Data integration in microbial genomics ... - Jacobs University

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4.2 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . 56 4.3 Development of MIMARKS . . . . . . . . . . . . . . . . . 58 4.4 Survey of published parameters . . . . . . . . . . . . . . . 61 4.5 The MIMARKS checklist . . . . . . . . . . . . . . . . . . . 61 4.6 Conclusions and call for action . . . . . . . . . . . . . . . . 65 5 Megx.net 67 5.1 Abstract . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67 5.2 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . 68 5.3 New database structure and content . . . . . . . . . . . . 69 5.4 User Access . . . . . . . . . . . . . . . . . . . . . . . . . . . 73 5.5 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76 6 Domains of unknown function 79 6.1 Abstract . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79 6.2 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . 80 6.3 Material and Methods . . . . . . . . . . . . . . . . . . . . . 80 6.4 Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81 6.5 Conclusion . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84 7 Summary and discussion 87 7.1 Development of MIxS standard-compliant tools . . . . . 87 7.2 GSC standards development . . . . . . . . . . . . . . . . . 89 7.3 Megx.net: A unified view on the data . . . . . . . . . . . 92 7.4 In silico Hypothesis Generation . . . . . . . . . . . . . . . 93 7.5 Getting the most out of the data . . . . . . . . . . . . . . 94 8 Conclusion and outlook 97 8.1 Life Sciences: The transition to a data-driven field of science . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97 8.2 Projects on the horizon . . . . . . . . . . . . . . . . . . . . 98 8.3 A contextual data utopia . . . . . . . . . . . . . . . . . . . 99 9 Acknowledgements 119
CHAPTER 1 INTRODUCTION “We’re drowning in information and starving for knowledge.” (Rutherford D. Rogers, NY Times, 1988) In this introductory chapter, the basic concepts and a theoretical framework are presented to set the stage. The focus of this doctoral thesis is put into a broader context. Subsequently, the relevant bioinformatic approaches and problems are presented that are tackled by the research aims. The chapter finishes with an overview about the overall structure of the thesis. It is the intention to guide a reader not familiar with the subject of this thesis towards an understanding that helps to fully appreciate the motivation of the research aims and the studies conducted. 1.1 From data to knowledge “Of our mundane and technical concepts information is currently one of the most important, most widely used and least understood.” [Floridi, 2003] Information as well as data and knowledge are central terms in this thesis. They are defined in the following. This happens without claiming to offer the only philosophically valid definitions for these terms, but to establish a consistent vocabulary that will be used throughout this work. Information scientists agree that on the lowest level there are signs that are defined in alphabets (see figure 1.1). These signs can be com-
Page 1: Max Planck Institute for Marine Mic
Page 4 and 5: List of abbreviations BLAST Basic L
Page 6 and 7: Thesis abstract Deoxyribonucleic ac
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Page 24 and 25: 16 1. Introduction tual data acquis
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CHAPTER 4 MIMARKS The Minimum infor
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4.2. Introduction 57 edge generatio
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4.3. Development of MIMARKS 59 in t
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4.4. Survey of published parameters
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4.5. The MIMARKS checklist 63 Resul
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4.6. Conclusions and call for actio
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CHAPTER 5 MEGX.NET Integrated datab
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5.3. New database structure and con
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5.3. New database structure and con
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5.4. User Access 73 5.4 User Access
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5.4. User Access 75 tal context, co
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5.5. Summary 77 access charge: Max
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CHAPTER 7 SUMMARY AND DISCUSSION Th
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7.2. GSC standards development 89 T
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7.4. In silico Hypothesis Generatio
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7.5. Getting the most out of the da
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98 8. Conclusion and outlook nities
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102 BIBLIOGRAPHY [Beynon-Davies, 20
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104 BIBLIOGRAPHY oceanic regions by
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106 BIBLIOGRAPHY [Giovannoni et al.
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108 BIBLIOGRAPHY [Kitano, 2002] Kit
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110 BIBLIOGRAPHY pathways in marine
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112 BIBLIOGRAPHY [Ramette, 2007] Ra
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114 BIBLIOGRAPHY (2006). Microbial
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116 BIBLIOGRAPHY [Williamson et al.
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CHAPTER 9 ACKNOWLEDGEMENTS First, I
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