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