# Presentation: 097151

## Terminology Curation with Biomed GT (Semantic MediaWiki)

- Terminology and the Semantic MediaWiki

- 04/18/2007

## What is Biomed GT

- Biomedical Grid Terminology
- An open, collaboratively developed terminology for translational research
- Based on the NCI Thesaurus
- Goal: Evolve BiomedGT into a set of subterminologies that can be
- Federated
- Maintained by experts in the relevant research communities

- Terminology and the Semantic MediaWiki

- 04/18/2007

## Nature of the Project

- Provide a mechanism for the research and clinical communities to collaboratively create and edit biomedical terminology used by the Cancer Bioinformatics Grid community and other interested users

- Terminology and the Semantic MediaWiki

- 04/18/2007

## What is biomedgt.org

- A wiki site
- A new tool for collaborative terminology authoring
- Developed by:
- _[National Cancer Institute Center for Bioinformatics](http://ncicb.nci.nih.gov/NCICB/)__ _
- Apelon, Inc.
- Significant collaboration and contribution from Mayo Clinic Division of Biomedical Informatics

- Terminology and the Semantic MediaWiki

- 04/18/2007

## History

- The Original Task
- Evaluate the roles, categories and organization of the National Cancer Institute (NCI)’s Cancer Thesaurus with respect to:
- Upper Level Ontological Principles
- ISO TC37 & Related principles
- Approach
- Gather appropriate upper level ontologies (BFO, Dolce Lite, Top Bio, UMLS Semantic Net and OBO Relations Ontology) into a single, readily referenced format
- Load NCI Thesaurus into same format
- Multiple parties review, annotate, recommend and categorize
- Publish, analyze and evaluate results

- Terminology and the Semantic MediaWiki

- 04/18/2007

## Solution

- By using the Semantic MediaWiki (SMW), we were able to accomplish all of the goals in a (very) reasonable period of time

- Terminology and the Semantic MediaWiki

- 04/18/2007

## Slide 7

- Terminology and the Semantic MediaWiki

- 04/18/2007

## Slide 8

- Terminology and the Semantic MediaWiki

- 04/18/2007

## Internal Hyperlink to Semantic Net

- External Hyperlink to OMIM

- Text Rendering of DL “Some” Statement

- Curation Status Tracking

- Terminology and the Semantic MediaWiki

- 04/18/2007

## Discussion

- We also discovered that, with some extensions, the SMW could be useful for publishing, annotating and cross-referencing other terminological resources.

- Terminology and the Semantic MediaWiki

- 04/18/2007

## The Question

- Could this approach be more generally applied to the task of terminology authoring /curation

- Terminology and the Semantic MediaWiki

- 04/18/2007

## The Answer	

- In short, “yes”
- Load and browse terminologies
- Query by concept code  or preferred name
- Generic search with semantic assistance (Halo Extension)
- Create and Edit proposals or change requests to the Biomed GT terminology

- Terminology and the Semantic MediaWiki

- 04/18/2007

## Slide 13

- Terminology and the Semantic MediaWiki

- 04/18/2007

## Terminology Workflow 2008

- Controlled
- Terminology

- Curation

- (1)

- Distribution

- (2)

- (3)

- (5)

- Common
- Distribution
- Model

- Online
- Services

- (4)

- Terminology and the Semantic MediaWiki

- 04/18/2007

**Notes:**
Over the past 10+ years, the advent of a common distribution model and common services have enabled a more standardized distribution mechanism

Terminology was curated by a committee or organization composed of subject matter experts.
The distribution process now involves transforming the content into the terms of a common model and/or publishing it via standarized online services
A common model allows multiple terminology to be absorbed and integrated for common consumption
 Standardized API’s allow direct access to terminological content
The feedback mechanism, while improved by having the common model semantics at its disposal, is still limited and, in large, ad-hoc

## Terminology Workflow 2008

- Controlled
- Terminology

- Curation

- (1)

- Distribution

- (2)

- (3)

- (5)

- Common
- Distribution
- Model

- Online
- Services

- (4)

- Controlled
- Terminology
- B

- Terminology and the Semantic MediaWiki

- 04/18/2007

**Notes:**
The common model and services allow multiple terminologies to be merged, published together. 

It also enables the user base to write generalized tools that can utilize mutliple terminologies

## Workflow and Feedback

- Controlled
- Terminology

- Curation

- (1)

- Distribution

- (2)

- (3)

- (5)

- Common
- Distribution
- Model

- Online
- Services

- (4)

- Terminology and the Semantic MediaWiki

- 04/18/2007

## The Feedback Component

- Curation

- Terminology and the Semantic MediaWiki

- 04/18/2007

**Notes:**
Requirements
Enable community commentary and input
Provide access to editing and veting process (<Torah commentary>)
Status tracking (submitted, approved, denied, accepted, included in version X)
Community sanctioning (<sanger>)
Adhere to existing semantics (LexGrid, OWL, SKOS(?), etc).

## The Feedback Component

- Curation

- Semantic
- MediaWiki (++)

- Annotations and
- Change Requests

- Community
- Review

- Distribution

- Common
- Distribution
- Model

- Online
- Services

- Version
- Staging

- Controlled
- Terminology

- Terminology and the Semantic MediaWiki

- 04/18/2007

## Why Version Staging/Curation

- We don’t *want* to change the terminology content on the fly

- Terminology and the Semantic MediaWiki

- 04/18/2007

## Clinical / Research Terminology

- Quality and content is important
- Needs central vetting, integration, QA
- Central model doesn’t scale
- Need input from (many) experts
- Need visible, active feedback loop

- Terminology and the Semantic MediaWiki

- 04/18/2007

## Clinical / Research Terminology

- Centrally curated
- Central to the practice of medicine
- Insurance and reporting
- Regulatory
- Research
- Clinical Practice
- Information Sharing
- ICD-9, CPT-4, SNOMED, ...

- Terminology and the Semantic MediaWiki

- 04/18/2007

## How is it Working?

- Very well!

- Terminology and the Semantic MediaWiki

- 04/18/2007

## Status

- BiomedGT Alpha 1 release is live
- Alpha 2 in Late January early February
- Collaboration on TCDE
- Apelon w/ DTS Server / LexBIG
- Mayo with Protégé Server
- Workflow
- NCI / Apelon
- Identifier resolution / hyperlinks
- Tools
- Semantic Templates
- Halo Extension
- Hover over
- WYSWIG editing
- ...

- Terminology and the Semantic MediaWiki

- 04/18/2007

## Questions?

- _[BGTsupport@apelon.com](mailto:BGTsupport@apelon.com)_
- _[hsolbrig@apelon.com](mailto:hsolbrig@apelon.com)_
- _[rhamm@apelon.com](mailto:rhamm@apelon.com)__ _
- _[http://biomedgt.org](http://biomedgt.org/)__ _
- _[http://wiki.ontoworld.org/index.php/Semantic_MediaWiki](http://wiki.ontoworld.org/index.php/Semantic_MediaWiki)_

- Terminology and the Semantic MediaWiki

- 04/18/2007