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

Yuxin MaoCCNT Lab of Zhejiang University

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Outline

Background Ontology Modeling Ontology Development Ontology Reuse Applications

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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

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Background(2)

TCM Research requires a great deal of knowledge from different sources TCM herbal medicine, TCM diseases, TCM EMRs, TCM Li

teratures… The size of existing TCM knowledge base is too larg

e for any TCM scientist or doctor to handle. A large-scale ontology is critical in the sharing and in

tegration of information and knowledge in TCM to overcome the problem of semantic heterogeneity and encode domain knowledge in reusable format

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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

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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

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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

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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)

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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

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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

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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

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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

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Ontology Reuse

Locality of knowledge reference A typical application can only use a small propor

tion of the TCM OntologySub-ontologies are context-specific p

ortions of the TCM ontologySub-ontology cache can hold SubOs

as cache blocks for ontology reuse.

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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.

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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.

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Thank YouQ&A