Data integration in microbial genomics ... - Jacobs University

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16 1. Introduction tual data acquisition tool MetaBar (chapter 2), which aims to support biologists to capture contextual data from sampling to sequencing. CDinFusion (chapter 3) is a tool to prepare contextualized sequence data submissions. It helps to prepare contextual data enriched sequence submissions to the INSDC. At the interface between data and information is a chapter about the GSC contextual data standard “Minimum Information about a MARKer Sequence” (MIMARKS) (chapter 4), this standard extends and refines the previously published checklist “Minimum Information about a Genome Sequence” (MIGS)/ ”Minimum Information about a Metagenome Sequence“ (MIMS) [Field et al., 2008] that are collectively called MIxS. At the interface between information and knowledge is a chapter about the megx.net platform (chapter 5), an internet portal that provides users with a unified view on integrated sequence, environmental and geographic data. It provides tools to access and analyse these data with graphical user interfaces. The thesis finishes, close to the top of the pyramid, with a chapter about in silico hypothesis and knowledge generation, in a study where metagenomic sequence data were analysed in their environmental context (chapter 6). 1.8 Publication overview 1) MetaBar - A tool for consistent contextual data acquisition and standards compliant submission Authors: Wolfgang Hankeln, Pier Luigi Buttigieg, Dennis Fink, Renzo Kottmann, Pelin Yilmaz and Frank Oliver Glöckner Published in: BMC Bioinformatics, June 2010 Personal Contribution: Developed and implemented MetaBar and wrote the initial manuscript. Relevance: To provide the life science community with a tool that allows to capture contextual data consistently, that accumulate, when samples are collected and processed. 2) CDinFusion Submission-ready, on-line Integration of sequence and contextual data
1.8. Publication overview 17 Authors: Wolfgang Hankeln, Norma Johanna Wendel, Jan Gerken, Jost Waldmann, Pier Luigi Buttigieg, Ivaylo Kostadinov, Renzo Kottmann, Pelin Yilmaz, Frank Oliver Glöckner Submitted to: PLoS ONE, April 2011 Personal Contribution: Developed and implemented CDinFusion together with Norma Johanna Wendel, Jan Gerken and Jost Waldmann. Wrote the initial manuscript. Relevance: To provide the life science community with a tool to enrich sequence data with contextual data prior to submission to the INSDC. 3) 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,
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
Page 8 and 9: 4.2 Introduction . . . . . . . . .
Page 10 and 11: 2 1. Introduction syntax: data leve
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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
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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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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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