Data integration in microbial genomics ... - Jacobs University

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22 2. MetaBar is given a unique identifier and at any stage the sheets can be uploaded to the MetaBar database server. To label samples, identifiers can be printed as barcodes. An intuitive web interface provides quick access to the contextual data in the MetaBar database as well as user and project management capabilities. Export functions facilitate contextual and sequence data submission to the International Nucleotide Sequence Database Collaboration (INSDC), comprising of the DNA DataBase of Japan (DDBJ), the European Molecular Biology Laboratory database (EMBL) and GenBank. MetaBar requests and stores contextual data in compliance to the Genomic Standards Consortium specifications. The MetaBar open source code base for local installation is available under the GNU General Public License version 3 (GNU GPL3). Conclusion: The MetaBar software supports the typical workflow from data acquisition and field-sampling to contextual data enriched sequence submission to an INSDC database. The integration with the megx.net marine Ecological Genomics database and portal facilitates georeferenced data integration and metadata-based comparisons of sampling sites as well as interactive data visualization. The ample export functionalities and the INSDC submission support enable exchange of data across disciplines and safeguarding contextual data. 2.2 Background The technological advancement in molecular biology facilitates investigations of biodiversity and functions on a temporal and geospatial scale. Improved sampling and laboratory methods, together with fast and affordable sequencing technologies [Hall, 2007], provide the framework to create a network of data points capable to answer basic ecological questions such as: ‘Who is out there?’ and ‘What are these organisms doing?’ To shed light on the complex interplay, adaptation and survival mechanisms of organisms in times of global change, contextual data describing the surrounding environment of sampling locations are of crucial importance [Field et al., 2008]. At the very least, the latitude and longitude (x, y),the depth/altitude (z) in relation to sea level, and the sampling date and time (t) must be provided to allow anchoring
2.2. Background 23 molecular sequence data to their environmental context. If every sequence entry in the INSDC databases, comprising of DDBJ, EMBL and GenBank, would be thus georeferenced, researchers would have the post factum opportunity to contextualize these sequences with environmental data [Wieczorek et al., 2004]. The power of contextual data enriched sequence data sets for the environmental and medical field has been recently documented [DeLong et al., 2006, Janies et al., 2007, Ramette, 2007, Fuhrman et al., 2006, Pommier et al., 2007, Parks et al., 2009, Green et al., 2008, Schriml et al., 2010, Field, 2008]. Unfortunately, a survey in the EMBL sequence repository has shown that only a minor set of sequences are accompanied by a relevant amount of contextual data. For example, latitude, longitude (INSDC: lat lon), and time (INSDC: collection date), elements of the key contextual data tuple (x,y,z,t), are only reported in 7.3% and 7.2% of all submissions [Guy Cochrane, personal communication, October 2009]. But even if these data are available, correctness is not guaranteed. The paucity of sequence associated contextual data has been recognized by the primary database providers and biocuration efforts are currently underway for specific subsets. The National Center for Biotechnology Information (NCBI), for example, curates the Reference Sequence (RefSeq) database which aims to provide a comprehensive, non-redundant, well-annotated set of sequences, including genomic DNA, transcripts and proteins (http://www.ncbi.nlm.nih.gov/RefSeq/). The European Molecular Biology Laboratory (EMBL) provides the UniProt/Swiss-Prot Knowledgebase which focuses on high quality protein sequence annotations (http://www.ebi.ac.uk/uniprot/) [Consortium, 2010]. However, the common aim of these efforts is to enhance the quality of the sequence or protein data and annotations rather than to provide more information on the data processing or the environment where the sample or organism has been taken. To improve the quantity and quality of contextual data describing the environment of a sample is currently addressed by several projects which systematically collect georeferenced sequence data, environmental parameters, and further curated metadata [Howe et al., 2008]. SILVA [Pruesse et al., 2007] or RDP II [Cole et al., 2005] are examples for specialized databases that offer users curated and quality checked ribosomal RNA sequences that are often enriched with more reliable
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 24 and 25: 16 1. Introduction tual data acquis
Page 26 and 27: 18 1. Introduction Doug Wendel, Owe
Page 29: CHAPTER 2 METABAR A tool for consis
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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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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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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