LexEVS

Semantic Tooling Advancements

Kevin PetersonMayo Clinic

Mayo 2009

LexEVS 5.0

• What is LexEVS?

• LexEVS is a 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.

LexEVS 5.0

The LexEVS 5.0 Release includes the following components:

• Java API - A Java interface based on the LexGrid 5.0 Object Model

• REST/HTTP Interface - Offers an HTTP based query mechanism. Results are returned in either XML or HTML formats

• SOAP/Web Services Interface - Provides a programming language neutral Service-Oriented Architecture (SOA)

• Distributed LexBIG (DLB) API - A Java interface based on the LexGrid 2009/01 data model and relies on a LexEVS Proxy and *Distributed LexEVS Adapter to provide remote clients access to the native LexEVS API

• LexEVS 5.0 Grid Service - An interface which uses the caGRID infrastructure to provide access to the native LexEVS API via he caGRID Services

LexEVS 5.0

What’s New for 5.0• Retirement of EVS Model and API• Model Changes (LexGrid Model Version 2009/01)• caCORE SDK/Data Grid Service• New Migration Guide and Wiki Documentation

LexEVS 5.0

Retirement of EVS Model and API• The EVS caCORE 3.2 Model and API (deprecated in LexEVS 4.2) have been

removed in LexEVS API.• Simplifies the Code Base and exposes the LexEVS API directly to the users.• Existing applications will need to migrate to the new API.

LexEVS 5.0

Model Changes• Accommodate entities other than concept/instance/association • Converge attributes (e.g. associated properties) to ‘Entity’ superclass • Single resource can be defined as multiple types • Allow more granular version tracking (e.g. per concept or per property) • Extensive updates to value domain and pick list representation • Remove antiquated packages & classes (e.g. LDAP) • Accuracy and alignment of internal lexicon (URNMap -> URIMap) • Influenced by CTS2, OWL, XMDR, GE/IHC • Formalized (EA model available)

LexEVS 5.0

caCORE SDK/Data Grid Service• New caGRID Data Service to go along with the existing LexEVS Analytical Service.• The Analytical Service exposes the LexEVS API, the Data Service directly exposes

the LexGrid Domain Model.

• Uses standard caCORE SDK API• CQL

• Query-By-Example

• HQL

• Detached Criteria

• SOAP

• REST

LexEVS 5.0

New Migration Guide and Wiki Document• All existing LexBIG/LexEVS documentation has been converted to Wiki format.• Searchable and more accessible.• Migration Guide

• Provides existing applications with a migration path from the EVS API and Domain Model to the LexEVS 5.0 API and Domain Model.

LexWiki

• An open source, high-capacity editor for distributed terminology development.

• Based on the integration of semantic wiki and LexGrid technology.

• Developed by Mayo Clinic with collaborations of National Cancer Institute (NCI), World Health Organization (WHO) , Stanford University.

LexWiki Architecture

•Domain experts interact with the LexWiki editor created from Semantic Forms. Those Editors are based on the LexWiki templates created from the Semantic Wiki Core. •When changes are detected, they are sent to Protégé for verification and passed to LexGrid for persistence to the mySQL database.•When information is requested by the domain expert, LexGrid retrieves the data from the database and passes it to Protégé which is able to export/load the LexWiki template.

LexWiki Components

• LexWiki Templates

• LexWiki representation of terminology contents and semantics

• LexWiki Editor

• Based on Semantic Forms

• LexWiki Extension

• A Semantic MediaWiki Extension

• Provide Functions to access, manipulate and parse the LexWiki Semantics

• LexWiki Protégé Tab Plugin

• Import/Export among LexWiki, LexBIG, and Protégé

• Changeset detection

• Workflow management

• LexWiki Workflow Management

• My Workflow extension

Vocabulary Browser

•Users of the Vocabulary Browser at bioMedGT can view the NanoParticle Ontology concepts in a hierarchy tree.•Clicking on a concept in the hierarchy tree opens a page outlining its informational and operational properties.

Informational / Operational Properties

•The properties of the concept depend on the ontology but usually include the concept code, preferred name, definition and associations.•Alpha Aminoacid Sidechain has a “part_of” association. Clicking “part_of” would open a page listing all concepts which share that association.

Collaboration Platform

•The LexWiki is also being used as a collaboration platform in order to help domain experts author ontologies. •CTCAE used the LexWiki on the bioMedGT site to create a new version of their ontology by editing adverse event names and grades for those events. •After the editing process ended, we collated the results and a final version was created.

Fosters Discussion & Proposals

Another form of collaboration is seen with BGT. There are tabs across the top of the properties page for users with appropriate permissions.

Clicking on the discussion tab allows domain experts to talk about the concept as well as any proposals in a free form format.

Proposals may be made to the properties of the concept by opening the propose changes tab. On this page is a more formal format where experts may propose changes to any of the properties listed.

Domain experts may also propose a new child for the concept by opening the propose child concept tab.

Workflow Tracker

•There is also a workflow tracker included in the LexWiki. The workflow tracker lists all the proposals you have made using the LexWiki. This allows you to follow the progress of your proposals through the collaboration workflow from initial creation to final completion.

LexWiki Installation Package

• Zip file includes everything required to install a LexWiki.

• Command line driven using Ant

• Prerequisites

• Linux/Windows/Mac OSX.

• A Web Sever (Apache 2 or Microsoft IIS / PWS)

• MySQL 5.x or above is installed

• PHP 5 or above is installed.

• Java 1.5 or above is installed.

• Ant 1.6.5 or above is installed.

• Software Stack included

• MediaWiki

• Semantic MediaWiki extension

• Semantic Forms extension

• SMW Halo extension

• LexWiki Extension

New EVS Browsers

Semantic Tooling Advancements

Sherri de CoronadoNCI CBIIT

May 2009

New NCI Thesaurus Browser

• Will replace the current (deprecated) DTS based browser

• Expected release date: late May 2009• New look and feel, very nice, very user friendly• Improved search• Improved performance• Easy access to terminology subsets in NCIt

NCIt Browser Welcome Page

•Front page of the browser with description of features, links, easy access to the search bar.

Tabbed for Easy Viewing

•The concept information is tabbed for easy viewing, or you can view all the concept information together in the last tab.•Also buttons to view in the hierarchy – opens tree to the hierarchy position.

Relationships Tab

•Second Tab shows relationships.•Related concepts are hyperlinked.

Synonym Source and TermType

•Source information and term type available in Synonym Details tab (or by link from main tab).

Click “View in Hierarchy”

•Click Open in Hierarchy, see Angiogenesis in the NCI Thesaurus hierarchy (in red).

Results of “Begins With” Search

•Results of “Begins With” search for Angiogenesis

Results of “Contains” Search

•P53 Contains search.

Subsets Readily Accessible

•Subsets Readily Visible in Browser, click Subsets (near top).

Subsets

•Click on Terminology Subset previous page, and then View in Hierarchy – •Shows the hierarchy of subsets tagged in NCI Thesaurus.

New NCI Metathesaurus Browser

•NCI Metathesaurus Browser still in development, here’s a screen shot of the prototype. The existing NCI Meta Browser will remain available until this is shown to be a suitable alternative.

Concept Pages Similar to NCIt Browser

•Concept page is similar to that in NCI Thesaurus browser.

Parent, Child & Associated Concepts

•You can see parents, children and relationships. Concepts are hyperlinked.

Both Browsers Use LexBig API for Data Access

•Both browsers access data through the LexBIG API.•N-tier architecture.