Semantic Web Development for Traditional Chinese Medicine
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Transcript of Semantic Web Development for Traditional Chinese Medicine
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Semantic Web Development for Traditional Chinese Medicine
Tong Yu, Zhejiang University. China.
July. 15th, 2008, IAAI, Chicago, Il.
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Outline
• Overview of TCM Semantic Web• Ontology Engineering and Reuse• Semantic Mapping and Integration• Semantic Query, Search and
Navigation• Semantic Graph Mining • Summary
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The Semantic Web: “A Giant Graph of Things”
• Based on the Internet and the Web• Formal Semantics
o Use URIs as names for thingso RDF information about things available through HTTP URIso Use RDF statements for semantic links between things
• Global network of databases
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Project Background
• Preservation and Modernization of TCM
• Integrative Medicine • Connecting the data• A Student Project
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The ultimate vision: Make a connection between TCM and modern medicine
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User Scenario
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TCM Ontology Platform
• Domain Categorizationo The current TCM ontology contains 15 major
categories for each sub-domain.
• Ontology Structureo A typing system as a concept hierarchyo A semantic network defining the associations between concepts
• Scaleo More than 20,000 classes and 100,000 instances
defined in the current ontology
• Access Controlo layered privilege mechanism that defines users as
reader, editor, checker and administrator.
• Serviceo Web APIs for ontology-based applications.
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The 15 Categories Defined in the TCM Ontology
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Ajax-based Ontology Viewer and Editor
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Ontology Fusion and Reuse
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Visualized Mapper: An Eclipse Plugin
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Visualized Mapper: The Ajax-based Tool
• http://ec2-67-202-22-44.compute-1.amazonaws.com:8890/demo/mapper/
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Semantic Search Portal
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Semantic Graph Mining
• We envision that intelligent agents could work on the Semantic Web of structured data, and assist their masters to solve problems, who can o discover important Web resourceso discern latent semantic associationso interpret interesting graph patterns.
• Existing methods of data mining, especially graph mining, can be adopted to implement these intelligent agents.
• We propose a methodology, called Semantic Graph Mining (SGM), for building agents that discover knowledge on the Semantic Web.
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TCM Semantic Graph
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The Network of Herbs
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The Process for Analyzing the Network of Herbs
1.Data Modeling2.Data
Transformation & Integration :
3.Entity Disambiguation
4.Interaction Identification
5.Network Mapping6.Network Analysis
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Semantic Graph Resource Importance
• the in-degree centrality CI of a resource is measured by the weighted sum of statements with the resource as object, and the out-degree centrality is measured by the weighted sum of statements with the resource as subject.
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Semantic Graph Resource Importance
• The Closeness Centrality of a resource r is defined as the inverse of the sum of the distance from r to all other resources.
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Semantic Graph Resource Importance
• The Betweenness Centrality of a resource r is defined as the ratio of shortest paths across the resource in the graph.
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Frequent Semantic Subgraph
SG1 SG2
SG3
SG4SG5
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Frequent Semantic Subgraph
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Pattern Interpretation
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Interactive Mining of TCM Knowledge
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Conclusion
• We took the first systematic approach to leverage the progress of Biomedical Informatics to address the modernization of TCM.
• Domain experts evaluate the platform’s major technical features as original and productive in Drug Safety and Efficacy analysis.
• This case study demonstrates the Semantic Web’s advantages in representation, integration, and discovery of knowledge with complex domain models.
• Contributes to the Preservation and Modernization of TCM as intangible cultural heritage.
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Reference
• TCM Ontology Engineering and Reuseo Y. Mao, et al. Dynamic Sub-Ontology Evolution for Traditional Chinese
Medicine Web Ontology. Journal of Biomedical Informatics, 2008 (In progress)
o Y. Mao et al. Sub-Ontology Based Resource Management for Web-based e-Learning. IEEE Transactions on Knowledge and Data Engineering, 2008 (In Progress)
• Data Mapping and Integrationo Zhao-hui Wu, Hua-jun Chen. 2008. Semantic Grid:Model,
Methodology,and Applications (Monograph). Co-published by Zhejiang University Press and Springer-Verlag GmbH.
o Huajun Chen et al. RDF/RDFS-based Relational Database Integration. ICDE 2006
o Huajun Chen et al.From Legacy Relational Databases to the Semantic Web: an In-Use Application for Traditional Chinese Medicine. ISWC 2006.
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Reference
• Semantic Search, Query, and Navigationo Huajun Chen et al. Towards semantic e-science for traditional chinese
medicine. BMC Bioinformatics, 8(Suppl 3):56, 2007.• Knowledge Discovery for TCM
o Yi Feng et al. Knowledge discovery in traditional Chinese medicine: State of the art and perspectives, AI in Medicine, 38(3): 219-236, 2006.
o Xuezhong Zhou et al. Integrative mining of traditional Chinese medicine literature and MEDLINE for functional gene networks. AI in Medicine (2007) 41, 87—104.
• Semantic Graph Miningo Tong Yu et al. Semantic Graph Mining for Biomedical Complex Network
Analysis. WWW ’08 Workshops: HCLS.o Huajun Chen et al. Semantic Graph Mining for Biomedical Complex
Network Analysis. Brief. In Bioinformatics ( In progress).
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Thanks for your time!