Data integration in microbial genomics ... - Jacobs University

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70 5. Megx.net to PostgreSQL. PostGIS implements the ‘Simple Features Specification for SQL’ standard recommended by the Open Geospatial Consortium (OGC; http://www.opengeospatial.org/), and therefore offers hundreds of geospatial manipulation functions. MegDB is comprised of (i) MetaStorage, which stores georeferenced DNA sequence data from a collection of genomes, metagenomes and genes of molecular environmental surveys, with their contextual data, and (ii) OceaniaDB, which stores georeferenced quantitative environmental data (Figure 5.1). Figure 5.1: General architecture of megx.net: DNA sequence data (from INSDC) is integrated with contextual data from diverse resources (i.e. manual literature mining and the GOLD database) and interpolated environmental data. MegDB integrates the data conforming to OGC standards and MIGS/MIMS specification. The core megx.net tools, Genes Mapserver and Geographic-BLAST access the MegDB content. Contextual and sequence data content Sequences in MetaStorage are retrieved from the International Nucleotide Sequence Database Collaboration (INSDC, http://www.insdc. org/). However, as of September 2009, GOLD reported 5776 genome projects, of which, only 1095 were finished and published (http://www. genomesonline.org/gold.cgi). As most of the sequenced functional diversity is contained in these draft and shotgun datasets, megx.net was extended to host draft genomes and whole genome shotgun data. Cur-
5.3. New database structure and content 71 rently, MegDB contains 1832 prokaryote genomes (940 incomplete or draft) and 80 marine shotgun metagenomes from the GOS microbial dataset. Marine viruses are a missing link in the correlation of microbial sequence data with contextual information to elucidate diversity and function. Consequently, megx.net now incorporates all sequenced marine phage genomes in MegDB, the first step towards a community call for integration of viral genomic and biogeochemical data [Brussaard et al., 2008]. In an effort towards integrating microbial diversity with specific sampling sites, megx.net has been extended to include georeferenced small and large subunit rRNA sequences from the SILVA rRNA databases project [Pruesse et al., 2007]. Currently, only 9% (16S/18S) and 2% (23S/28S) of over 1 million sequences in SILVA SSUParc (16S/18S) and LSUParc (23S/28S) databases are georeferenced. With the implementation of the Minimal Information about an Environmental Sequence (MIENS) standard for marker gene sequences (http://gensc.org/gc_ wiki/index.php/MIENS), efforts are ongoing to significantly improve this situation. All genomic sequences in megx.net are supplemented by contextual data from GOLD [Liolios et al., 2008] and NCBI Genome Projects (http://www.ncbi.nlm.nih.gov/genomes/MICROBES/microbial_taxtree.html). The database is designed to store all contextual data recommended by the Genomics Standards Consortium, and is thus compliant with the Minimum Information about a Genome Sequence (MIGS) standard and its extension, Minimum Information about a Metagenome Sequence (MIMS) [Field et al., 2008, Kottmann et al., 2008]. Furthermore, megx.net is the first resource to provide a manually annotated collection of genomes using terms from EnvO-Lite (Rev. 1.4), a subset of the Environment Ontology (EnvO) [Hirschman et al., 2008]. An EnvO-Lite term was assigned to each genome project, identifying the environment where its original sample material was obtained. The annotation can be browsed on the megx.net portal using, e.g. tag clouds, and may be used as a categorical variable in comparative analyses. Environmental data content OceaniaDB was added to MegDB to supplement the georeferenced molecular data of MetaStorage with interpolated environmental pa-
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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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10 1. Introduction marker genes hel
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16 1. Introduction tual data acquis
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18 1. Introduction Doug Wendel, Owe
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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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Page 110 and 111: 102 BIBLIOGRAPHY [Beynon-Davies, 20
Page 112 and 113: 104 BIBLIOGRAPHY oceanic regions by
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Page 118 and 119: 110 BIBLIOGRAPHY pathways in marine
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Page 127: CHAPTER 9 ACKNOWLEDGEMENTS First, I
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