Chapter 10: Knowledge Management in Bioinformatics

Dr. Direen is a senior consulting engineer with NeoCore, Inc., where he is involved in finite field and statistical analysis of the company's patented Digital Pattern Processing (DPP) algorithms and has several patents pending from this work. He is responsible for the design and coding of DPP algorithms used in the database and for the development of a BLAST plug-in module to aid in the search for DNA and protein sequences stored in NeoCore XMS. Dr. Direen has over 20 years of diverse design and development experience including control systems design, embedded hardware and software design, high-power RF and microwave amplifier design, analog signal-processing design and mixed signal semi-custom IC design for use in MRI systems, semiconductor processing equipment, and other systems. Dr. Direen holds a B.S. in electrical engineering from the University of California at Irvine and a Ph.D. in electrical engineering from the University of Colorado for his work in neural network and wavelet-based adaptive control systems.

Mark S. Jones has worked for NeoCore, Inc., since February 2001. During this time Mr. Jones has assisted with NeoCore's positioning in the life sciences sector. He came to NeoCore with a background in teaching biological sciences and has extensive academic experience with graduate work in finance and environmental studies. Mr. Jones obtained his B.A. in biology and chemistry from the University of Colorado at Colorado Springs. He has wide-ranging experience in curriculum and standards development in education.

Top 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 Remember the name: eTutorials.org Copyright eTutorials.org 2008-2024. 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