Data integration in microbial genomics ... - Jacobs University

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CHAPTER 4 MIMARKS The Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications Authors: Pelin Yilmaz, Renzo Kottmann, Dawn Field, Rob Knight, James R Cole, Linda Amaral-Zettler, Jack A Gilbert, Ilene Karsch- Mizrachi, Anjanette Johnston, Guy Cochrane, Robert Vaughan, Christopher Hunter, Joonhong Park, Norman Morrison, Philippe Rocca-Serra, Peter Sterk, Manimozhiyan Arumugam, Mark Bailey, Laura Baumgartner, Bruce W Birren, Martin J Blaser, Vivien Bonazzi, Tim Booth, Peer Bork, Frederic D Bushman, Pier Luigi Buttigieg, Patrick S G Chain, Emily Charlson, Elizabeth K Costello, Heather Huot-Creasy, Peter Dawyndt, Todd DeSantis, Noah Fierer, Jed A Fuhrman, Rachel E Gallery, Dirk Gevers, Richard A Gibbs, Inigo San Gil, Antonio Gonzalez, Jeffrey I Gordon, Robert Guralnick, Wolfgang Hankeln, Sarah Highlander, Philip Hugenholtz, Janet Jansson, Andrew L Kau, Scott T Kelley, Jerry Kennedy, Dan Knights, Omry Koren, Justin Kuczynski, Nikos Kyrpides, Robert Larsen, Christian L Lauber, Teresa Legg, Ruth E Ley, Catherine A Lozupone, Wolfgang Ludwig, Donna Lyons, Eamonn Maguire, Barbara A Methé, Folker Meyer, Brian Muegge, Sara Nakielny, Karen E Nelson, Diana Nemergut, Josh D Neufeld, Lindsay K Newbold, Anna E Oliver, Norman R Pace, Giriprakash Palanisamy, Jörg Peplies, Joseph Petrosino, Lita Proctor, Elmar Pruesse, Christian Quast, Jeroen Raes, Sujeevan Ratnasingham, Jacques Ravel, David A Relman, Susanna Assunta-Sansone, Patrick D Schloss, Lynn Schriml, Rohini Sinha, Michelle I Smith, Erica Sodergren, Aymé Spor, Jesse Stombaugh, James M Tiedje, Doyle V Ward, George M Weinstock,
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Max Planck Institute for Marine Mic
Page 4 and 5:
List of abbreviations BLAST Basic L
Page 6 and 7:
Thesis abstract Deoxyribonucleic ac
Page 8 and 9:
4.2 Introduction . . . . . . . . .
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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
Page 54 and 55: 46 3. CDinFusion offered the option
Page 56 and 57: 48 3. CDinFusion AMD Opteron TM pro
Page 58 and 59: 50 3. CDinFusion able separately an
Page 60 and 61: 52 3. CDinFusion and upload it with
Page 64 and 65: 56 4. MIMARKS Doug Wendel, Owen Whi
Page 66 and 67: 58 4. MIMARKS troducing additional
Page 68 and 69: 60 4. MIMARKS Report type Item Desc
Page 70 and 71: 62 4. MIMARKS and sequencing contex
Page 72 and 73: 64 4. MIMARKS plays MIxS-compliant
Page 74 and 75: 66 4. MIMARKS Note: Supplementary i
Page 76 and 77: 68 5. Megx.net ronmental parameters
Page 78 and 79: 70 5. Megx.net to PostgreSQL. PostG
Page 80 and 81: 72 5. Megx.net rameters. When suffi
Page 82 and 83: 74 5. Megx.net such as temperature,
Page 84 and 85: 76 5. Megx.net NCBI Genome 5.5 Summ
Page 87 and 88: CHAPTER 6 DOMAINS OF UNKNOWN FUNCTI
Page 89 and 90: 6.4. Results 81 bations are grouped
Page 91 and 92: 6.4. Results 83 employed indirect g
Page 93: 6.5. Conclusion 85 dients and accom
Page 96 and 97: 88 7. Summary and discussion for a
Page 98 and 99: 90 7. Summary and discussion and de
Page 100 and 101: 92 7. Summary and discussion http:/
Page 102 and 103: 94 7. Summary and discussion tive f
Page 105 and 106: CHAPTER 8 CONCLUSION AND OUTLOOK
Page 107 and 108: 8.3. A contextual data utopia 99 mi
Page 109 and 110: Bibliography [Ackoff, 1989] Ackoff,
Page 111 and 112: BIBLIOGRAPHY 103 throughput communi
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BIBLIOGRAPHY 105 [Floridi, 2003] Fl
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BIBLIOGRAPHY 107 [Hewson and Fuhrma
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BIBLIOGRAPHY 109 [Ludwig and Schlei
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BIBLIOGRAPHY 111 [Norvig, 2009] Nor
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BIBLIOGRAPHY 113 Hoffman, J. M., Re
Page 123 and 124:
BIBLIOGRAPHY 115 [van der Staay et
Page 125:
BIBLIOGRAPHY 117 [Zehr and Kudela,
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