# Presentation: 667337

## The cancer Biomedical Informatics Grid (caBIG):  LexGrid Vocabulary Services for caBIG (LexBIG) – Year 1 Development

- Solbrig, Harold; Armbrust, Daniel; Johnson, Thomas; Buntrock, James; Chute, Christopher1;
- Hartel, Frank; Fragosos, Gilberto; Safran, Tracy; Ong, Kim; Oberthaler, James2
- 1Mayo Clinic College of Medicine
- 2National Cancer Institute Center of Bioinformatics

## Outline

- Overview (5 min)
- Demonstration and Code Sample (15 min)
- Question and Answer

## Overview – Terminologies Today

- Different representation formats
- Standardized - RRF, OWL
- Non-standard - CSV, proprietary spreadsheet or database, HTML, PDF, ...
- Different distribution methods
- Periodic release cycle
- Self-contained or tightly coupled packaging
- Different access and tooling
- Programmatic access changes with provider and distribution format
- Different tools to Browse / Edit / Maintain Lifecycle

## Overview - The Lexical Grid

- Terminology as a commodity resource
- Accessible online, under a common model, in web-space on web-time
- Federated distribution
- Cross-linked, loosely coupled, published individually on demand
- Open source building blocks and tools
- Simplify vocabulary access and integration
- Provide the consistency and standardization required to move beyond the cottage industry to support large-scale terminology adoption and use

## Overview – What’s in a Name‘LexGrid’ vs. ‘LexBIG’

- LexGrid
- A brand and vision for Mayo vocabulary research providing ...
- Common building blocks such as a vocabulary information model, flexible persistence, and tooling
- Architectural consistency across components grounded in standards (e.g. HL7 CTS, OMG LQS)
- LexBIG
- A project with specific timelines and deliverables to meet the needs of caBIGTM
- Software to be used as the underlying terminology engine for NCI Enterprise Vocabulary Services (EVS)
- Built on top of LexGrid technology base; extended where necessary

## Overview – LexBIG Design Philosophy

- Model Driven
- LexGrid model is core component of design
- XML Schema as master, rendered in XMI, EMF, UML, Java
- Conscious separation of service and data classes
- Deferred query resolution
- Specific extensions points for load, index, search, and convenience methods
- Provide vocabulary mapping for common formats

## LexBIG Runtime ScenariosConsolidated Host – EVS Access

- LexBIG Host

- LexBIG
- DataStore

- caBIO Server / Java Runtime

- Editors

- Browsers

- Query
- Tools

- EVS
- Clients

- LexBIG
- Java API

- EVS
- Service

- Mediator
- (‘LexRPC’)

**Notes:**
Depicts EVS access with all server layers deployed to a single system.  EVS service is expected to invoke methods through mediation layer.  The mediator is anticipated to be similar in function to current DTS RPC, in that services may be fulfilled by different implementations.  In this case service is fulfilled via direct invocation of LexBIG API within the same JVM.

## LexBIG Runtime ScenariosDirect Programmatic Access

- LexBIG Host

- LexBIG
- DataStore

**Notes:**
Depicts programmatic access to LexBIG functions via direct reference to the Java API.

## LexBIG Runtime ScenariosEnterprise Java Beans

## LexBIG Import/Export

- Draft

**Notes:**
Basic import and export scenarios.  Input files are downloaded and accessible prior to import.  Data store typically shown here to reside on same server, but may be accessed remotely.

## Demonstration

- Acquiring Software
- Stepping through installation process
- Environment Verification Tests
- Loading Content
- Review Available Documentation
- Step through a Sample Query

## Demonstration – Acquiring Software

## Demonstration - Installation

## Demonstration – Environment Verification

## Demonstration – Loading Vocabularies

## Demonstration - Documentation

## Demonstration – Sample Query

## Resources

- LexGrid Project_[http://](http://informatics.mayo.edu/LexGrid)__[informatics.mayo.edu](http://informatics.mayo.edu/LexGrid)__[/LexGrid](http://informatics.mayo.edu/LexGrid)_
- LexBIG Forge Site_[http://](http://gforge.nci.nih.gov/projects/lexbig)__[gforge.nci.nih.gov/projects/lexbig](http://gforge.nci.nih.gov/projects/lexbig)_
- caBIG LexBIG CVS_[http://cabigcvs.nci.nih.gov/viewcvs.cgi/lexgrid](http://cabigcvs.nci.nih.gov/viewcvs.cgi/lexgrid)_