Bioinformatics: Managing Scientific Data (The Morgan Kaufmann Series in Multimedia Information and Systems) - Hardcover

Hardcover

ISBN 10: 155860829X ISBN 13: 9781558608290

Publisher: Morgan Kaufmann, 2003

Synopsis

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.

About this title

About the Authors

Dr. Zoé Lacroix is currently a Research Assistant Professor at Arizona State University. She received a Ph.D. in Computer Science in 1996 from the University of Paris XI (France). Her research interests cover various aspects of data management. She has published over twenty journal articles, conference papers, and book chapters. She also has served in numerous conference program committees, she has organized several panels and workshops, and she was an active member in the working groups XML Query Language and XML Forms at the World Wide Web Consortium (W3C). Dr. Lacroix has been involved in bioinformatics for over seven years. She has interacted with the Center of Bioinformatics at the University of Pennsylvania, and worked for two biotech companies: Gene Logic Inc. and SurroMed Inc. Her contributions in bioinformatics include publications, invited talks (Symposium on Bioinformatics organized at the National University of Singapore) and data integration middlewares such as the Object-Web Wrapper currently used at SmithKlineGlaxo.

Dr. Terence Critchlow is a computer scientist in the Center for Applied Scientific Computing at Lawrence Livermore National Laboratory, and leads the DataFoundry project. His involvement in bioinformatics began over seven years ago as part of a collaboration between the University of Utah Computer Science department and the Utah Human Genome Center. Since completing his dissertation and joining LLNL in 1997, he has been an active member of the research community publishing in both computer science and informatics forums, giving invited talks, participating in program committees, and organizing the XML Enabled Searches in Bioinformatics workshop.

From the Back Cover

This is the first book that focuses on the managements systems for biological data. It is an exciting compilation by leaders of an emerging community that addresses the key issues in biological data management. The book should be useful not only for the biologists but for data managers who are new to the biology domain. It would also be a great resource for courses at the interface of biology and data management.
-Sylvia Spengler, Lawrence Berkeley National Laboratory

This book very effectively tees up many of the technical challenges underlying biological data management and integration, through in-depth presentations of a good assortment of commercial and academic approaches. I found it to be a useful reference for much of the current thinking on this topic, in both theory and practice.
-David B. Searls, GlaxoSmithKline Pharmaceuticals

The life sciences face unique challenges in bringing leading-edge computing technologies to bear on their highly heterogeneous collections of data. Bioinformatics: Managing Scientific Data outlines these challenges and then explores--in exacting detail--how they've been met by eight data-integration systems devised by life scientists working in a wide range of fields.

This is critical, hard-to-find information for a necessarily diverse audience: life science researchers with a hands-on role in analysis of their data, computer scientists working with biodata, and managers who want a better understanding of the processes they oversee. It's also a valuable resource for all students whose work will be affected by the growing importance of computing throughout the life sciences.

Features
- Begins with a working definition of bioinformatics and sketches the steps that typically comprise the development of a bioinformatics system.
- Details the challenges involved in applying computing technologies to bioinformation and accounts for the failures of conventional approaches.
- Provides first-hand accounts of eight bioinformatics systems used in academia and industry, including BioKris, TAMBIS, K2, GeneExpress, P/FDM, KIND, SRS, and DiscoveryLink.
- Presents a detailed methodology for evaluating these and other systems, allowing the readers to determine the best way to realize their research aims or assess a system already in use.
- Includes a useful summary of challenges, a comparison of approaches, a glossary defining all major terms, and a list of scientific resources.

Edition details

• Publisher: Morgan Kaufmann
• Publication date: 2003
• Language: English
• ISBN 10: 155860829X
• ISBN 13: 9781558608290
• Binding: Hardcover
• Number of pages: 464
• Editor: Lacroix Zoé, Critchlow Terence