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Duhaime MB, Kottmann R, Field D, et al. Enriching public descriptions of marine phages using the Genomic Standards Consortium MIGS standard. Stand Genomic Sci. 2011;4(2):271-85doi: 10.4056/sigs.621069.
Duhaime, M. B., Kottmann, R., Field, D., & Glöckner, F. O. (2011). Enriching public descriptions of marine phages using the Genomic Standards Consortium MIGS standard. Standards in genomic sciences, 4(2), 271-85. https://doi.org/10.4056/sigs.621069
Duhaime, Melissa Beth, et al. "Enriching public descriptions of marine phages using the Genomic Standards Consortium MIGS standard." Standards in genomic sciences vol. 4,2 (2011): 271-85. doi: https://doi.org/10.4056/sigs.621069
Duhaime MB, Kottmann R, Field D, Glöckner FO. Enriching public descriptions of marine phages using the Genomic Standards Consortium MIGS standard. Stand Genomic Sci. 2011 Apr 29;4(2):271-85. doi: 10.4056/sigs.621069. PMID: 21677864; PMCID: PMC3111985.
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Stand Genomic Sci. 2011 Apr 29;4(2):271-85. doi: 10.4056/sigs.621069.

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

Standards in genomic sciences

Melissa Beth Duhaime, Renzo Kottmann, Dawn Field, Frank Oliver Glöckner

PMID: 21677864 PMCID: PMC3111985 DOI: 10.4056/sigs.621069

Abstract

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.

Keywords: contextual data; genome standards; marine phages; markup language

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