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Chapter 10. Knowledge Management in Bioinformatics
Harry G. Direen, Jr. Mark S. Jones
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Title
TOC
Preface
P.1 What Is XML?
P.2 XML Concepts
P.3 XML-Related Technologies
P.4 XML Data Management
P.5 How This Book Is Organized
P.6 Who Should Read This Book
P.7 Resources
Acknowledgments
Chapter 8
Chapter 12
Chapter 13
Chapter 14
Chapter 19
Part I: What Is XML?
Chapter 1. Information Modeling with XML
1.1 Introduction
1.2 XML as an Information Domain
1.3 How XML Expresses Information
1.4 Patterns in XML
1.5 Common XML Information-Modeling Pitfalls
1.6 A Very Simple Way to Design XML
1.7 Conclusion
Part II: Native XML Databases
Chapter 2. Tamino-Software AG's Native XML Server
2.1 Introduction
2.2 Tamino Architecture and APIs
2.3 XML Storage
2.4 Querying XML
2.5 Tools
2.6 Full Database Functionality
2.7 Conclusion
Chapter 3. eXist Native XML Database
3.1 Introduction
3.2 Features
3.3 System Architecture Overview
3.4 Getting Started
3.5 Query Language Extensions
3.6 Application Development
3.7 Technical Background
3.8 Conclusion
Chapter 4. Embedded XML Databases
4.1 Introduction
4.2 A Primer on Embedded Databases
4.3 Embedded XML Databases
4.4 Building Applications for Embedded XML Databases
4.5 Conclusion
Part III: XML and Relational Databases
Chapter 5. IBM XML-Enabled Data Management Product Architecture & Technology
5.1 Introduction
5.2 Product and Technology Offering Summaries
5.3 Current Architecture and Technology
5.4 Future Architecture and Technology
5.5 Conclusion
Notices
Chapter 6. Supporting XML in Oracle9i
6.1 Introduction
6.2 Storing XML as CLOB
6.3 XMLType
6.4 Using XSU for Fine-Grained Storage
6.5 Building XML Documents from Relational Data
6.6 Web Access to the Database
6.7 Special Oracle Features
6.8 Conclusion
Chapter 7. XML Support in Microsoft SQL Server 2000
7.1 Introduction
7.2 XML and Relational Data
7.3 XML Access to SQL Server
7.4 Serializing SQL Query Results into XML
7.5 Providing Relational Views over XML
7.6 SQLXML Templates
7.7 Providing XML Views over Relational Data
7.8 Conclusion
Chapter 8. A Generic Architecture for Storing XML Documents in a Relational Database
8.1 Introduction
8.2 System Architecture
8.3 The Data Model
8.4 Creating the Database
8.5 Connecting to the Repository
8.6 Uploading XML Documents
8.7 Querying the Repository
8.8 Further Enhancements
8.9 Conclusion
Chapter 9. An Object-Relational Approach to Building a High-Performance XML Repository
9.1 Introduction
9.2 Overview of XML Use-Case Scenario
9.3 High-Level System Architecture
9.4 Detailed Design Descriptions
9.5 Conclusion
Part IV: Applications of XML
Chapter 10. Knowledge Management in Bioinformatics
10.1 Introduction
10.2 A Brief Molecular Biology Background
10.3 Life Sciences Are Turning to XML to Model Their Information
10.4 A Genetic Information Model
10.5 NeoCore XMS*
10.6 Integration of BLAST into NeoCore XMS
Conclusion
Chapter 11. Case Studies of XML Used with IBM DB2 Universal Database
11.1 Introduction
11.2 Case Study 1: "Our Most Valued Customers Come First"
11.3 Case Study 2: "Improve Cash Flow"
11.4 Conclusion
Notices
Chapter 12. The Design and Implementation of an Engineering Data Management System Using XML and J2EE
12.1 Introduction
12.2 Background and Requirements
12.3 Overview
12.4 Design Choices
12.5 Future Directions
12.6 Conclusion
Chapter 13. Geographical Data Interchange Using XML-Enabled Technology within the GIDB System
13.1 Introduction
13.2 GIDB METOC Data Integration
13.3 GIDB Web Map Service Implementation
13.4 GIDB GML Import and Export
13.5 Conclusion
Chapter 14. Space Wide Web by Adapters in Distributed Systems Configuration from Reusable Components
14.1 Introduction
14.2 Advanced Concept Description: The Research Problem
14.3 Integration of Components with Architecture
14.4 Example
14.5 Future Generation NASA Institute for Advanced Concepts, Space Wide Web Research, and Boundaries
14.6 Advanced Concept Development
14.7 Conclusion
Chapter 15. XML as a Unifying Framework for Inductive Databases
15.1 Introduction
15.2 Past Work
15.3 The Proposed Data Model: XDM
15.4 Benefits of XDM
15.5 Toward Flexible and Open Systems
15.6 Related Work
15.7 Conclusion
Chapter 16. Designing and Managing an XML Warehouse
16.1 Introduction
16.2 Architecture
16.3 Data Warehouse Specification
16.4 Managing the Metadata
16.5 Storage and Management of the Data Warehouse
16.6 DAWAX: A Graphic Tool for the Specification and Management of a Data Warehouse
16.7 Related Work
16.8 Conclusion
Part V: Performance and Benchmarks
Chapter 17. XML Management System Benchmarks
17.1 Introduction
17.2 Benchmark Specification
17.3 Benchmark Data Set
17.4 Existing Benchmarks for XML
17.5 Conclusion
Chapter 18. The Michigan Benchmark: A Micro-Benchmark for XML Query Performance Diagnostics
18.1 Introduction
18.2 Related Work
18.3 Benchmark Data Set
18.4 Benchmark Queries
18.5 Using the Benchmark
18.6 Conclusion
Chapter 19. A Comparison of Database Approaches for Storing XML Documents
19.1 Introduction
19.2 Data Models for XML Documents
19.3 Databases for Storing XML Documents
19.4 Benchmarking Specification
19.5 Test Results
19.6 Related Work
19.7 Summary
Chapter 20. Performance Analysis between an XML-Enabled Database and a Native XML Database
20.1 Introduction
20.2 Related Work
20.3 Methodology
20.4 Database Design
20.5 Discussion
20.6 Experiment Result
20.7 Conclusion
Chapter 21. Conclusion
References
Contributors
Editors
Chapter 1: Information Modeling with XML
Chapter 2: Tamino-Software AG's Native XML Server
Chapter 3: eXist Native XML Database
Chapter 4: Embedded XML Databases
Chapter 5: IBM XML-Enabled Data Management Product Architecture and Technology
Chapter 6: Supporting XML in Oracle9i
Chapter 7: XML Support in Microsoft SQL Server 2000
Chapter 8: A Generic Architecture for Storing XML Documents in a Relational Database
Chapter 9: An Object-Relational Approach to Building a High-Performance XML Repository
Chapter 10: Knowledge Management in Bioinformatics
Chapter 11: Case Studies of XML Used with IBM DB2 Universal Database
Chapter 12: The Design and Implementation of an Engineering Data Management System Using XML and J2EE
Chapter 13: Geographical Data Interchange Using XML-Enabled Technology within the GIDB System
Chapter 14: Space Wide Web by Adapters in Distributed Systems Configuration from Reusable Components
Chapter 15: XML as a Unifying Framework for Inductive Databases
Chapter 16: Designing and Managing an XML Warehouse
Chapter 17: XML Management System Benchmarks
Chapter 18: The Michigan Benchmark: A Micro-Benchmark for XML Query Performance Diagnostics
Chapter 19: A Comparison of Database Approaches for Storing XML Documents
Chapter 20: Performance Analysis between an XML-Enabled Database and a Native XML Database
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