1. CCNT Lab of Zhejiang University
Web Ontology Engineering and Applications: A Case Study in Traditional Chinese Medicine
Yuxin Mao
CCNT Lab of Zhejiang University
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2. Outline Background Ontology Modeling Ontology Development
Ontology Reuse
Applications
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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
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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
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5. 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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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
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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
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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)
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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
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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
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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
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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
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13. 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.
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14. 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.
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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.
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16. Thank You
Q&A
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