Data integration in microbial genomics ... - Jacobs University

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List of abbreviations BLAST Basic Local Alignment and Search Tool DIKW ”data information knowledge wisdom hierarchy” DDBJ DNA Data Bank of Japan DNA deoxyribonucleic acid DUF Domain of Unknown Function ENA European Nucleotide Archive FOL First Order Logic GOS Global Ocean Survey GSC Genomic Standards Consortium HMM Hidden Markov Model INSDC International Nucleotide Sequence Database Collaboration KEGG Kyoto Encyclopedia of Genes and Genomes MarMic Marine Microbiology MIMARKS “Minimum Information about a MARKer Sequence” MIGS “Minimum Information about a Genome Sequence” MIMS ”Minimum Information about a Metagenome Sequence“ MIxS Minimum Information about any (x) Sequence NCBI National Center for Biotechnology Information NGS Next Generation Sequencing ORF Open Reading Frame RNA ribonucleic acid rRNA ribosomal ribonucleic acid WOA World Ocean Atlas
“To me, bioinformatics has an inherent ’cool factor’ because it challenges our approaches to analytics, pushes the envelope on performance, and offers a compelling example for a web services-based industry.” (James Gosling, O’Reilly Media, 2003)
Page 1: Max Planck Institute for Marine Mic
Page 6 and 7: Thesis abstract Deoxyribonucleic ac
Page 8 and 9: 4.2 Introduction . . . . . . . . .
Page 10 and 11: 2 1. Introduction syntax: data leve
Page 12 and 13: 4 1. Introduction used to derive ne
Page 14 and 15: 6 1. Introduction croorganisms thri
Page 16 and 17: 8 1. Introduction the middle at the
Page 18 and 19: 10 1. Introduction marker genes hel
Page 20 and 21: 12 1. Introduction what kind and wh
Page 22 and 23: 14 1. Introduction possibilities li
Page 24 and 25: 16 1. Introduction tual data acquis
Page 26 and 27: 18 1. Introduction Doug Wendel, Owe
Page 29 and 30: CHAPTER 2 METABAR A tool for consis
Page 31 and 32: 2.2. Background 23 molecular sequen
Page 33 and 34: 2.2. Background 25 printing of data
Page 35 and 36: 2.4. Results 27 KML export function
Page 37 and 38: 2.4. Results 29 Figure 2.3: Screens
Page 39 and 40: 2.5. Discussion 31 taking samples i
Page 41 and 42: 2.5. Discussion 33 Handlebar MetaBa
Page 43 and 44: 2.6. Conclusion 35 rine Microbiolog
Page 45: 2.6. Conclusion 37 RK advised progr
Page 48 and 49: 40 3. CDinFusion Genomic Standards
Page 50 and 51: 42 3. CDinFusion sortium (GSC), an
Page 52 and 53: 44 3. CDinFusion tiFASTA file with
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46 3. CDinFusion offered the option
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48 3. CDinFusion AMD Opteron TM pro
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50 3. CDinFusion able separately an
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52 3. CDinFusion and upload it with
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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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80 6. Domains of unknown function 6
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82 6. Domains of unknown function F
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84 6. Domains of unknown function p
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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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7.2. GSC standards development 91 o
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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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100 8. Conclusion and outlook plina
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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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Data integration in microbial genomics ... - Jacobs University

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