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 TM

1  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.

2 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

3 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™)

4 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 in other clinical trials involving agents known to affect these specific pathways, and identify any studies in model organisms involving tissues with similar pathway activity.

5 Semantic interoperability Syntactic interoperability Interoperability ability of a system to access and use the parts or equipment of another system

6 SYNTACTIC SEMANTIC caBIG Compatibility Guidelines

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

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9 caCORE Bioinformatics ObjectsEnterprise VocabularyCommon Data Elements SECURITYSECURITY

10 Bioinformatics Objects

11  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 standard for Common Data Elements (CDEs). Common Data Elements

12 Preferred Name Synonyms Definition Relationships Concept Code Enterprise Vocabulary Description Logic

13 caCORE Software Development Kit

14 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 caCORE SDK Generates a caBIG Silver-Compliant System

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

16 From Silver to Gold: caGrid

17 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

18 Gold Cancer Center Cancer Center NCI OTHER caBIG SERVICE PROVIDERS OTHER TOOLKITS Silver

19 caGrid 1.0 Architecture Grid Communication Protocol Service Description Service Business Process Service Registry Security Semantic service Resource Management Functions Quality of Service ID Resolution Transport GSI DORIAN GT4 Workflow GLOBUS Toolkit caDSR EVSGT4 Portal caDSR GME GTS Index IntroduceFQE Grid ID

20 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)

21 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

22 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

23 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  caGrid –Avinash Shanbhag, NCI –Joel Saltz and colleagues, Ohio State U. –Ian Foster and colleagues, U. Chicago/Argonne –Booz Allen Hamilton –SAIC –SemanticBits

24 Links  caBIG: –  caGrid –  caCORE –