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NCBO Fabric and Service-Oriented Architecture Advancing biology and medicine with tools and methodologies for the structured organization of knowledge. Benjamin Dai December 18, 2008. Overview. Consuming REST Services NCBO Services Overview SOA Infrastructure. NCBO Services Overview.
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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
Overview • Consuming REST Services • NCBO Services Overview • SOA Infrastructure
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
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
Separation of Concerns Verbs Noun Representation http://rest.blueoxen.net/cgi-bin/wiki.pl?RestTriangle
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
Example 2: NLM License Server Integration for UMLS Note: NLM License Services implements a local license cache.
Example 2: DEMO • Walk-through • NLM License Services • Integration with UMLS Prototype Service
Example 3: OBO to OWL Converter Wrapper Note: Requests can be throttled by number of threads with specified queue size.
Example 3: DEMO • Walk-through
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