Data integration in microbial genomics ... - Jacobs University

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108 BIBLIOGRAPHY [Kitano, 2002] Kitano, H. (2002). Computational systems biology. Nature, 420(6912):206–210. [Kottmann et al., 2008] Kottmann, R., Gray, T., Murphy, S., Kagan, L., Kravitz, S., Lombardot, T., Field, D., Glöckner, F. O., and Consortium, G. S. (2008). A standard migs/mims compliant xml schema: toward the development of the genomic contextual data markup language (gcdml). OMICS, 12(2):115–121. [Kottmann et al., 2010] Kottmann, R., Kostadinov, I., Duhaime, M. B., Buttigieg, P. L., Yilmaz, P., Hankeln, W., Waldmann, J., and Glöckner, F. O. (2010). Megx.net: integrated database resource for marine ecological genomics. Nucleic Acids Res, 38(Database issue):D391–D395. [Krcmar, 2009] Krcmar, H. (2009). Informationsmanagement. Springer, Berlin, 5 edition. [Lenzerini, 2002] Lenzerini, M. (2002). Data integration: a theoretical perspective. In Proceedings of the twenty-first ACM SIGMOD- SIGACT-SIGART symposium on Principles of database systems, PODS ’02, pages 233–246, New York, NY, USA. ACM. [Liolios et al., 2008] Liolios, K., Mavromatis, K., Tavernarakis, N., and Kyrpides, N. C. (2008). The genomes on line database (gold) in 2007: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res, 36(Database issue):D475–D479. [Lombardot et al., 2006] Lombardot, T., Kottmann, R., Pfeffer, H., Richter, M., Teeling, H., Quast, C., and Glöckner, F. O. (2006). Megx.net–database resources for marine ecological genomics. Nucleic Acids Res, 34(Database issue):D390–D393. [Ludwig et al., 1994] Ludwig, W., Dorn, S., Springer, N., Kirchhof, G., and Schleifer, K. H. (1994). Pcr-based preparation of 23s rrnatargeted group-specific polynucleotide probes. Appl Environ Microbiol, 60(9):3236–3244. [Ludwig and Schleifer, 1994] Ludwig, W. and Schleifer, K. H. (1994). Bacterial phylogeny based on 16s and 23s rrna sequence analysis. FEMS Microbiol Rev, 15(2-3):155–173.
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Max Planck Institute for Marine Mic
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List of abbreviations BLAST Basic L
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Thesis abstract Deoxyribonucleic ac
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4.2 Introduction . . . . . . . . .
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2 1. Introduction syntax: data leve
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4 1. Introduction used to derive ne
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6 1. Introduction croorganisms thri
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8 1. Introduction the middle at the
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10 1. Introduction marker genes hel
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12 1. Introduction what kind and wh
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14 1. Introduction possibilities li
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16 1. Introduction tual data acquis
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18 1. Introduction Doug Wendel, Owe
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CHAPTER 2 METABAR A tool for consis
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2.2. Background 23 molecular sequen
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2.2. Background 25 printing of data
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2.4. Results 27 KML export function
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2.4. Results 29 Figure 2.3: Screens
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2.5. Discussion 31 taking samples i
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2.5. Discussion 33 Handlebar MetaBa
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2.6. Conclusion 35 rine Microbiolog
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2.6. Conclusion 37 RK advised progr
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40 3. CDinFusion Genomic Standards
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42 3. CDinFusion sortium (GSC), an
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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
Page 65 and 66: 4.2. Introduction 57 edge generatio
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Page 69 and 70: 4.4. Survey of published parameters
Page 71 and 72: 4.5. The MIMARKS checklist 63 Resul
Page 73 and 74: 4.6. Conclusions and call for actio
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Page 81 and 82: 5.4. User Access 73 5.4 User Access
Page 83 and 84: 5.4. User Access 75 tal context, co
Page 85: 5.5. Summary 77 access charge: Max
Page 88 and 89: 80 6. Domains of unknown function 6
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Page 95 and 96: CHAPTER 7 SUMMARY AND DISCUSSION Th
Page 97 and 98: 7.2. GSC standards development 89 T
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Page 106 and 107: 98 8. Conclusion and outlook nities
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Page 110 and 111: 102 BIBLIOGRAPHY [Beynon-Davies, 20
Page 112 and 113: 104 BIBLIOGRAPHY oceanic regions by
Page 114 and 115: 106 BIBLIOGRAPHY [Giovannoni et al.
Page 118 and 119: 110 BIBLIOGRAPHY pathways in marine
Page 120 and 121: 112 BIBLIOGRAPHY [Ramette, 2007] Ra
Page 122 and 123: 114 BIBLIOGRAPHY (2006). Microbial
Page 124 and 125: 116 BIBLIOGRAPHY [Williamson et al.
Page 127: CHAPTER 9 ACKNOWLEDGEMENTS First, I
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