Mayo LexWiki: A Prototype of Collaborative Platform for

Terminology/Ontology Content Development

Guoqian Jiang, Ph.D.

Division of Biomedical Informatics,

Mayo Clinic College of Medicine.NCBO DevCon 2007 (Stanford)

December 13, 2007

Outline

• Why Semantic Wikis?

• LexWiki machine prototype– LexWiki Editor– LexWiki Protégé Tab

• LexWiki Features

• LexWiki/Protégé Interface

• Future vision

Why Semantic Wiki?

• The infrastructure and culture of the semantic wiki is being considered as a promising workbench for collaborative ontology engineering.– Easy to learn tool– Open content development platform– Change history management– Formal output rendering (RDF export)– …

Semantic Annotations in SMW

Attribute Annotation

Relation Annotation

Relation Annotation

LexWiki Machine: A Collaboration Platform

Wiki Core Semantic Wiki

Semantic Forms

MySQLLexBIG

Export/Load

Domain Experts

Protégé

Authoring

Change setsDetection

Templates

LexWiki Editor

LexWiki Tab

LexWiki Use Cases

• LexWiki ICD10+– A WHO project– To realize collaborative ICD11 editing process

• BiomedGT– A NCI project– To realize collaborative NCI Thesaurus

development process

LexWiki Features• Browsing support

– Hierarchical View – Data elements

• Basic data (Lexical)• Concept Property• Association (Relation)

– Association Graph

• Authoring support– Workflow for Proposals (LexWiki Editor)

• Change proposal• New concept proposal

– Workflow for change set detection• RDF output from LexWiki• Annotation Ontology Mapping

Proposed Change

Proposed Association

All Proposals

Changeset Model by Annotation Ontology (Protégé/LexWiki Interface)

Export/Load Change SetInto Collaborative Protege

Portable ChangeSetIn RDF format

ChAO: Change and Annotations Ontology

N. Noy, A Framework for Ontology Evolution in Collaborative Environments, ISWC06

Generating ChAO Instances

LexWiki TabDiff Algorithm

OntologyVersion1

LexWiki EditorEditingInput

Proposals

Produces

Produces

Authoring SupportIn Collaborative Protégé

Updates

Authoring Support in Collaborative Protégé

Instances of Changes

Summary

• We have a dream: the emergence of a semantic web

• We have a problem: the creation of complete and well-defined ontologies

• We have a solution: to create these ontologies with collaborative ontology-editing tools

• We have a problem: we do not have such tools available

• We have a partial tested solution: LexWiki prototype

WIKI LOCAL/WEBSMEs Curators

LW Editor Ontology Editor

Propose ChangesPropose New Concepts

Commit ChangesCommit New ConceptsCheck Consistency

LexWiki Simple Forms Protégé Frames/OWLProtégé Web Server

LexGrid ModelTerminology Services

Collaborative Content Authoring (Prototype)

WIKI WIKISMEs Curators

LW Editor Ontology Editor

Propose ChangesPropose New Concepts

Commit ChangesCommit New ConceptsCheck Consistency

Wiki Text EditorLexWiki Simple Forms

Wiki-basedProtégé Editor

LexGrid ModelTerminology Services

Collaborative Content Authoring (Future)

Tool CollaborationOpen-source distributed authoring

• Mayo Clinic, Division of Biomedical Informatics• Apelon – terminology consultants• WHO – World Health Organization

– ICD11 editing task

• NCI – National Cancer Institute– caBIG – Bioinformatics Grid– NCI Thesaurus development task

• Stanford – Biomedical Informatics Research– Developers of Protégé and Collaborative Protégé – National Center for Biomedical Ontologies

Acknowledgements

• LexWiki development team in Mayo BMI– Deepak Sharma– Kevin Peterson– Jyotishman Pathak, Ph.D.– Guoqian Jiang, Ph.D.– Thomas Johnson (LexGrid Team Leader)– James Buntrocks