Peter A. Covitz, Ph.D. Chief Operating Officer National Cancer Institute

1. TM 0 caBIG and caGrid: Interoperable Computing Infrastructure for the Nation’s [and World’s] Cancer Research Enterprise Peter A. Covitz, Ph.D. Chief Operating Officer National Cancer Institute Center for Bioinformatics

2. The Center for Bioinformatics is the NCI’s strategic and tactical arm for research information management • We collaborate with both intramural and extramural groups • Mission to integrate and harmonize disparate biomedical research data • Production, service-oriented organization. Evaluated based upon customer and partner satisfaction.

3. The Problem 1,372,910 new cancer cases and 570,280 deaths due to cancer expected in the U.S. in 2005 Jemal et al.,CA Cancer J Clin 2005; 55:10-30

4. A National Response • Enable investigators and research teams nationwide to combine and leverage their findings and expertise. • Create scalable, actively managed organization that will connect members of the NCI-supported cancer enterprise by building a biomedical informatics network The Cancer Biomedical Informatics Grid™ (caBIG™)

5. Scenario from caBIG Strategic Plan A researcher involved in a phase II clinical trial of a new targeted therapeutic for brain tumors observes that cancers derived from one specific tissue progenitor appear to be strongly affected. The trial has been generating proteomic and microarray data. The researcher would like to identify potential biochemical and signaling pathways that might be different between this cell type and other potential progenitors in cancer, deduce whether anything similar has been observed inother clinical trials involving agents known to affect these specific pathways, and identify any studies inmodel organisms involving tissues with similar pathway activity.

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

7. SEMANTIC SEMANTIC SEMANTIC SYNTACTIC caBIG Compatibility Guidelines

8. Model Driven Architecture + Computable Semantics = Platform for Syntactic and Semantic Interoperability caCORE

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

11. Bioinformatics Objects

12. Common Data Elements • What do all those UML data Classes and Attributes actually mean, anyway? • UML model components are mapped to semantic concepts drawn from Enterprise Vocabulary sources, then registered in the Cancer Data Standards Repository (caDSR). • caDSR is a metadata registry, implements ISO/IEC 11179 standard for Common Data Elements (CDEs).

13. Description Logic Enterprise Vocabulary Concept Code Relationships Preferred Name Definition Synonyms

14. caCORE Software Development Kit

15. caCORE SDK 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

16. 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

17. From Silver to Gold:caGrid

18. Use cases not satisfied by caCORE alone • 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

19. Silver Silver Silver Silver Gold Silver Silver Silver OTHER TOOLKITS NCI OTHER caBIG SERVICE PROVIDERS Cancer Center Cancer Center Cancer Center Cancer Center Cancer Center

20. caGrid 1.0 Architecture Functions Quality of Service Semanticservice ID Resolution Workflow Business Process Portal caDSR DORIAN Security Resource Management Service Registry Grid ID Service FQE Introduce GSI GME caDSR Service Description Index Grid Communication Protocol GLOBUS Toolkit GTS GT4 EVS GT4 Transport

21. Data Object Semantics, Metadata, and Schemas • Object oriented, APIs, well-defined data types • Classes defined in UML and converted into ISO/IEC 11179, registered in the caDSR • Definitions drawn from Enterprise Vocabulary Services (EVS), relationships semantically described • XML serialization of objects adhere to XML schemas registered in the Global Model Exchange (GME)

22. Service Data Elements • Two types of top-level grid services defined • Data Services • Analytical Services • Service Data Elements (SDEs) describe services so clients can discover what they do

23. Integrating with other Grids • caGrid intentionally focused on federated data and analytic service interoperability, not computing power • Adoption of standard grid tooling intended to facilitate integration other grids with compute power focus • Seeking partnership with established compute grids to install caGrid Analytical Service nodes that would be transparently available to caGrid users

24. caGrid Avinash Shanbhag, NCI Joel Saltz and colleagues, Ohio State U. Ian Foster and colleagues, U. Chicago/Argonne Booz Allen Hamilton SAIC SemanticBits Acknowledgements • caCORE • Denise Warzel • George Komatsoulis • Avinash Shanbhag • Frank Hartel • Dianne Reeves • Sherri De Coronado • Gilberto Fragoso • SAIC • Terrapin Systems • Oracle • Ekagra • ScenPro • Apelon • MSD

25. Links • caBIG: • https://cabig.nci.nih.gov • caGrid • https://cabig.nci.nih.gov/News_Folder/caGrid_1.0_Beta_Release • caCORE • http://ncicb.nci.nih.gov/NCICB/infrastructure/cacore_overview