Download - 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
JAASAuthorization &Authentication
JBoss Application Server
JMSMessaging
Java Mail
Generic Subsystem
OracleDatabase
Soap ServicesExternal access
WebDAVFile access
module
Apache Web Server
User InterfaceJSF, JSP, Servlets,
Applets, CSS, HTML
Message DrivenBeans
Session Beans
Entity Beans
PROMPT APIProtégé APILexGrid API
cBIOArchitecture
File / VersionSubmission
Basic Validation
Further Validation
BackgroundProcessing
File toHolding Bin
User NotifiedBy Email
OBO Librarian Review
Convert file toLexGrid DB Schema
Indexing Using LexGrid
Alignment - PROMPT
User Interface
Control back to UI Success?
DB StatusChange
cBIO Workflow Ontology Submission
Format Validation
Success?
Success?
Success?
DB StatusChange
Yes
No
Yes
Yes
No
No
Yes
General Aspects
• Ontology Storage and Management
• Query and Access
• File Format Conversions
• LexGrid and Protégé Integration
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
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
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
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
Versioning
• Support for multiple versions of an ontology
• Provide basic administration utilities for loading, activating, deactivating, retiring, and special tagging.
LexBIO
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
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
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
LexBIO
LexBIG High Level Components
LexBIG Service and Subsystems
LexBIG Service
Service Metadata
Query Service
Service Manager Extensions
Lexical Set Operations
Graph Operations
History
Loaders
Coding Scheme Metadata
Plug-ins
Licensing
Indexers
Discovery
Service Manager Subsystem
Service Manager
Service Administration
LexGrid
Loaders
OWL
OBO
Protégé
Other
Loader Administration
Extendable
Indexers
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
Query Service Subsystem
Query Service
History Lexical Set Operations Graph Operations
Common Terminology Services(CTS)
LexGRID Mayo Terminology Services
CTSII
Extension Subsystem
Extensions
Loaders
Search/Index
General Purpose
Classifiers (future)
Schedule3/1/06 3/15 4/1 4/15 7/15/15 6/15/1 6/15 7/15 8/1 8/15
RequirementsAnalysis
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
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
FunctionalityReplication / Update
NCIReplica
DataStore
Mayo
NCIReplica
DataStore
Stanford
NCI
DataStore
NCI
Update
Subscribe
ChangeLog
ChangeLog
ChangeLog
“Push”“Pull”
FunctionalityCross References
NCI
DataStore
UMLS
DataStore
SemanticNET
DataStoreUMLS_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”
FunctionalityIndices
NCI
DataStore
NCI
Update
IndexService
Subscribe
“Push”
ReasoningService
Subscribe
“Push”
• Questions