lexevs overview mayo clinic rochester, minnesota june 2009

LexEVS Overview

Mayo Clinic

Rochester, Minnesota

June 2009

What is LexGrid?

• The LexGrid package represents a comprehensive set of software and services to load, publish, and access vocabulary or ontological resources.

• Built on common information model representing multiple vocabularies

• Utilize common repositories, software components, APIs, and tools

• Ground in standards (e.g. HL7 CTS, ISO 11179)

What is LexGrid?

•The LexGrid package represents a comprehensive set of software and services to load, publish, and access vocabulary or ontological resources. •Built on common information model representing multiple vocabularies•Utilize common repositories, software components, APIs, and tools•Ground in standards (e.g. HL7 CTS, ISO 11179)

Source

OMG LQS

…OWL

Standards

ISO 11179

XML

HL7 CTS

Other

OBO

Content

Represent

LexGridModel

Data

Index

Export

ImportOWL

XML

OBO

Text

Protégé

RRF

XML

Tools

Access

SERVICES

JavaAPI

Lex*

CTS2

CTS

Embed

.NET

Web Clients

Grid Clients

Documentation

Examples

Open

What is LexBIG?

• A specific API to serve vocabularies based on the LexGrid model, developed for the Cancer Biomedical Informatics Grid (caBIG®) community.• Coordinated infrastructure for Cancer Research

• Clinical Trials, Integrative Cancer Research, Tissue Banking and Pathology Tools, In vivo Imaging

• Vocabulary, Common Data Elements, Architecture

• Open source implementation.

• Underpins current NCI Enterprise Vocabulary Services (EVS).

• Represents the next generation EVS API.

• Additional contributions and tuning to meet the needs of the NCBO community, based on development of NCBO BioPortal services.

What is LexEVS?

• Adopted as project name to describe merging of LexGrid model and LexBIG API as the mainstream EVS interfaces.

• Collection of programmable interfaces that provide users with the ability to access controlled terminologies supplied by the NCI Enterprise Vocabulary Services (EVS) Project. The controlled terminologies hosted by the NCI EVS Project are published via the Open-Source LexEVS Terminology Server.

• Introduced as Distributed API and grid-level services in EVS version 4.x, and completing transition to caCORE SDK-generated interfaces (RESTFul API, SOAP services, etc) in EVS 5.0.

What is LexEVS 5.0?

• LexEVS 5.0 is the first release to completely shift from the EVS Model and EVS API to LexEVS API and LexGrid Model.

• The 2008/01 model is updated to the 2009/01 LexGrid Model

• New Data Services are now provided for the Grid and web service interfaces

• XSL transformations are provided for legacy LexGrid data.

• Unified OWL loader (Migration from the NCI OWL loader and a generic OWL loader to a single loader)

• Updated to work with caCORE SDK 4.1

• LexEVS 5.0 introduces LexGrid-based Query-By-Example (QBE) services

LexEVS Conceptual Overview

•LexEVS consists of LexGrid Model & Storage, LexEVS Java API, LexEVS Distributed Service and LexEVS caGrid Service.

LexEVS caGrid Service

LexEVS Distributed Service

LexEVS Java API

LexGridModel & Storage

Browsers and Applications

LexEVS API

•Now we will discuss LexEVS API.

LexEVS Java API


LexEVS API – Characteristics

• API coverage• Administrative FunctionsAdministrative Functions

• Query Code Systems and Available MetadataQuery Code Systems and Available Metadata

• Query Concepts, Concept Properties, and QualificationsQuery Concepts, Concept Properties, and Qualifications

• Query Concept Relationships and QualificationsQuery Concept Relationships and Qualifications

• API characteristics• Conscious separation of service and data classesConscious separation of service and data classes

• Deferred query resolutionDeferred query resolution

• Payload optimizationPayload optimization

• Support iterationSupport iteration

• Defined extension points (loaders, exporters, sort algorithms, filters, Defined extension points (loaders, exporters, sort algorithms, filters, convenience methods)convenience methods)

LexEVS API - Distributed

•Now we will discuss LexEVS Distributed API.


LexEVS Java API


LexEVS API - Distributed

• Same API functions; requires change to service declaration only• Does not expose administration options

Database Server

Distributed LexEVS Server

RMI

LexEVS on Local System

LexEVS Install

Database Server

LexEVS Install

JDBC

JDBC

Direct

Distributed

LexBIG API Proxy

Client System

LexEVS Client Proxy

LexEVS API – caGrid Service

•Now we will discuss LexEVS caGrid Service

LexEVS caGrid Service


LexEVS Java API


•The caGrid Service consists of client system, caGrid Host Server, Distributed LexEVS Server and Database Server.

Database Server

Distributed LexEVS Server

RMI

LexEVS on Local System

LexEVS Install

Database Server

LexEVS Install

JDBC

JDBC

Direct

Distributed

Database Server

LexBIG API Proxy

Client System

caGrid Host ServerClient System Distributed LexEVS Server

RMI

LexEVS Install

Grid

JDBCTCP

LexEVS Proxy

LexEVS Client Proxy

LexEVS Client Proxy



•caGrid Services use same API functions and only require change to service declaration only.

Client caGrid Service Distributed LexBIGCalls caGrid ‘getSupportedCodingSchemes()’

Calls Distributed LexBIG‘getSupportedCodingSchemes()

Returns result of call to caGrid Service

Results are returned to clientwith all appropriate caGrid security mechanisms

LexEVS caCORE SDK APIs

•Now we will discuss LexEVS caCORE SDK APIs.

caCORE SDK APIs


• Query-by-example (QBE) system

• Based on LexGrid model

• Java Language Binding

• Web Services (SOAP)

• Web Services (REST HTTP / XML)

caCORE EVS Server

Web ServicesWeb Services

XML / HTMLXML / HTML

Java QBEJava QBE

LexBIG Install

DAO

Cache

Service L

ayer

Database Server

JDBC

LexEVS caCORE SDK APIs

Hibernate

caCORE SDK APIs – QBE Example

•SDK-Generated Query by Example User Interface is demonstrated by the domain class browser.

SDK-Generated Query by Example User Interface:

caCORE SDK APIs – Rest Example

•SDK Generated REST request output in HTML (XML is also available).

Example Restful Request (HTML)…

Example Restful Output (HTML shown, XML also available)…


•Now we will discuss browsers and applications that utilize LexEVS.

LexBIG/EVS caGrid Service

LexBIG/EVS Distributed Service

LexBIG/EVS Java API




•The LexEVS GUI Provides graphical interface to exercise API functionality.

LexBIG GUI

Provides graphical interface to exercise API functionality.

caBIG LexEVS Adopters

LexEVS is used in various projects within the caBIG community. For example:

• Meta Data Registry and UK Cancer Grid (cgMDR)

cgMDR is a collaborative development effort with involving the NCI CBIIT MDR Team and the team from the UK Cancer Grid to build plugins that will facilitate meta data reuse and development amongst the caBIG community.

https://gforge.nci.nih.gov/projects/cgmdr/• Cancer Models Database (caMOD)

caMOD provides information about animal models for human cancer to the public research community.

https://cabig.nci.nih.gov/tools/caMOD• Cancer Data Standards Registry and Repository (caDSR)

The caDSR is a database and a set of APIs and tools used to create, edit, control, deploy and find common data elements (CDEs) for metadata consumers and for UML model development.

http://ncicb.nci.nih.gov/NCICB/infrastructure/cacore_overview/cadsr

https://cabig.nci.nih.gov/tools/caMOD

LexEVS Resources

• LexEVS Project

http://gforge.nci.nih.gov/projects/lexevs/

• caBIG® Vocabulary Knowledge Center Wiki

Comprehensive resource for LexEVShttps://cabig-kc.nci.nih.gov/Vocab/KC/index.php/Main_Page

• caBIG® Vocabulary Knowledge Center Forums

Provides ability to ask LexEVS questions and find answershttps://cabig-kc.nci.nih.gov/Vocab/forums/

• LexEVS 5.0 Migration Guide

Documentation to assist adopters to migrate to LexEVS 5.0https://cabig-kc.nci.nih.gov/Vocab/KC/index.php/LexEVS_5.0_Migration_Guide

lexevs overview mayo clinic rochester, minnesota june 2009

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