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Benjamin Dai December 18, 2008

Explore the structured organization of knowledge in biology and medicine with NCBO's Fabric and Service-Oriented Architecture. Learn how to consume REST services and utilize ontology, data, and annotation services. Discover examples like Protégé 4 Plugin for BioPortal and BioPortal FOAF User integration. Witness the collaboration with Zepheira on the resource-oriented architecture. Dive into the world of NCBO services for a seamless integration experience.

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Benjamin Dai December 18, 2008

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  1. NCBO – Internal Use Only NCBO Fabric and Service-Oriented ArchitectureAdvancing biology and medicine with tools and methodologiesfor the structured organization of knowledge. Benjamin Dai December 18, 2008

  2. Overview • Consuming REST Services • NCBO Services Overview • SOA Infrastructure

  3. NCBO Services Overview Ontology services (OBS) Data service (OBR) Annotation service (OBA) BioPortal services UMLS services Users UCSF Laboratree CollabRx UCHSC PharmGKB, JAX HGMD Users BioPortal UI PDB/PLoS I2B2 NextBio IO informatics Users BioPortal Resources tab Knewco IO informatics

  4. Consuming of NCBO REST Services

  5. REST • Representational State Transfer • Described in Roy Fielding’s Ph.D. thesis • URLs locate resources in Internet-sized address spaces • Client passes all state in request

  6. Separation of Concerns Verbs Noun Representation http://rest.blueoxen.net/cgi-bin/wiki.pl?RestTriangle

  7. NCBO and Service Oriented Architecture • Enables simple consumption of and integration with NCBO services. • Four Examples for 2009: • Protégé 4 Plugin for BioPortal (re-use of Protégé TONES plugin) • NLM License Server Integration for UMLS vocabularies • OBO to OWL Converter Wrapper • BioPortal FOAF User

  8. Example 1: Protégé 4 Plugin for BioPortal

  9. Example 2: NLM License Server Integration for UMLS Note: NLM License Services implements a local license cache.

  10. Example 2: DEMO • Walk-through • NLM License Services • Integration with UMLS Prototype Service

  11. Example 3: OBO to OWL Converter Wrapper Note: Requests can be throttled by number of threads with specified queue size.

  12. Example 3: DEMO • Walk-through

  13. Example 4: BioPortal FOAF User

  14. Example 4: Demo

  15. NetKernel • NCBO SOA Infrastucture leverages NetKernel. • Collaboration with Zepheira (Eric Miller) • What is it? • Resource-Oriented Architecture • Modern, microkernel architecture • Takes the best of • REST, Unix Pipes, SOA • Open Source w/ Dual License

  16. Resource Oriented Environment

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