An Open-Access, Standards-Supportive Publication that Rapidly Disseminates Concise Genome and Metagenome Reports in Compliance with MIGS/MIMS Standards

Oranmiyan W. Nelson, Department of Microbiology and Molecular Genetics, Michigan State University; George M. Garrity, Department of Microbiology and Molecular Genetics, Michigan State University

Abstract


The Standards in Genomic Sciences eJournal (SIGS; http://standardsingenomics.org) is a newly established standards-supportive publication being developed to report on the exponentially increasing volume of genomic and metagenomic data1. SIGS will also include coverage of detailed standard operating procedures, meeting reports, reviews and commentaries, data policies, and white papers and other gray literature that are relevant to genomic sciences, but absent from the scholarly literature. To achieve standards compliance, SIGS has been designed to support the specification for the minimum information about a genome sequence (MIGS)2. MIGS is developed and maintained by the Genomic Standards Consortium (GSC), a group formed to promote the development of standardized annotations of genomic investigations. As a specification and checklist, MIGS has helped inspire formal models for gathering information routinely included in primary publications such as environmental context, biotic relationship, relationship to oxygen, source material identifier(s), nucleic acid sequence and sample metadata as well as the sequencing assay and genome annotation protocol. MIGS has been developed to address the genomic information of bacteria, archaea, eukaryotes, plasmids, viruses, and organelles. MIGS has been extended into a specification of minimum information about a metagenome sequence (MIMS). The editorial workflow utilizes Open Journal Systems  from the Public Knowledge Project (http://pkp.sfu.ca/ojs), because that application supports custom-specification of checklists that can be integrated into the submission and peer review process, and has an extensible plugin architecture with hook callback and registration features. We have already pilot-tested the software with a sampling of content. SIGS is the first standards-based journal in the life sciences and will provide open access to its content from the outset, on the principle that making research freely available supports a global exchange of knowledge to better accelerate scientific discovery.

1. Garrity, G. M., Field, D., Kyrpides, N., Hirschman, L., Sansone, S. A., Angiuoli, S., Cole, J. R., Glöckner, F. O., Kolker, E., Kowalchuk, G., Moran, M. A., Ussery, D., and White, O. 2008. Toward a standards-compliant genomic and metagenomic publication record. OMICS 12:157-60.

2. Field, D. et al. 2008. The minimum information about a genome sequence (MIGS) specification.  Nat Biotechnol 26:541-7.


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