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56 4. MIMARKS Doug Wendel, Owen White, Andrew Whiteley, Andreas Wilke, Jennifer R Wortman, Tanya Yatsunenko and Frank Oliver Glöckner Submitted to: nature biotechnology, accepted April 2011 Personal Contribution: Initial talk with the title: “Survey results: MInimal list of contextual data fields for ENvironmental Sequences (MIENS)” at the 6th meeting of the GSC at the EBI (Hinxton, UK) October 2008, which was the starting point for the development of this standard, that was later renamed to MIMARKS. Contributed suggestions for improvements of the data fields, during implementation work of this standard in the tools MetaBar and CDinFusion. Relevance: Standards development for contextual data. 4.1 Abstract Here we present a standard developed by the Genomic Standards Consortium (GSC) for reporting marker gene sequences—the minimum information about a marker gene sequence (MIMARKS). We also introduce a system for describing the environment from which a biological sample originates. The ‘environmental packages’ apply to any genome sequence of known origin and can be used in combination with MIMARKS and other GSC checklists. Finally, to establish a unified standard for describing sequence data and to provide a single point of entry for the scientific community to access and learn about GSC checklists, we present the minimum information about any (x) sequence (MIxS). Adoption of MIxS will enhance our ability to analyze natural genetic diversity documented by massive DNA sequencing efforts from myriad ecosystems in our ever-changing biosphere. 4.2 Introduction Without specific guidelines, most genomic, metagenomic and marker gene sequences in databases are sparsely annotated with the information required to guide data integration, comparative studies and knowl-
4.2. Introduction 57 edge generation. Even with complex keyword searches, it is currently impossible to reliably retrieve sequences that have originated from certain environments or particular locations on Earth—for example, all sequences from ‘soil’ or ‘freshwater lakes’ in a certain region of the world. Because public databases of the International Nucleotide Sequence Database Collaboration (INSDC; comprising DNA Data Bank of Japan (DDBJ), the European Nucleotide Archive (EBI-ENA) and GenBank (http://www.insdc.org/)) depend on author-submitted information to enrich the value of sequence data sets, we argue that the only way to change the current practice is to establish a standard of reporting that requires contextual data to be deposited at the time of sequence submission. The adoption of such a standard would elevate the quality, accessibility and utility of information that can be collected from INSDC or any other data repository. The GSC has previously proposed standards for describing genomic sequences— the ’minimum information about a genome sequence’ (MIGS) — and metagenomic sequences — the ’minimum information about a metagenome sequence’ (MIMS) [Field et al., 2008]. Here we introduce an extension of these standards for capturing information about marker genes. Additionally, we introduce ‘environmental packages’ that standardize sets of measurements and observations describing particular habitats that are applicable across all GSC checklists and beyond [Taylor et al., 2008]. We define ‘environment’ as any location in which a sample or organism is found, e.g., soil, air, water, humanassociated, plant-associated or laboratory. The original MIGS/MIMS checklists included contextual data about the location from which a sample was isolated and how the sequence data were produced. However, standard descriptions for a more comprehensive range of environmental parameters, which would help to better contextualize a sample, were not included. The environmental packages presented here are relevant to any genome sequence of known origin and are designed to be used in combination with MIGS, MIMS and MIMARKS checklists. To create a single entry point to all minimum information checklists from the GSC and to the environmental packages, we propose an overarching framework, the MIxS standard (http://gensc.org/gc_ wiki/index.php/MIxS). MIxS includes the technology-specific checklists from the previous MIGS and MIMS standards, provides a way of in-
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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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Page 110 and 111: 102 BIBLIOGRAPHY [Beynon-Davies, 20
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106 BIBLIOGRAPHY [Giovannoni et al.
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CHAPTER 9 ACKNOWLEDGEMENTS First, I
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