# Presentation: 645323

## Vocabulary Knowledge Center

- VCDE/Architecture Workspace Face to Face Meeting
***Birds of a Feather Session***

**October 29, 2008**

## Agenda

**Introduction to the Vocabulary Knowledge Center**
**Overview of the VKC Website**
**Supported Tools**
**Conclusions**
**Feedback and Discussion**

**Long-standing pioneer in health-information semantic research**
**Over 20 years of active research and development in terminology services and related ontology infrastructures**
**Expertise in standards and terminology development and management**
- Common Terminology Services (CTS)
- ICD-11, HL7, CTCAE, SNOMED, ICD, HITSP
- Partner with the National Center for Biomedical Ontology (NCBO)
**Extensive experience with biomedical vocabularies and formats**
- Open Biomedical Ontologies (OBO)
- Text-delimited
- NLM Rich Release Format (RRF)
- Web Ontology Language (OWL)

## Vocabulary KCOrganization and Management

**Technical Resources**
*SemanticBits*

- Patrick McConnell & Joshua Phillips
*Technical Managers*

*Senior Software Engineer, Tech Writer*

## Vocabulary Knowledge Center

**SERVICE AND SUPPORT**
**Web-based support for vocabulary authoring and management tools**
*- Documentation and Training*
- Technical documentation (e.g., installation)
- User's guides
- Training materials
- Information and FAQ’s on tools
*- Community Outreach*
- caBIG participants
- The broader cancer and biomedical research community
*- Discussion forums*
*- Bug reports, feature requests*
*- Source code repository*

## Slide 6

## Slide 7

## Slide 8

## Slide 9

## Agenda

**Introduction to the Vocabulary Knowledge Center**
**Overview of the VKC Website**
**Supported Tools**
**Conclusions**
**Feedback and Discussion**

## caBIG® Knowledge Centers

- https://cabig-kc.nci.nih.gov/MediaWiki/index.php/Main_Page

## Knowledge Centers

## Vocabulary Knowledge Center Website

- https://cabig-kc.nci.nih.gov/Vocab/KC

## Vocabulary Knowledge Center Website

**Vocabulary Knowledge Center ****Website**

## Forums

- Visitors may post general questions   and comments related to the Knowledge Center's domain
- Questions and/or comments related to each tool under the Knowledge Center's stewardship
- Each tool as a end user forum and a developer forum

## LexBIG End User Forum

## Bugs/Feature Requests

## Knowledge Center Bug Tracking System

Used for every Knowledge Center 

Central bug tracker that allows users and developers to report defects and request features for specific tools and versions. 

Feature requests are treated like defects (aka "bugs"). 

Use the Search for or Report a Bug functions to search for and/or report both defects and feature requests. 

- Used for every Knowledge Center
- Central bug tracker that allows users and developers to report defects and request features for specific tools and versions.
- Feature requests are treated like defects (aka "bugs").
- Use the Search for or Report a Bug functions to search for and/or report both defects and feature requests.

**Bugzilla**

## Code Repository

## Code Repository

- Contains released versions of tools
- Contains development code for caBIG® tools under the stewardship of the caBIG ® Knowledge Centers.** **

## Code Repository	

- Code Repository is for developers that wish to participate in open source development efforts.
- Storage for the code for tools currently in open development.
- Stores previous and current **released** versions of supported tools
- will be posted as downloadable executable files on the web server,
- will be accessible through the Tools Landing Pages on the VKC.
- will be available through the Subversion tool
- "General Edit Users" will be able to download code from the repository. Only a select group of advanced users, primarily members of the development team, will be able to upload/commit code to the repository.
- The subversion online manual is a complete guide to this tool's functions and processes.

## Vocabulary Knowledge Center Website

- https://cabig-kc.nci.nih.gov/Vocab/KC/index.php/Main_Page

## LexBIG Resource page

## LexBIG Frequently Asked Questions

## Agenda

**Introduction to the Vocabulary Knowledge Center**
**Overview of the VKC Website**
**Supported Tools**
**Conclusions**
**Feedback and Discussion**

## Tools – Scope of Support

_*The Vocabulary Knowledge Center will provide:*_
- Web-based support for vocabulary authoring and management tools
- Support will be provided through
- Domain expertise
- Searchable knowledge base
- Installation packages for supported tools
- Administration of open source development by the community
- Collection and monitoring of defect reports and feature requests
- Training materials

## Tool Descriptions

- LexBIG

**LexBIG**
- Common access point for representing and accessing terminology content
- Step toward making terminologies an interoperable component of caBIG

**Semantic MediaWiki**
- Federated environment for users to browse and discuss the use and structure of the terminology
- System that allows users to suggest changes to the terminology providers in a way that can be managed effectively

**Protégé**
- Facilitates terminology management and editing
- Integrated with LexBIG and Semantic MediaWiki

## Supported Tools – LexGrid/LexBIG

**Terminology infrastructure and services **are provided by the LexGrid system, which includes both Java and caGrid-based interfaces.

## LexGrid

**	****A model of terminology that is:**
- An ongoing line of research that encapsulates Mayo activity in vocabularies and ontologies
- Unified by common underpinnings and direction that:
*Build on a common information model capable of representing multiple vocabulary sources*
*Focus on developing and enabling software components, APIs, and tools to support the model*
*Provides architectural consistency across the model and components, grounded in standards (eg HL7 CTS, ISO 11179) *
- Not a single well-defined software deliverable
- Not a single project; rather an ongoing effort to further standards and interoperability

## LexBIG

**System for standardized storage of and access to**
**       ****terminologies**
- Common model and API
**Supports distributed terminologies**
- Provides an open source implementation of EVS-compliant vocabulary services.
- Provides flexible implementation for vocabulary storage and persistence.
- Provides standard tooling for load and distribution of vocabulary content**.**
**Development by the Mayo Clinic**
- Based on a long history of development of terminology services
- Software developed to be initially used as the underlying terminology engine for NCI   	Enterprise Vocabulary Services (EVS)
- Built on top of LexGrid technology base; extended where necessary

## LexBIG Packaging

**Major components ...**
**Service Management** tools to load, index, and manage vocabulary content for the vocabulary server.
**Application Programming Interface** (API) providing Java interfaces to various functions including Lexical queries, Graph representation and traversal, and NCI change event history.
**Graphical User Interface **providing access to service management and API functions; geared toward expert users.
**Documentation **consisting of JavaDocs, Administrator and Programmer Guides.
**Examples** providing sample source code for common vocabulary queries.
**Source** for all code developed for the LexBIG project.
**Test Suite **to validate the LexBIG installation.

## LexBIG Packaging

**Not included in LexBIG**
- Authoring or curation tools
- End user tools (e.g. browser for those not familiar with API)
- Application Server / Web Services
- Vocabulary content
- Data Repository

## LexGrid and LexBIG

**       ****	****   ****An in-depth look ****	****	****	****	****      at ****	****	****	****	**** LexGrid and LexBIG ****	****	****	****    with ****	**
**     ****Vocabulary Knowledge Center         ****	****Subject Matter Expert –**
**                ****Tom Johnson**

## LexBIG/EVS API Overview

**October 2008**

## What is LexBIG?

**A specific API to serve vocabularies based on the ****Lex****Grid model, developed for the Cancer Biomedical Informatics Grid (ca****BIG****®) community.**
**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.**

## LexBIG Architecture

**LexBIG Architecture**

**Each LexGrid ‘Node’ provides the software, metadata, indexes, and backing data store to service one or more vocabularies.**
**Each LexBIG Installation represents one LexGrid Node and Java API to administer and query data.**

- File System:
- Metadata &
- Indexes

## Conceptual Overview

- LexBIG/EVS caGrid Service

- LexBIG/EVS Distributed Service

- LexBIG/EVS Java API

**Conceptual Overview**

- LexGrid
- Model & Storage

**Browsers and Applications**

## LexBIG/EVS API

**LexBIG/EVS API**

- LexGrid
- Model & Storage

## LexBIG/EVS API – Characteristics

**API coverage**
- Administrative Functions
- Query Code Systems and Available Metadata
- Query Concepts, Concept Properties, and Qualifications
- Query Concept Relationships and Qualifications
**API characteristics**
- Conscious separation of service and data classes
- Deferred query resolution
- Payload optimization
- Support iteration
- Defined extension points (loaders, exporters, sort algorithms, filters, convenience methods)

**Notes:**
Use Cases and requirements demanded a rich (LexBIG) API, as opposed to the existing HL7 CTS specification.

## LexBIG/EVS API – Example

**Prerequisites**
- ICD-9-CM loaded from UMLS distribution (RRF source files)

**LoadUMLSFiles [-s null] [-mf uri] [-v int] [-lp uri] [-nf] -in uri [-t id] [-mh int] [-a]**
**Example: **
**LoadUMLSFiles -in **_[file:///path/to/directory/](file:///path/to/directory/)_** -s “ICD9CM" -nf -a**
- -s,--sources Comma-delimited list of source vocabularies to load.
- -mh,--mrhier <int> Process hierarchical relationships stored by the MRHIER file. 0=none, 1=HCD-tagged items (default)
- -a,--activate ActivateScheme on successful load.
- -in,--input <uri> URI or path specifying the directory containing the NLM files.
- -lp,--loadPrefs <uri> URI or path specifying location of the Loader Preferences file.
- -mf,--manifest <uri> URI or path specifying location of the manifest file.
- -nf,--noFail If specified, indicates that processing should not stop for recoverable errors.
- -t,--tag <id> An optional tag ID (e.g. 'PRODUCTION' or 'TEST') to assign.
- -v,--validate <int> Validation only; no load. If specified, 'nf', 'a' and 't‘ are ignored. 0 to verify files exist.

## LexBIG/EVS API – Example

**Let’s query some concepts ...**
**Target a code system**
_**Define a new LexBIGService as starting point.**_
_**Define a concept ‘space’ (a codedNodeSet) for ICD-9-CM, version 2007**_
- Note: Initially unrestricted and unresolved

**LexBIGService lbs = new LexBIGServiceImpl();**
**CodedNodeSet cns = lbs.getCodingSchemeConcepts("ICD-9-CM", null);**

## LexBIG/EVS API – Example

**Prerequisites**
- ICD-9-CM loaded from UMLS distribution (RRF source files)
**Target a code system**
- Define a concept ‘space’ (a codedNodeSet) for ICD-9-CM, version 2007
- Initially unrestricted and unresolved
**Restrict the space based by adding constraints**
_**Property ‘Semantic Type’ -> **__***exact match***__** -> “Disease or Syndrome”**_

- LexBIGService lbs = new LexBIGServiceImpl();
- CodedNodeSet cns = lbs.getCodingSchemeConcepts("ICD-9-CM", null);
**cns.restrictToMatchingProperties( Constructors.*****createLocalNameList*****(**
**   ****"Semantic_Type"), null, "Disease or Syndrome", “exactMatch", null);**

## LexBIG/EVS API – Example

**Prerequisites**
- ICD-9-CM loaded from UMLS distribution (RRF source files)
**Target a code system**
- Define a concept ‘space’ (a codedNodeSet) for ICD-9-CM, version 2007
- Initially unrestricted and unresolved
**Restrict the space based by adding constraints**
- Property ‘Semantic Type’ -> *exact match* -> “Disease or Syndrome”
_**Primary text match -> **__***sounds like***__** -> ‘infeksion’**_

- LexBIGService lbs = new LexBIGServiceImpl();
- CodedNodeSet cns = lbs.getCodingSchemeConcepts("ICD-9-CM", null);
- cns.restrictToMatchingProperties( Constructors.*createLocalNameList*(
-    "Semantic_Type"), null, "Disease or Syndrome", “exactMatch", null);
**cns.restrictToMatchingDesignations("infeksion", SearchDesignationOption.     **
**    ****PREFERRED_ONLY, “DoubleMetaphoneLuceneQuery”, null);**

## LexBIG/EVS API – Example

**Prerequisites**
- ICD-9-CM loaded from UMLS distribution (RRF source files)
**Target a code system**
- Define a concept ‘space’ (a codedNodeSet) for ICD-9-CM, version 2007
- Initially unrestricted and unresolved
**Restrict the space based by adding constraints**
- Property ‘Semantic Type’ -> *exact match* -> “Disease or Syndrome”
- Primary text match -> *sounds like* -> ‘infeksion’
_**Any text stemmed match -> ‘classify’ (to match ‘classified’, ‘classifying’, etc)**_

- LexBIGService lbs = new LexBIGServiceImpl();
- CodedNodeSet cns = lbs.getCodingSchemeConcepts("ICD-9-CM", null);
- cns.restrictToMatchingProperties( Constructors.createLocalNameList(
-    "Semantic_Type"), null, "Disease or Syndrome", “exactMatch", null);
- cns.restrictToMatchingDesignations("infeksion", SearchDesignationOption.
-     PREFERRED_ONLY, “DoubleMetaphoneLuceneQuery”, null);
**cns.restrictToMatchingDesignations("classify", SearchDesignationOption.ALL, **
**    ****"StemmedLuceneQuery“, null);**

## LexBIG/EVS API – Example

**Prerequisites**
- ICD-9-CM loaded from UMLS distribution (RRF source files)
**Target a code system**
- Define a concept ‘space’ (a codedNodeSet) for ICD-9-CM, version 2007
- Initially unrestricted and unresolved
**Restrict the space based by adding constraints**
- Property ‘Semantic Type’ -> *exact match* -> “Disease or Syndrome”
- Primary text match -> *sounds like* -> ‘infeksion’
- Any text stemmed match -> ‘classify’ (to match ‘classified’, ‘classifying’, etc)
_**Concept must be active**_

- LexBIGService lbs = new LexBIGServiceImpl();
- CodedNodeSet cns = lbs.getCodingSchemeConcepts("ICD-9-CM", null);
- cns.restrictToMatchingProperties( Constructors.createLocalNameList(
-    "Semantic_Type"), null, "Disease or Syndrome", “exactMatch", null);
- cns.restrictToMatchingDesignations("infeksion", SearchDesignationOption.
-     PREFERRED_ONLY, “DoubleMetaphoneLuceneQuery”, null);
- cns.restrictToMatchingDesignations("classify", SearchDesignationOption.ALL,
-     "StemmedLuceneQuery“, null);
**cns.restrictToStatus(ActiveOption.ACTIVE_ONLY, null);**

## LexBIG/EVS API – Example

**Prerequisites**
- ICD-9-CM loaded from UMLS distribution (RRF source files)
**Target a code system**
- Define a concept ‘space’ (a codedNodeSet) for ICD-9-CM, version 2007
- Initially unrestricted and unresolved
**Restrict the space based by adding constraints**
- Property ‘Semantic Type’ -> ***exact match*** -> “Disease or Syndrome”
- Primary text match -> ***sounds like*** -> ‘infeksion’
- Any text stemmed match -> ‘classify’ (to match ‘classified’, ‘classifying’, etc)
- Must contain a property with name -> ‘UMLS_CUI’
- Concept must be active
**Indicate sort preferences and limit number returned**
_**Sort by code, ascending**_
_**Limit to top 5**_

- ...
- cns.restrictToStatus(ActiveOption.ACTIVE_ONLY, null);
**ResolvedConceptReferenceList list = cns.resolveToList(**
**    ****Constructors.createSortOptionList(new String[] { "matchToQuery", "code" }),**
**    ****null, null, 5);**

**Notes:**
Indicate that the resulting list should be sorted, with best results first and then sorted by code if there is a tie.
Still nothing computed yet; no heavyweight database access, etc.
Perform the query and resolve the sorted/filtered list, with a maximum of 6 items returned ...

## LexBIG/EVS API – Example 

**Prerequisites**
- ICD-9-CM loaded from UMLS distribution (RRF source files)
**Target a code system**
- Define a concept ‘space’ (a codedNodeSet) for ICD-9-CM, version 2007
- Initially unrestricted and unresolved
**Restrict the space based by adding constraints**
- Property ‘Semantic Type’ -> ***exact match*** -> “Disease or Syndrome”
- Primary text match -> ***sounds like*** -> ‘infeksion’
- Any text stemmed match -> ‘classify’ (to match ‘classified’, ‘classifying’, etc)
- Must contain a property with name -> ‘UMLS_CUI’
- Concept must be active
**Indicate sort preferences and limit number returned**
- Sort by code, ascending
- Limit to top 5
**Resolve!**

## LexBIG/EVS API – Example 2

**OK, now find some relationships...**
**Target a code system**
_**Define an unrestricted graph for a target ontology (e.g. ICD-9-CM)**_

**CodedNodeGraph **_**cng**_** = lbs.getNodeGraph("ICD-9-CM", null, null);**

## LexBIG/EVS API – Example 2

**OK, now find some relationships...**
**Target a code system**
- Define an unrestricted graph for a target ontology (e.g. ICD-9-CM)
**Restrict by adding constraints**
_**Restrict to hierarchical relationships (UMLS-defined ‘CHD’ = has child)**_

- CodedNodeGraph _cng_ = lbs.getNodeGraph("ICD-9-CM", null, null);
**cng.restrictToAssociations(Constructors.createNameAndValueList(“CHD"), null);**

## LexBIG/EVS API – Example 2

**OK, now find some relationships...**
**Target a code system**
- Define an unrestricted graph for a target ontology (e.g. ICD-9-CM)
**Restrict by adding constraints**
- Restrict to hierarchical relationships (UMLS-defined ‘CHD’ = has child)
**Indicate extent of navigation**
_**Set focal point (008 = ‘Intestinal infections due to other organisms’)**_
_**Maximum 2 levels, full reporting at all levels**_
_**Moving only in forward direction**_
_**No application of filter extensions, etc**_
_**Maximum 50 nodes resolved overall**_

- CodedNodeGraph _cng_ = lbs.getNodeGraph("ICD-9-CM", null, null);
- cng.restrictToAssociations(Constructors.createNameAndValueList(“CHD"), null);
**cng.resolveAsList(**
**  ****Constructors.*****createConceptReference*****("008", "ICD-9-CM"), true, false, 2, 2,   **
**  ****null, null, null, null, 50);**

## LexBIG/EVS API – Example 2

**OK, now find some relationships...**
**Target a code system**
- Define an unrestricted graph for a target ontology (e.g. ICD-9-CM)
**Restrict by adding constraints**
- Restrict to parent/child relationships (UMLS-defined ‘PAR’ = has parent)
- Restrict to the codedNodeSet defined in the previous example
**Indicate extent of navigation**
- Set focal point (008 = ‘Intestinal infections due to other organisms’)
- Maximum 2 levels, moving in forward direction
- Maximum 50 nodes resolved overall
**Resolve!**

## LexBIG API - Distributed

- LexBIG/EVS Java API

**LexBIG API - Distributed**

- LexGrid
- Model & Storage

## LexBIG/EVS API – Distributed

**LexBIG/EVS API – Distributed**

- Distributed LexBIG Server

- RMI

- JDBC

- JDBC

**Direct**

**Distributed**

- LexBIG API Proxy

- LexBIG Client Proxy

## LexBIG/EVS API – Distributed

**// Set the URL (for distributed access) and establish a remote service ...**
**String evsUrl = “http://evsapi.nci.nih.gov/evsapi41/http/remoteService”;**
**LexBIGService lbSvc =  EVSApplicationService.getRemoteInstance(evsUrl);**
**// Additional code is unchanged ...**
- CodedNodeSet cns = lbs.getCodingSchemeConcepts("ICD-9-CM", null);
- cns.restrictToMatchingProperties( Constructors.createLocalNameList(
-    "Semantic_Type"), null, "Disease or Syndrome", “exactMatch", null);
- cns.restrictToMatchingDesignations("infeksion", SearchDesignationOption.
-     PREFERRED_ONLY, “DoubleMetaphoneLuceneQuery”, null);
- cns.restrictToMatchingDesignations("classify", SearchDesignationOption.ALL,
-     "StemmedLuceneQuery“, null);
- ...

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

## LexBIG/EVS API - caGrid

- LexBIG/EVS Distributed Service

- LexBIG/EVS Java API

**LexBIG/EVS API - caGrid**

- LexGrid
- Model & Storage

## LexBIG/EVS API - caGrid

**LexBIG/EVS API - caGrid**

- Distributed LexBIG Server

- RMI

- JDBC

- JDBC

**Direct**

**Distributed**

- LexBIG API Proxy

- caGrid Host Server

- Distributed LexBIG Server

- RMI

**Grid**

- JDBC

- TCP

- LexBIG Proxy

- LexBIG Client Proxy

- LexBIG Client Proxy

## Same API Functionality

- Client

- caGrid Service

- Distributed LexBIG

- Calls caGrid ‘getSupportedCodingSchemes()’

- Calls Distributed LexBIG
- ‘getSupportedCodingSchemes()

- Returns result of call
- to caGrid Service

- Results are returned to client
- with all appropriate caGrid
- security mechanisms

**LexBIG/EVS API - caGrid**

## caCORE SDK APIs

**caCORE SDK APIs**

- LexGrid
- Model & Storage

##  Query-by-example (QBE) system
 Based on LexGrid model
Java Language Binding
Web Services (SOAP)
Web Services (REST HTTP / XML)             

** ****Based on LexGrid model**
- Java Language Binding
- Web Services (SOAP)
- Web Services (REST HTTP / XML)

- caCORE EVS Server

**caCORE SDK APIs**

- Hibernate

## caCORE SDK APIs - Example

- SDK-Generated Query by Example User Interface:

## caCORE SDK APIs - Example

- Example Restful Request (HTML)...

- Example Restful Output (HTML shown, XML also available)...

## Browsers and Applications

- LexBIG/EVS caGrid Service

- LexBIG/EVS Distributed Service

- LexBIG/EVS Java API

**Browsers and Applications**

- LexGrid
- Model & Storage

**Browsers and Applications**

## User Interfaces - LexBIG GUI

## User Interfaces - BioPortal

## Project Links

**LexEVS Project**
_**[http://gforge.nci.nih.gov/projects/lexevs/](http://gforge.nci.nih.gov/projects/lexevs/)**_
**caBIG® Vocabulary Knowledge Center**
_**[https://cabig-kc.nci.nih.gov/Vocab/KC/index.php/Main_Page](https://cabig-kc.nci.nih.gov/Vocab/KC/index.php/Main_Page)**_

## Supported Tools – Semantic MediaWiki

**Collaborative authoring tools** provide a distributed authoring environment. NCI BiomedGT and LexWiki are extensions of Semantic MediaWiki.

## Semantic MediaWiki

**Open source extension of MediaWiki (e.g., Wikipedia)**
**Adds semantic annotations to wiki content**
- Resource Description Framework (RDF)
- Encodes more information than text and hyperlinks
- Allows more advanced searching than simply key words
**Application to terminology management**
- Creation of change proposals
- Dynamic editing of proposal content and relationships between proposals
**Development by the Mayo Clinic and NCI**
- Interface for collaborative authoring environments
- LexWiki (in partnership with NCI and Apelon)
- An implementation of Semantic MediaWiki
- Browse terminology content
- Create and modify change proposals
- Integrated with LexBIG and Protégé

## LexWiki

**An open source, high-capacity editor for **
**    ****distributed terminology development.**
**Based on the integration of Semantic Mediawiki and LexGrid technology.**
**Developed by the Mayo Clinic with collaborations of National Cancer Institute (NCI), World Health Organization (WHO) , Stanford University and Apelon Inc**

## Semantic MediaWiki and LexWiki	

**	****	****     ****An in-depth look ****	****	****	****        at ****	****	****	****  Semantic MediaWiki ****	****	****        and LexWiki **
**by ****	**
**     ****Vocabulary Knowledge Center ****	****Subject Matter Expert **
**	****	****        ****- Jyoti Pathak**

## Supported Tools – Protégé	

**Terminology editing tools** enable terminology owners to review and make proposed changes then publish and update to the terminology server.

## Protégé

**	****Open source platform of tools**
- Plug-in architecture and Java-based API
- Originally developed by Stanford (NCBO)
**	****Terminology management**
- Ontology editor and knowledge-base framework
- Supports the creation, visualization, and manipulation of ontologies in various representation formats
**	****Development by the Mayo Clinic and NCI**
- Plug-ins for integration with LexGrid and Semantic MediaWiki
- Protégé –Frames
- Protégé - OWL

## Protégé – Mayo and NCI Plug-Ins

**Mayo Plug-In**
- 	In order to add more powerful functionality (e.g., inferencing, editing) to the existing infrastructure and align LexGrid more closely with various Semantic Web technologies, the LexOWL plugin for Protégé 4 provides a way for representing the ontologies modeled within the LexGrid environment in OWL (Web Ontology Language). Essentially, the plugin provides a "bridge" that glues the LexBIG (an interface that implements the LexGrid model) and OWL APIs (an interface that implements OWL) seamlessly.
** ****NCI Plug-In**

*NCI Protégé *is a collection of Protégé plug-ins developed for the NCI-specific editing
- environment. NCI Protégé provides a customized OWL editing environment tailored to
- the needs of NCI terminologies, including additional editing and querying capabilities
- that are not available in the Protégé OWL plug-in. The NCI-specific plug-ins have been implemented as a tabbed interface.

## Protégé

**                  ****An in-depth look ****	****	****	****	****          at ****	****	****	****	****              Protégé ****	****	****	****	****                    by ****	**
**       ****Vocabulary Knowledge Center ****	****  ****	****  Subject Matter Expert,****	****	****	****           Jyoti Pathak.**

## Agenda

**Introduction to the Vocabulary Knowledge Center**
**Overview of the VKC Website**
**Supported Tools**
**Conclusions**
**Feedback and Discussion**

## Future Development – VKC wiki

**“****Always keeping in mind our customers needs”**
**Initial Focus**
**	****	**Operations and Organization
**Focus Areas for the Future  **
- content
- needs of community
- usability of information within website
- outreach/Collaborations

## Tools – What’s Happening?

**Terminology editing tools** enable terminology owners to review and make proposed changes then publish and update to the terminology server.

**Collaborative authoring tools** provide a distributed authoring environment. NCI BiomedGT and LexWiki are extensions of Semantic MediaWiki.

**Terminology infrastructure and services **are provided by the LexGrid system, which includes both Java and caGrid-based interfaces.

## Tool News 

_**LexGrid/LexBIG**_
- Release of LexBIG 2.3.0 on October 13, 2008
- EVS is transitioning from using Apelon DTS software for terminology services to using the open-source LexBIG software, developed by Mayo Clinic.
- Visit the VKC wiki to discuss/respond to a request for a LexEVS boot camp for this transition. There is a discussion forum dedicated to this request. _[EVS API 4.x to 5.0 Migration forum](https://cabig-kc.nci.nih.gov/Vocab/forums/viewforum.php?f=23)_.
_**Semantic MediaWiki/LexWiki**_
- LexWiki package being created for users – will be available on the VKC wiki by mid-November 2008.
- SMW Project SMW 1.4 alpha released for extension developers on Oct 26 2008.
- For developers
- Unifies the treatment of "special properties" and normal user-defined properties**. **

## Tool News (continued)

**Protégé**
- Protégé 3.4 beta (build 513) released on October 24, 2008
- New OWL parser (for OWL 1.0)
- Database backend support
- Protégé 4.0 beta (build 103) released on October 15, 2008
- Based on the new Manchester OWL API (for OWL 2.0)
- Faster, scalable, & better reasoner integration

## Contact Information

-  **vocabkc@mayo.edu **
**https://cabig-kc.nci.nih.gov/Vocab/KC**

## Agenda

**Introduction to the Vocabulary Knowledge Center**
**Overview of the VKC Website**
**Supported Tools**
**Conclusions**
**Feedback and Discussion**

## Feedback and Discussion	

**What are your needs as a community?**
**What kind(s) of documentation are most needed?**
- End-User
- Technical
**What kind(s) of education and training are in demand?**
- General
- End-User
**Discussion**

**Email:  ****vocabkc@mayo.edu**
**Website: ****https://cabig-kc.nci.nih.gov/Vocab/KC**