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

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Presentation on theme: "LexGrid for cBIO Division of Biomedical Informatics Mayo Clinic Rochester, MN."— Presentation transcript:

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 JAAS Authorization & Authentication JBoss Application Server JMS Messaging Java Mail Generic Subsystem Oracle Database Soap Services External access WebDAV File access module Apache Web Server User Interface JSF, JSP, Servlets, Applets, CSS, HTML Message Driven Beans Session Beans Entity Beans PROMPT APIProtégé APILexGrid API cBIO Architecture

4 File / Version Submission Basic Validation Further Validation Background Processing File to Holding Bin User Notified By Email OBO Librarian Review Convert file to LexGrid DB Schema Indexing Using LexGrid Alignment - PROMPT User Interface Control back to UI Success? DB Status Change cBIO Workflow Ontology Submission Format Validation Success? DB Status Change Yes No Yes No Yes

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

6 LexGrid Goal 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 1. Direct LexGrid API access 2. Cross Ontology Search 3. Versioning 4. Validation 5. Protégé and OWL Support 6. 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 ) 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 and Subsystems LexBIG Service Service Metadata Query Service Service ManagerExtensions Lexical Set Operations Graph Operations History Loaders Coding Scheme Metadata Plug-ins Licensing Indexers Discovery

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

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 HistoryLexical Set OperationsGraph Operations Common Terminology Services (CTS) LexGRID Mayo Terminology Services CTSII

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

22 Schedule 3/1/063/154/14/157/15/156/15/16/157/158/18/15 Requirements Analysis OWL/OBO Loader 9/1 Software Testing LexBIO Development Completed Planned LexBIO 0.5 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 Functionality Replication / Update NCI Replica DataStore Mayo NCI Replica DataStore Stanford NCI DataStore NCI Update Subscribe Change Log Change Log Change Log “Push” “Pull”

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

26 Functionality Indices NCI DataStore NCI Update Index Service Subscribe “Push” Reasoning Service Subscribe “Push”

27 Questions

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