo rk s p a c e W rk s p a c e In te gg ra tiv e In te ra tiv e C aa n c e r C ncer R ee s e a rc h R s e a rc h W oo rk s p a c e W rk s p a c e In VV iv o In iv o Im aa g in g Im g in g W oo rk s p a c e W rk s p a c e TT is s u e is s u e B aa n k s& B nks & PP a th o lo g y a th o lo g y TT o o ls o o ls W oo rk s p a c e W rk s p a c e TT ra in in g ra in in g W oo rk s p a c e W rk s p a c e D aa taSS h a rin g& D ta h a rin g & In te lle cc tu a l In te lle tu a l C aa p ita l C p ita l W oo rk s p a c e W rk s p a c e cc a B IG T MVV o c a b u la rie saa n dC oo m m o nD aa taEE le m e n tsW oo rk s p a c e a B IG T M o c a b u la rie s n d C m m o n D ta le m e n ts W rk s p a c e cc a B IG T MA rc hh ite c tu reW oo rk s p a c e a B IG T M A rc ite c tu re W rk s p a c e National Cancer Institute 2006 Clinical Trial Tools Development Activities • caAERS • Patient Study Calendar • Lab Data Hub • Making other CTMS systems caBIG compatible National Cancer Institute Clinical Research IT Infrastructure Translation Service HL7v2.x, other HL7v3 HL7/ CAM SDK Clinical Systems Clinical Trials etc. External Reporting HL7-v3, Janus HL7-v3, Janus Lifecycle Management Adverse Events Labs, EMR, Tissue, etc. HL7 transactional database Participant Registry EDC FDA Clinical Research Information Exchange SPONSOR NCI other Clinical Data Mgmt Patient Health Record De-identification Services Research Data Warehouse National Cancer Institute Integrated Cancer Research • Microarray Repositories • Data Analysis & Statistics • Informatics for Proteomics • Genome Annotation • Pathways Tools • Translational Tools • Population Sciences and Cancer Control National Cancer Institute National Cancer Institute National Cancer Institute National Cancer Institute 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 caTISSUE Core: National Cancer Institute Register Specimen Group National Cancer Institute 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). • • • National Cancer Institute National Cancer Institute caBIG™ Compatibility • • caBIG™ is all about Interoperability – – – – Key is to create tools for sharing information Expandable and modular software to plug into existing systems so current development efforts are not wasted Encourages relationships between academic, government and industry Compatibility guidelines are being translated into certification procedures Extensible infrastructure • • • Ensures partnerships Evolving Compatibility Guidelines at https://cabig.nci.nih.gov/guidelines_documentation National Cancer Institute Interoperability ability of a system to access and use the parts or equipment of another system Syntactic interoperability Semantic interoperability National Cancer Institute caCORE S E C U R I T Y Bioinformatics Objects Common Data Elements Enterprise Vocabulary National Cancer Institute Professional Documentation National Cancer Institute 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 National Cancer Institute National Cancer Institute 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. National Cancer Institute Test bed Infrastructure caGrid 0.5 Test Bed National Cancer Institute Cancer Biomedical Informatics Grid™ (caBIGTM) • caBIG™ infrastructure and tools are widely applicable outside cancer • caBIG™ components may be used by anyone National Cancer Institute 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 National Cancer Institute Additional Background and Detail • The following slides were not included in the presentation. 26 National Cancer Institute 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 27 National Cancer Institute Four Domain Workspaces and two Cross Cutting Workspaces have been launched DOMAIN WORKSPACE 1 Clinical Trial Management Systems DOMAIN WORKSPACE 2 Integrative Cancer Research DOMAIN WORKSPACE 3 Tissue Banks & Pathology Tools DOMAIN WORKSPACE 4 Imaging Addresses the need for consistent, open and comprehensive tools for clinical trials management. Provides tools and systems to enable integration and sharing of information. Provides for the integration, development, and implementation of tissue and pathology tools. Provides for the sharing and analysis of in vivo imaging data. Responsible for evaluating, developing, and integrating CROSS CUTTING WORKSPACE 1 systems for vocabulary and ontology content, Vocabularies & Common standards, and software systems for content delivery. Data Elements Developing architectural standards and architecture necessary for other workspaces. CROSS CUTTING WORKSPACE 2 Architecture 28 National Cancer Institute 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. 29 National Cancer Institute REMBRANDT: Building a robust translational research framework for brain tumor studies REpository of Molecular BRAin Neoplasia DaTa http://rembrandt.nci.nih.gov 30 National Cancer Institute Rembrandt Knowledgebase Expression array data caIntegrator DataMart Better understanding SNPArray data Better treatments Clinical data Proteomics data caBIG Analytic Tools 31 National Cancer Institute 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 32 SYNTACTIC SEMANTIC SEMANTIC caBIG Compatibility Guidelines SEMANTIC 33 National Cancer Institute National Cancer Institute 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 34 National Cancer Institute 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 35 National Cancer Institute 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 36 National Cancer Institute 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 37 • • National Cancer Institute caCORE Architecture Middleware A P I A P I A P I Clients Data HTTP Clients Web Application Server Interfaces Java Biomedical Data SOAP Clients SOAP Perl Clients XML Domain Domain Objects Objects [Gene, [Gene, Disease, Disease, etc.] Agent, etc.] Data Access Objects Common Data Elements Java Applications A P I Data Access Objects Enterprise Vocabulary Authorization 38 National Cancer Institute 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 39 National Cancer Institute 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 40 National Cancer Institute caGrid Service-Oriented Architecture Functions Globus BPEL Management Mobius Workflow Resource Management Service GRAM Globus Metadata Management Schema Management Service Registry ID Resolution OGSA-DAI Service Description Globus Toolkit Grid Communication Protocol Transport myProxy GSI caCORE CAS Security Globus OGSA Compliant - Service Oriented Architecture 41 National Cancer Institute 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. 42 National Cancer Institute 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 43 National Cancer Institute 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/ 44