CCNT Lab of Zhejiang University Web Ontology Engineering and Applications: A Case Study in Traditional Chinese Medicine Yuxin Mao CCNT Lab of Zhejiang University @ HCLS 2008

Outline Background Ontology Modeling Ontology Development Ontology Reuse Applications @ HCLS 2008

Background Ontologies are the specification of conceptualizations, used for programs and humans to share knowledge. Semantic Web facilitates the engineering of various large-scale online ontologies: UMLS for integrating biomedical terminology Gene Ontology for gene product and MGED Ontology for microarray experiment @ HCLS 2008

Background(2) TCM Research requires a great deal of knowledge from different sources TCM herbal medicine, TCM diseases, TCM EMRs, TCM Literatures… The size of existing TCM knowledge base is too large for any TCM scientist or doctor to handle. A large-scale ontology is critical in the sharing and integration of information and knowledge in TCM to overcome the problem of semantic heterogeneity and encode domain knowledge in reusable format @ HCLS 2008

Ontology Modeling Here we present the upper-level framework for modeling the TCM ontology. The current TCM ontology contains 12 major categories for each sub-domain. The TCM ontology includes 2 components: concept system semantic system @ HCLS 2008

Semantic System We have defined 59 semantic relationships between content classes and 104 TCM semantic types According to the time, function, space, entity and class attributes of TCM domain knowledge plus all the semantic types from UMLS @ HCLS 2008

Concept System The concept system defines the concepts in TCM domain, and it contains content classes and implemental classes. Content class represents the concrete domain knowledge of the TCM discipline. In order to unify class structure, we formulize key properties and relationships of content class as implemental classes: Name Class represents various name terms (e.g. alias, English name, or synonym) of an instance Definition Class represents the scientific definition of a in-stance Explanation Class represents additional explanations to instance definition Relation Class represents the relationship between two instances @ HCLS 2008

Ontology Development Requirements of the Ontology development environment (ODE) for TCM Ontology: Facilitate professional ontology development The TCM ontology is developed collaboratively by experts from several institutions, so the ODE should enable remote access and modification on the ontology The TCM ontology is divided into several categories both logically and geographically, so the ODE should enable ontology integration and federation in a distributed environment like the Web We have built a Web-based ODE, called TOtE (TCM Ontology Editor) @ HCLS 2008

Web-based Ontology Editor TOtE is an editor that allows users to edit and explore ontology online TOtE runs on the server-side and publishes large-scale TCM ontologies to users through Web services Users can browse and edit TCM ontologies anywhere with their Web browsers. Incorporates a back-end database for ontology storage Compatible with popular ontology formats @ HCLS 2008

Web-based Ontology Editor(2) The user interface incorporates an open-source AJAX framework a tree-based view for classes and a form-based view for instances of an ontology, similar with Protégé employ a layered privilege mechanism in TOtE and users that play different roles in the process of ontology development hold different privileges @ HCLS 2008

Development Procedure Analyze and determine knowledge sources Construct upper-level conceptual framework Determine and assign developing tasks Extend conceptual hierarchy Materialize ontology contents Check and revise contents Publish ontology user interface @ HCLS 2008

Major Result there have been more than 20,000 classes and 100,000 instances defined in the current knowledge base of the TCM ontology The ontology under development is still part of the complete one The TCM ontology has become a distributed large-scale knowledge base for TCM domain knowledge and can be accessed on-line @ HCLS 2008

Ontology Reuse Locality of knowledge reference A typical application can only use a small proportion of the TCM Ontology Sub-ontologies are context-specific portions of the TCM ontology Sub-ontology cache can hold SubOs as cache blocks for ontology reuse. @ HCLS 2008

Applications Database Integration Informatics Search Engine DartGrid: a semantic-based database grid platform we adopt the semantics of the TCM ontology to integrate massive amount of TCM databases based on the Grid infrastructure Informatics Search Engine DartSearch: a semantic-based search engine for TCM informatics Provides users with a Google-like search interface to perform semantic search We harness the ontology semantics to improve searching experience in DartSearch. @ HCLS 2008

Conclusion Ontology engineering is a key issue for realizing the Semantic Web vision. we propose a comprehensive approach to model, develop, and reuse large-scale Web ontology for the TCM discipline. The scale of the TCM ontology has reached 20,000 classes and 100,000 instances by now. The TCM ontology has been used to support several semantic-based applications for TCM. @ HCLS 2008

Thank You Q&A @ HCLS 2008