Data integration in microbial genomics ... - Jacobs University

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24 2. MetaBar contextual and taxonomic information than originally annotated by the sequence submitters. Furthermore, there are projects which curate the contextual data associated to the primary sequence data to facilitate specific analysis purposes. For example the Genomes On- Line Database (GOLD) collects metadata for ongoing and completed genome sequencing projects [Liolios et al., 2008]. The Visualization and Analysis of Microbial Population Structures (VAMPS) project, with its integrated collection of tools for researchers, aims to visualize and analyze data for microbial population structures and distributions. All the contextual data in VAMPS comes from the MI- CROBIS database management system of the International Census of Marine Microbes (ICoMM: http://icomm.mbl.edu/microbis/). The megx.net portal (www.megx.net) [Kottmann et al., 2010] systematically integrates environmental parameters and sequence data of marine microbial genomes and metagenomes using georeferencing as an anchor. In 2005 the international Genomic Standards Consortium (GSC) introduced checklists to promote standardized contextual data acquisition and storage. So far the Minimum Information about a Genome (Metagenome) Sequence (MIGS/MIMS) has been published [Field et al., 2008] and the Minimum Information about an Environmental Sequence (MIENS) is in development (http://gensc.org/gc_wiki/index.php/MIENS). For data exchange, the Genomic Contextual Data Markup Language (GCDML) [Kottmann et al., 2008] has been developed. A corollary of these ongoing efforts is the need to support field scientists in the consistent capture, storage and submission of both contextual and sequence data. Handlebar, a lightweight Laboratory Information Management System (LIMS) for the management of barcoded samples, in part addresses this issue by supporting the acquisition and processing of contextual data compliant with GSC standards [Booth et al., 2007]. The Barcode of Life Database (BOLD) initiative, which aims to identify and classify all eukaryotic life on Earth [Ratnasingham and Hebert, 2007], also includes an advanced data acquisition and submission system. Unfortunately the system only supports phylogenetic markers which serve the eukaryotic domain e.g. the cytochrome c oxidase I (COI), which is only present in Eukarya and absent in the other domains of life, and so far exclude Archaea and Bacteria. Furthermore, it does not support the
2.2. Background 25 printing of database identifiers as barcodes to label collected samples. Even though initiatives and tools exist to enhance the quantity and quality of contextual data subsequent to sequence submission, the amount of contextual data in the INSDC databases remains an issue. In summary, the most likely reasons for the persisting scarcity of consistent contextual data are: (1) Contextual data that are recorded in the field are often not stored electronically in structured databases. Consequently contextual data get rapidly unlinked from the sequence data and finally ‘forgotten’ in the sequence submission process. (2) There is a lack of automatic quality checking mechanisms active before data submission. Unfortunately, the flood of data entering the public databases prevents any manual curation process. (3) The sheer amount of potential contextual data with respect to the different fields of research ranging from textual data to images or even videos would rapidly exceed the capacities of the INSDC databases. Consequently, only a commonly agreed and standardized subset of data can be stored and made available. Here the user-centric, web-based tool MetaBar is presented. MetaBar offers all the required features for sample identification and barcode labeling allowing robust sample tracking and inventorying. MetaBar is focused on the acquisition of contextual data recorded during sampling in the field ‘offline’ using spreadsheets. All recorded contextual data can be subsequently uploaded and consistently stored in an underlying database. The web Graphical User Interface (GUI) provides advanced user management and access to data and barcodes. Vitally, the tool captures GSC standards compliant data and it is integrated into a set of tools to facilitate further data usage such as integration, visualization and analysis available from the Marine Ecological Genomics database and portal, megx.net. Finally, MetaBar supports contextual data enriched sequence submission to the INSDC databases. The tool is not restricted to any given research field or domain of life, but can universally be applied to capture the contextual data of any biological sample. It is designed to support the complete workflow from the sampling event up to the sequence submission to an INSDC database.
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
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Page 29 and 30: CHAPTER 2 METABAR A tool for consis
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Page 43 and 44: 2.6. Conclusion 35 rine Microbiolog
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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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CHAPTER 7 SUMMARY AND DISCUSSION Th
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98 8. Conclusion and outlook nities
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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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