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

LexWiki Machine: A Collaboration Platform Wiki Core Semantic Wiki Semantic Forms MySQL LexBIG Export/Load Domain Experts Protégé Authoring Change sets Detection 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 Set Into Collaborative Protege Portable ChangeSet In RDF format

ChAO: Change and Annotations Ontology N. Noy, A Framework for Ontology Evolution in Collaborative Environments, ISWC06

Generating ChAO Instances LexWiki Tab Diff Algorithm Ontology Version1 LexWiki Editor Editing Input Proposals Produces Authoring Support In 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/WEB SMEs Curators LW Editor Ontology Editor Propose Changes Propose New Concepts Commit Changes Commit New Concepts Check Consistency LexWiki Simple Forms Protégé Frames/OWL Protégé Web Server LexGrid Model Terminology Services Collaborative Content Authoring (Prototype)

WIKI SMEs Curators LW Editor Ontology Editor Propose Changes Propose New Concepts Commit Changes Commit New Concepts Check Consistency Wiki Text Editor LexWiki Simple Forms Wiki-based Protégé Editor LexGrid Model Terminology Services Collaborative Content Authoring (Future)

Tool Collaboration Open-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