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Enriching public descriptions of marine phages using the Genomic Standards Consortium MIGS standard

Duhaime, Melissa Beth; Kottmann, Renzo; Field, Dawn; Glockner, Frank Oliver. 2011 Enriching public descriptions of marine phages using the Genomic Standards Consortium MIGS standard. Standards in Genomic Sciences, 4 (2). 271 -285. 10.4056/sigs.621069

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Abstract/Summary

In any sequencing project, the possible depth of comparative analysis is determined largely by the amount and quality of the accompanying contextual data. The structure, content, and storage of this contextual data should be standardized to ensure consistent coverage of all sequenced entities and facilitate comparisons. The Genomic Standards Consortium (GSC) has developed the “Minimum Information about Genome/Metagenome Sequences (MIGS/MIMS)” checklist for the description of genomes and here we annotate all 30 publicly available marine bacteriophage sequences to the MIGS standard. These annotations build on existing International Nucleotide Sequence Database Collaboration (INSDC) records, and confirm, as expected that current submissions lack most MIGS fields. MIGS fields were manually curated from the literature and placed in XML format as specified by the Genomic Contextual Data Markup Language (GCDML). These “machine-readable” reports were then analyzed to highlight patterns describing this collection of genomes. Completed reports are provided in GCDML. This work represents one step towards the annotation of our complete collection of genome sequences and shows the utility of capturing richer metadata along with raw sequences.

Item Type: Publication - Article
Digital Object Identifier (DOI): 10.4056/sigs.621069
Programmes: CEH Topics & Objectives 2009 onwards > Biodiversity > BD Topic 1 - Observations, Patterns, and Predictions for Biodiversity > BD - 1.1 - Standards for data collection, quality, management and integration ...
CEH Sections: Hails
ISSN: 1944-3277
Additional Information. Not used in RCUK Gateway to Research.: Open Access article - click on the Official URL link for full text
Additional Keywords: marine phages, contextual data, genome standards, markup language
NORA Subject Terms: Ecology and Environment
Data and Information
Date made live: 07 Sep 2011 10:11
URI: http://nora.nerc.ac.uk/id/eprint/15053

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