Bruza / Weeber Literature-based Discovery

1. Auflage 2008
ISBN: 978-3-540-68690-3
Verlag: Springer Berlin Heidelberg
Format: PDF
Kopierschutz: 1 - PDF Watermark

E-Book, Englisch, 198 Seiten

Reihe: Information Science and Knowledge Management

This is the first coherent book on literature-based discovery (LBD). LBD is an inherently multi-disciplinary enterprise. The aim of this volume is to plant a flag in the ground and inspire new researchers to the LBD challenge.

Autoren/Hrsg.

Bruza, Peter

Weeber, Marc

Inhaltsverzeichnis

1;Preface;5
2;Contents;6
3;Contributors;8
4;General Outlook and Possibilities;11
4.1;Literature-Based Discovery? The Very Idea;12
4.1.1;1 Complementarity of Hybridity and Cytology: The Birth of Cytogenetics;12
4.1.2;2 Suggestive Complementarity and the ABC Model;14
4.1.3;3 What People "Know" versus Recorded Knowledge;15
4.1.4;4 Fragmentation of Science;16
4.1.5;5 A Problem-Oriented Approach;17
4.1.6;6 Complementary but Disjoint Structures in the Literature of Science;18
4.1.7;7 Summing Up;19
4.1.7.1;7.1 Postscript: A Warning About Consequences;19
4.1.8;References;19
4.2;The Place of Literature-Based Discovery in Contemporary Scientific Practice;21
4.2.1;1 Introduction;21
4.2.2;2 A Case Study;22
4.2.3;3 Re-defining Success in LBD;25
4.2.4;4 Gold Standards;26
4.2.5;5 Concluding Remarks;28
4.2.6;References;28
4.3;The Tip of the Iceberg: The Quest for Innovation at the Base of the Pyramid;31
4.3.1;1 The Base of the Pyramid and Innovation;32
4.3.2;2 Disruptive Technologies;36
4.3.3;3 Application of Literature Based Discovery;37
4.3.4;4 Discovery: West to South;40
4.3.5;5 New Frontiers in Literature-Based Discovery;43
4.3.6;References;43
4.4;The ‘Open Discovery’ Challenge;46
4.4.1;1 Introduction;46
4.4.1.1;1.1 Text-Based Knowledge Discovery;47
4.4.1.2;1.2 General Approach;50
4.4.1.3;1.3 Previous LBD Applications;52
4.4.1.4;1.4 Improving on Co-Occurrences;53
4.4.1.5;1.5 Using History as a Guide to the Future;57
4.4.1.6;1.6 Literature Limitations;59
4.4.1.7;1.7 Integrating Gene Expression Measurements;60
4.4.2;2 Summary;60
4.4.3;References;61
4.5;Where is the Discovery in Literature-Based Discovery?;63
4.5.1;1 Discovery and Innovation Definitions;63
4.5.2;2 Radical Discovery;64
4.5.3;3 Literature-Based Discovery;65
4.5.4;4 Validating Potential Discovery (Vetting);67
4.5.5;5 Examples of Validation Issues;68
4.5.5.1;5.1 Use of MeSH Variables;68
4.5.5.2;5.2 Disjointness as Sufficient Condition;72
4.5.5.3;5.3 Definition of Prior Art;75
4.5.6;6 Summary and Conclusions;75
4.5.7;References;75
5;Methodology and Applications;79
5.1;Analyzing LBD Methods using a General Framework;80
5.1.1;1 Introduction;80
5.1.2;2 A Framework for Analyzing LBD Research and Development;81
5.1.2.1;2.1 LBD Framework;82
5.1.3;3 LBD for Postulating Gene–Disease Connections;84
5.1.3.1;3.1 G2D (Perez-Iratxeta et al. 2002);84
5.1.3.2;3.2 eVOC (Tiffin et al. 2005);86
5.1.3.3;3.3 BITOLA (Hristovski et al. 2001, 2003);87
5.1.3.4;3.4 Adamic et al. (2002);88
5.1.3.5;3.5 Wilkinson and Huberman (2004);89
5.1.3.6;3.6 Analysis of Gene-Disease LBD Approaches;90
5.1.4;4 General Purpose Biomedical LBD Systems;92
5.1.4.1;4.1 Manjal;94
5.1.4.2;4.2 Analysis of the General Purpose LBD Systems;95
5.1.5;5 Predicting Relationships from theWeb;96
5.1.5.1;5.1 Adamic and Adar (2003);96
5.1.5.2;5.2 Ben-Dov et al. (2004);97
5.1.5.3;5.3 Cory (1997);97
5.1.5.4;5.4 Kumar et al. (1999);98
5.1.5.5;5.5 Tan and Kumar (2001);99
5.1.5.6;5.6 Bernstein et al. (2002);99
5.1.5.7;5.7 Analysis of Web Based LBD;100
5.1.6;6 Conclusions;102
5.1.7;References;103
5.2;Evaluation of Literature-Based Discovery Systems;106
5.2.1;1 Introduction;106
5.2.2;2 Evaluation Metrics;107
5.2.2.1;2.1 Information Retrieval Metrics;107
5.2.2.2;2.2 Receiver Operating Characteristics (ROC) Curve;108
5.2.2.3;2.3 Probabilistic Approaches;109
5.2.3;3 Current Evaluation Approaches;109
5.2.3.1;3.1 Replicating Swanson’s Experiments;110
5.2.3.2;3.2 Using Statistical Evaluation Methods;112
5.2.3.3;3.3 Incorporating Expert Opinion;114
5.2.3.4;3.4 Publishing in the Medical Domain;115
5.2.4;4 User Interface Evaluation;116
5.2.5;5 Conclusion;117
5.2.6;References;117
5.3;Factor Analytic Approach to Transitive Text Mining using Medline Descriptors;119
5.3.1;1 Introduction;119
5.3.2;2 Methods ;122
5.3.2.1;2.1 Data;122
5.3.2.2;2.2 Matrix Decomposition;122
5.3.2.3;2.3 Factor Screening;123
5.3.3;3 Results;123
5.3.3.1;3.1 Raynaud’s Disease;123
5.3.3.2;3.2 Migraine;127
5.3.3.3;3.3 Cardiac Hypertrophy;129
5.3.3.4;3.4 Multiple Sclerosis;131
5.3.4;4 Discussion;132
5.3.5;5 Conclusion;133
5.3.6;References;133
5.4;Literature-Based Knowledge Discovery using Natural Language Processing;136
5.4.1;1 Introduction;136
5.4.2;2 Background ;137
5.4.2.1;2.1 Literature-Based Discovery;137
5.4.2.2;2.2 Natural Language Processing;139
5.4.3;3 Methods;142
5.4.3.1;3.1 Discovery Patterns;142
5.4.3.2;3.2 Integrated BioMedLEE and SemRep Output Format;146
5.4.4;4 Results;148
5.4.4.1;4.1 Rediscovering Fish Oil for Raynaud’s Disease;148
5.4.4.2;4.2 Insulin for Huntington Disease;149
5.4.4.3;4.3 Gabapentin for Parkinson’s Disease;150
5.4.4.4;4.4 Evaluation of BioMedLee and SemRep;151
5.4.5;5 Discussion and Further Work;152
5.4.6;6 Conclusions;153
5.4.7;References;154
5.5;Information Retrieval in Literature- Based Discovery;156
5.5.1;1 Introduction;156
5.5.2;2 Content;158
5.5.2.1;2.1 Bibliographic;158
5.5.2.2;2.2 Full-Text;159
5.5.2.3;2.3 Databases/Collections;160
5.5.3;3 Indexing;161
5.5.3.1;3.1 Controlled Vocabularies;162
5.5.3.2;3.2 Manual Indexing;163
5.5.3.3;3.3 Automated Indexing;165
5.5.4;4 Retrieval;167
5.5.4.1;4.1 Exact-Match;167
5.5.4.2;4.2 Partial-Match;168
5.5.5;5 Evaluation;169
5.5.5.1;5.1 System-Oriented;169
5.5.5.2;5.2 User-Oriented;171
5.5.6;6 IR Techniques for LBD;172
5.5.7;7 Conclusions;172
5.5.8;Suggested Readings;173
5.5.9;References;173
5.6;Biomedical Application of Knowledge Discovery;176
5.6.1;1 Overview of BioTermNet;176
5.6.2;2 System and Methods;178
5.6.2.1;2.1 Closed Discovery System;180
5.6.2.2;2.2 Open Discovery System;181
5.6.3;3 Comparison of Calculation Methods;182
5.6.4;4 Application to Pharmaco Genomics;187
5.6.5;5 Application to Linkage Analysis;188
5.6.6;6 Application to Microarray Analysis;191
5.6.7;7 Future Prospects;194
5.6.8;References;194
5.7;Index;196