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LexGrid for cBIO

LexGrid for cBIO. Division of Biomedical Informatics Mayo Clinic Rochester, MN. Outline. cBIO Architecture/Workflow (LexGrid) Mayo Activities LexGrid Goals cBIO Year 1 – Integration Points LexGrid Components Future Work and Integration Points. cBIO Architecture. Apache Web Server.

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LexGrid for cBIO

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  1. LexGrid for cBIO Division of Biomedical Informatics Mayo Clinic Rochester, MN

  2. Outline • cBIO Architecture/Workflow (LexGrid) • Mayo Activities • LexGrid Goals • cBIO Year 1 – Integration Points • LexGrid Components • Future Work and Integration Points

  3. cBIOArchitecture Apache Web Server WebDAV File access module JBoss Application Server User Interface JSF, JSP, Servlets, Applets, CSS, HTML Generic Subsystem JAAS Authorization &Authentication Session Beans Message DrivenBeans JMS Messaging Entity Beans Soap Services External access LexGrid API Protégé API PROMPT API Java Mail Oracle Database

  4. cBIO Workflow Ontology Submission File / VersionSubmission OBO Librarian Review User Interface Convert file toLexGrid DB Schema Basic Validation No Success? Control back to UI Yes Indexing Using LexGrid BackgroundProcessing Success? File toHolding Bin Format Validation Yes Alignment - PROMPT No Success? User NotifiedBy Email Yes Further Validation DB Status Change DB Status Change No Yes Success?

  5. General Aspects • Ontology Storage and Management • Query and Access • File Format Conversions • LexGrid and Protégé Integration

  6. LexGridGoal Terminology as a commodity resource • Available whenever and wherever it is needed • Online or downloadable • Push or pull update mechanism • Available 24x7 • Revised and updated in “real-time” • Cross-linked and indexed

  7. LexGrid for cBIO Roadmap • Direct LexGrid API access • Cross Ontology Search • Versioning • Validation • Protégé and OWL Support • OBO Plug-in API for Protégé

  8. Direct API for LexGrid • LexGrid for cBIO • Leverage Work with LexBIG • Common Set of Requirements • Administration, Functional, Serviceability, Performance, Architectural • Reviewed w/cBIO requirements • Provide most of the functionality for BioPortal 1.0

  9. Cross Ontology Search • Provide searching across multiple ontologies and versions • Limited to one LexGrid server instance • Additional requirements • Order and Precedence • E.g. return all concepts with name “lung” from current version

  10. Versioning • Support for multiple versions of an ontology • Provide basic administration utilities for loading, activating, deactivating, retiring, and special tagging.

  11. LexBIO

  12. Validation • Provide separate validation LexBIO API • Validation independent of loading • Syntactic validation only • Leverage Resource Reader Framework • Reads and absorbs source formats • Returns collection of errors encountered • Resource Headers (e.g <owl:ontology>) is possible to analyzed separately from content

  13. File Support • Generate Default Mappings to LexGrid • Parsing & Syntactic Validation of Protégé, Protégé OWL, and OBO • Content mapping (LexMap) • Source Format (Protégé, OWL, OBO) • Target Format (LexGrid) • Default mappings defined • User Defined mappings • Leverage Protégé and Protégé OWL APIs for validation • Leverage OMG ODM for OWL Mapping • Transformation using mappings • Content Indexing

  14. OBO Plug-in API for Protégé • OBO text file format • Reuse OBO parser/loader • Develop as API • Protégé Plug-in and LexGrid Converter • Basic integration into Protégé UI

  15. LexBIO

  16. LexBIG High Level Components

  17. LexBIG Service Service Metadata Coding Scheme Metadata Licensing Discovery Query Service Lexical Set Operations Graph Operations History Service Manager Extensions Loaders Plug-ins Indexers LexBIG Service and Subsystems

  18. Service Manager LexGrid Indexers OWL Extendable Loaders OBO Protégé Loader Administration Other Service Administration Service Manager Subsystem

  19. Query Design Philosophy • Model Driven • LexGrid model is core component of design • XML Schema is the master • Rendered in XMI, Java, and UML • Conscious separation of service and data classes • Deferred query resolution – support of iterators • Specific extensions points for load, index, search, and convenience methods • Provide vocabulary mapping for common formats

  20. Query Service Subsystem Query Service Lexical Set Operations Graph Operations History Common Terminology Services (CTS) CTSII LexGRID Mayo Terminology Services

  21. Extensions Loaders Search/Index General Purpose Classifiers (future) Extension Subsystem

  22. Schedule 3/1/06 3/15 4/1 4/15 5/1 5/15 6/1 6/15 7/1 7/15 8/1 8/15 9/1 Requirements Analysis OWL/OBO Loader LexBIO Development Software Testing LexBIO 0.5 Completed Planned LexBIO 0.6 LexBIO 0.7 LexBIO 0.8 LexBIO 0.9 LexBIO 1.0

  23. Future Points • Metadata Integration • Extension to Domains (OBD) • LexGrid Federation • Replication/Updates • Advertise and Discovery • Cross ontology and node search • Cross reference • Index Services • Synnorm • Reasoning

  24. Stanford NCI Replica NCI Replica NCI Mayo DataStore DataStore DataStore NCI FunctionalityReplication / Update Update Change Log Subscribe “Push” “Pull” Change Log Change Log

  25. NCI UMLS Semantic NET DataStore DataStore DataStore FunctionalityCross References ConceptCode: C222 entityDescription: Alkylsulfonate Compound Semantic_Type: SemNet:T123 UMLS_CUI: C0002072 Semantic_Type = URN:ISO:2.16.840.1.113883.6.56.1:T123 UMLS_CUI = URN:ISO:2.16.840.1.113883.6.56:C0002072 T123 – “Biologically Active Substance” C0002702 – “Alkanesulfonates”

  26. NCI DataStore NCI FunctionalityIndices Update Subscribe Subscribe “Push” “Push” Reasoning Service Index Service

  27. Questions

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