Bioinformatics: Managing Scientific Data

Terence Critchlow

Verlag: Elsevier, 2008
ISBN 10: 8181473728 / ISBN 13: 9788181473721
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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. Contents:- Introduction Zoe Lacroix and Terence Critchlow 1.1 Overview 1.2 Problem and Scope 1.3 Biological Data Integration 1.4 Developing a Biological Data Integration System 1.4.1 Specifications 1.4.2 Translating Specifications into a Technical Approach 1.4.3 Development Process 1.4.4 Evaluation of the System References 2 Challenges Faced in the Integration of Biological Information Su Yun Chung and John C. Wooley 2.1 The Life Science Discovery Process 2.2 An Information Integration Environment for Life Science Discovery 2.3 The Nature of Biological Data 2.3.1 Diversity 2.3.2 Variability 2.4 Data Sources in Life Science 2.4.1 Biological Databases Are Autonomous 2.4.2 Biological Databases Are Heterogeneous in Data Formats 2.4.3 Biological Data Sources Are Dynamic 2.4.4 Computational Analysis Tools Require Specific Input/Output Formats and Broad Domain Knowledge 2.5 Challenges in Information Integration 2.5.1 Data Integration 2.5.2 Meta-Data Specification 2.5.3 Data Provenance and Data Accuracy 2.5.4 Ontology 2.5.5 Web Presentations Conclusion References 3 A Practitioner`s Guide to Data Management and Data Integration in Bioinformatics Barbara A. Eckman 3.1 Introduction 3.2 Data Management in Bioinformatics 3.2.1 Data Management Basics 3.2.2 Two Popular Data Management Strategies and Their Limitations 3.2.3 Traditional Database Management 3.3 Dimensions Describing the Space of Integration Solutions 3.3.1 A Motivating Use Case for Integration 3.3.2 Browsing vs. Querying 3.3.3 Syntactic vs. Semantic Integration 3.3.4 Warehouse vs. Federation 3.3.5 Declarative vs. Procedural Access 3.3.6 Generic vs. Hard-Coded 3.3.7 Relational vs. Non-Relational Data Model 3.4 Use Cases of Integration Solutions 3.4.1 Browsing-Driven Solutions 3.4.2 Data Warehousing Solutions 3.4.3 Federated Database Systems Approach 3.4.4 Semantic Data Integration 3.5 Strengths and Weaknesses of the Various Approaches to Integration 3.5.1 Browsing and Querying: Strengths and Weaknesses 3.5.2 Warehousing and Federation: Strengths and Weaknesses 3.5.3 Procedural Code and Declarative Query Language: Strengths and Weaknesses 3.5.4 Generic and Hard-Coded Approaches: Strengths and Weaknesses 3.5.5 Relational and Non-Relational Data Models: Strengths and Weaknesses 3.5.6 Conclusion: A Hybrid Approach to Integration Is Ideal 3.6 Tough Problems in Bioinformatics Integration 3.6.1 Sema Printed Pages: 441. Buchnummer des Verkäufers 40591

Bibliografische Details

Titel: Bioinformatics: Managing Scientific Data
Verlag: Elsevier
Erscheinungsdatum: 2008
Einband: Hardcover
Zustand: New
Auflage: 5th or later edition.

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Lacroix, Zoe and Terence Critchlow:
Verlag: Morgan Kaufmann Publishers (2003)
ISBN 10: 155860829X ISBN 13: 9781558608290
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Buchbeschreibung Morgan Kaufmann Publishers, 2003. gebundene Ausgabe. Buchzustand: Gut. 441 Seiten Der Erhaltungszustand des hier angebotenen Werks ist trotz seiner Bibliotheksnutzung sehr sauber. Es befindet sich lediglich ein Bibliotheksstempel im Buch; ordnungsgemäß entwidmet. Sprache: Englisch Gewicht in Gramm: 990. Artikel-Nr. 1403559

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