Web Ontology Engineering and Applications: A Case Study in Traditional Chinese Medicine

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

2. Outline • Background • Ontology Modeling • Ontology Development • Ontology Reuse • Applications

3. 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

4. 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

5. Ontology Modeling • Here we present the upper-level framework for modeling the TCM ontology. • The current TCM ontology contains 12 major categories for eachsub-domain. • The TCM ontology includes 2 components: • concept system • semantic system

6. 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

7. 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

8. 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)

9. 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

10. 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

11. 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

12. 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

13. Ontology Reuse • Locality of knowledge reference A typical application can only use a small proportion of the TCM Ontology • Sub-ontologies arecontext-specific portions of the TCM ontology • Sub-ontology cache can hold SubOs as cache blocks for ontology reuse.

14. Applications • Database Integration • 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.

15. 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.

16. Thank You Q&A