Book description
Life science data integration and interoperability is one of the most challenging problems facing bioinformatics today. In the current age of the life sciences, investigators have to interpret many types of information from a variety of sources: lab instruments, public databases, gene expression profiles, raw sequence traces, single nucleotide polymorphisms, chemical screening data, proteomic data, putative metabolic pathway models, and many others. Unfortunately, scientists are not currently able to easily identify and access this information because of the variety of semantics, interfaces, and data formats used by the underlying data sources.Bioinformatics: Managing Scientific Data tackles this challenge head-on by discussing the current approaches and variety of systems available to help bioinformaticians with this increasingly complex issue. The heart of the book lies in the collaboration efforts of eight distinct bioinformatics teams that describe their own unique approaches to data integration and interoperability. Each system receives its own chapter where the lead contributors provide precious insight into the specific problems being addressed by the system, why the particular architecture was chosen, and details on the system's strengths and weaknesses. In closing, the editors provide important criteria for evaluating these systems that bioinformatics professionals will find valuable.
* Provides a clear overview of the state-of-the-art in data integration and interoperability in genomics, highlighting a variety of systems and giving insight into the strengths and weaknesses of their different approaches.
* Discusses shared vocabulary, design issues, complexity of use cases, and the difficulties of transferring existing data management approaches to bioinformatics systems, which serves to connect computer and life scientists.
* Written by the primary contributors of eight reputable bioinformatics systems in academia and industry including: BioKris, TAMBIS, K2, GeneExpress, P/FDM, MBM, SDSC, SRS, and DiscoveryLink.
Table of contents
- Cover image
- Title page
- Table of Contents
- The Morgan Kaufmann Series in Multimedia Information and Systems
- Copyright
- Contributors
- About the Authors
- Preface
- Chapter 1: Introduction
- Chapter 2: Challenges Faced in the Integration of Biological Information
-
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
- Chapter 4: Issues to Address While Designing a Biological Information System
- Chapter 5: SRS: An Integration Platform for Databanks and Analysis Tools in Bioinformatics
- Chapter 6: The Kleisli Query System as a Backbone for Bioinformatics Data Integration and Analysis
- Chapter 7: Complex Query Formulation Over Diverse Information Sources in TAMBIS
- Chapter 8: The Information Integration System K2
- Chapter 9: P/FDM Mediator for a Bioinformatics Database Federation
- Chapter 10: Integration Challenges in Gene Expression Data Management
- Chapter 11: DiscoveryLink
- Chapter 12: A Model-Based Mediator System for Scientific Data Management
- Chapter 13: Compared Evaluation of Scientific Data Management Systems
- Concluding Remarks
- Appendix: Biological Resources
- Glossary
- System Information
- Index
Product information
- Title: Bioinformatics
- Author(s):
- Release date: September 2003
- Publisher(s): Morgan Kaufmann
- ISBN: 9780080527987
You might also like
book
Bioinformatics for Vaccinology
"... this book was written from start to finish by one extremely dedicated and erudite individual. …
book
Bioinformatics and Functional Genomics, Second Edition
The bestselling introduction to bioinformatics and functional genomics—now in an updated edition Widely received in its …
book
Bioinformatics and Medical Applications
BIOINFORMATICS AND MEDICAL APPLICATIONS The main topics addressed in this book are big data analytics problems …
book
Computation in BioInformatics
COMPUTATION IN BIOINFORMATICS Bioinformatics is a platform between the biology and information technology and this book …