Front Cover -- Bioinformatics: Managing Scientific Data -- Copyright Page -- Table of Contents -- Contributors -- About the Authors -- Preface -- Chapter 1. Introduction -- 1.1 Overview -- 1.2 Problem and Scope -- 1.3 Biological Data Integration -- 1.4 Developing a Biological Data Integration System -- References -- Chapter 2. Challenges Faced in the Integration of Biological Information -- 2.1 The Life Science Discovery Process -- 2.2 An Information Integration Environment for Life Science Discovery -- 2.3 The Nature of Biological Data -- 2.4 Data Sources in Life Science -- 2.5 Challenges in Information Integration -- Conclusion -- References -- Chapter 3. A Practitioner's Guide to Data Management and Data Integration in Bioinformatics -- 3.1 Introduction -- 3.2 Data Management in Bioinformatics -- 3.3 Dimensions Describing the Space of Integration Solutions -- 3.4 Use Cases of Integration Solutions -- 3.5 Strengths and Weaknesses of the Various Approaches to Integration -- 3.6 Tough Problems in Bioinformatics Integration -- 3.7 Summary -- Acknowledgments -- References -- Chapter 4. Issues to Address While Designing a Biological Information System -- 4.1 Legacy -- 4.2 A Domain in Constant Evolution -- 4.3 Biological Queries -- 4.4 Query Processing -- 4.5 Visualization -- 4.6 Conclusion -- Acknowledgments -- References -- Chapter 5. SRS: An Integration Platform for Databanks and Analysis Tools in Bioinformatics -- 5.1 Integrating Flat File Databanks -- 5.2 Integration of XML Databases -- 5.3 Integrating Relational Databases -- 5.4 The SRS Query Language -- 5.5 Linking Databanks -- 5.6 The Object Loader -- 5.7 Scientific Analysis Tools -- 5.8 Interfaces to SRS -- 5.9 Automated Server Maintenance with SRS Prisma -- 5.10 Conclusion -- References -- Chapter 6. The Kleisli Query System as a Backbone for Bioinformatics Data Integration and Analysis.

6.1 Motivating Example -- 6.2 Approach -- 6.3 Data Model and Representation -- 6.4 Query Capability -- 6.5 Warehousing Capability -- 6.6 Data Sources -- 6.7 Optimizations -- 6.8 User Interfaces -- 6.9 Other Data Integration Technologies -- 6.10 Conclusions -- References -- Chapter 7. Complex Query Formulation Over Diverse Information Sources in TAMBIS -- 7.1 The Ontology -- 7.2 The User Interface -- 7.3 The Query Processor -- 7.4 Related Work -- 7.5 Current and Future Developments in TAMBIS -- Acknowledgments -- References -- Chapter 8. The Information Integration System K2 -- 8.1 Approach -- 8.2 Data Model and Languages -- 8.3 An Example -- 8.4 Internal Language -- 8.5 Data Sources -- 8.6 Query Optimization -- 8.7 User Interfaces -- 8.8 Scalability -- 8.9 Impact -- 8.10 Summary -- Acknowledgments -- References -- Chapter 9. P/FDM Mediator for a Bioinformatics Database Federation -- 9.1 Approach -- 9.2 Analysis -- 9.3 Conclusions -- Acknowledgment -- References -- Chapter 10. Integration Challenges in Gene Expression Data Management -- 10.1 Gene Expression Data Management: Background -- 10.2 The GeneExpress System -- 10.3 Managing Gene Expression Data: Integration Challenges -- 10.4 Integrating Third-Party Gene Expression Data in GeneExpress -- 10.5 Summary -- Acknowledgments -- Trademarks -- References -- Chapter 11. DiscoveryLink -- 11.1 Approach -- 11.2 Query Processing Overview -- 11.3 Ease of Use, Scalability, and Performance -- 11.4 Conclusions -- References -- Chapter 12. A Model-Based Mediator System for Scientific Data Management -- 12.1 Background -- 12.2 Scientific Data Integration Across Multiple Worlds: Examples and Challenges from the Neurosciences -- 12.3 Model-Based Mediation -- 12.4 Knowledge Representation for Model-Based Mediation -- 12.5 Model-Based Mediator System and Tools -- 12.6 Related Work and Conclusion -- Acknowledgments.

References -- Chapter 13. Compared Evaluation of Scientific Data Management Systems -- 13.1 Performance Model -- 13.2 Evaluation Criteria -- 13.3 Tradeoffs -- 13.4 Summary -- References -- Concluding Remarks -- Summary -- Looking Toward the Future -- Appendix: Biological Resources -- Glossary -- System Information -- Index.