Bioinformatics : managing scientific data / edited by Zoé Lacroix and Terence Critchlow.

Format:

Book

Contributor:

Lacroix, Zoé.

Critchlow, Terence

Constance L. Rosenthal Book Fund.

Series:

Morgan Kaufmann series in multimedia information and systems

The Morgan Kaufmann series in multimedia information and systems

Language:

English

Subjects (All):

Bioinformatics.

Physical Description:

xxi, 441 pages : illustrations ; 24 cm.

Place of Publication:

San Francisco, CA : Morgan Kaufmann Publishers, [2003]

Summary:

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 have 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 is also a valuable resource for all students whose work will be affected by the growing importance of computing throughout the life sciences

Contents:

1.3 Biological Data Integration 4

1.4 Developing a Biological Data Integration System 7

2 Challenges Faced in the Integration of Biological Information / Su Yun Chung, John C. Wooley 11

2.1 The Life Science Discovery Process 12

2.2 An Information Integration Environment for Life Science Discovery 14

2.3 The Nature of Biological Data 15

2.4 Data Sources in Life Science 17

2.5 Challenges in Information Integration 19

3 A Practitioner's Guide to Data Management and Data Integration in Bioinformatics / Barbara A. Eckman 35

3.2 Data Management in Bioinformatics 36

3.3 Dimensions Describing the Space of Integration Solutions 45

3.4 Use Cases of Integration Solutions 50

3.5 Strengths and Weaknesses of the Various Approaches to Integration 60

3.6 Tough Problems in Bioinformatics Integration 65

4 Issues to Address While Designing a Biological Information System / Zoe Lacroix 75

4.1 Legacy 78

4.2 A Domain in Constant Evolution 80

4.3 Biological Queries 86

4.4 Query Processing 92

4.5 Visualization 98

5 SRS: An Integration Platform for Databanks and Analysis Tools in Bioinformatics / Thure Etzold, Howard Harris, Simon Beaulah 109

5.1 Integrating Flat File Databanks 112

5.2 Integration of XML Databases 116

5.3 Integrating Relational Databases 124

5.4 The SRS Query Language 129

5.5 Linking Databanks 130

5.6 The Object Loader 133

5.7 Scientific Analysis Tools 137

5.8 Interfaces to SRS 139

5.9 Automated Server Maintenance with SRS Prisma 141

6 The Kleisli Query System as a Backbone for Bioinformatics Data Integration and Analysis / Jing Chen, Su Yun Chung, Limsoon Wong 147

6.1 Motivating Example 149

6.2 Approach 151

6.3 Data Model and Representation 153

6.4 Query Capability 158

6.5 Warehousing Capability 163

6.6 Data Sources 165

6.7 Optimizations 167

6.8 User Interfaces 175

6.9 Other Data Integration Technologies 179

7 Complex Query Formulation Over Diverse Information Sources in TAMBIS / Robert Stevens, Carole Goble, Norman W. Paton, Sean Bechhofer, Gary Ng, Patricia Baker, Andy Brass 189

7.1 The Ontology 192

7.2 The User Interface 195

7.3 The Query Processor 205

7.5 Current and Future Developments in TAMBIS 217

8 The Information Integration System K2 / Val Tannen, Susan B. Davidson, Scott Harker 225

8.1 Approach 229

8.2 Data Model and Languages 232

8.4 Internal Language 239

8.5 Data Sources 240

8.6 Query Optimization 242

8.7 User Interfaces 243

8.8 Scalability 244

8.9 Impact 245

9 P/FDM Mediator for a Bioinformatics Database Federation / Graham J. L. Kemp, Peter M. D. Gray 249

9.1 Approach 250

9.2 Analysis 266

10 Integration Challenges in Gene Expression Data Management / Victor M. Markowitz, John Campbell, I-Min A. Chen, Anthony Kosky, Krishna Palaniappan, Thodoros Topaloglou 277

10.1 Gene Expression Data Management: Background 278

10.2 The GeneExpress System 282

10.3 Managing Gene Expression Data: Integration Challenges 285

10.4 Integrating Third-Party Gene Expression Data in GeneExpress 291

Trademarks 299

11 DiscoveryLink / Laura M. Haas, Barbara A. Eckman, Prasad Kodali, Eileen T. Lin, Julia E. Rice, Peter M. Schwarz 303

11.1 Approach 306

11.2 Query Processing Overview 316

11.3 Ease of Use, Scalability, and Performance 327

12 A Model-Based Mediator System for Scientific Data Management / Bertram Ludascher, Amarnath Gupta, Maryann E. Martone 335

12.2 Scientific Data Integration Across Multiple Worlds: Examples and Challenges from the Neurosciences 338

12.3 Model-Based Mediation 343

12.4 Knowledge Representation for Model-Based Mediation 351

12.5 Model-Based Mediator System and Tools 360

13 Compared Evaluation of Scientific Data Management Systems / Zoe Lacroix, Terence Critchlow 371

13.1 Performance Model 371

13.2 Evaluation Criteria 376

13.3 Tradeoffs 385

Looking Toward the Future 394

System Information 425

SRS 425

Kleisli 425

TAMBIS 426

K2 426

P/FDM Mediator 427

GeneExpress 427

DiscoveryLink 428

KIND 428.

Notes:

Includes bibliographical references and index.

Local Notes:

Acquired for the Penn Libraries with assistance from the Constance L. Rosenthal Book Fund.

ISBN:

155860829X

OCLC:

51804737

Online:

Publisher description