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The Genomic Standards Consortium (GSC), an international initiative led by the Centre for Ecology & Hydrology and including representatives from a range of major sequencing and bioinformatics centres, has created a new guideline for describing genomes and metagenomes. The guideline, ‘Minimum Information about a Genome Sequence’ (MIGS), is published in the May issue of the journal Nature Biotechnology.
The new guideline is one of a number of emerging minimum information (MI) standards. Increased use of ultra-high-throughput sequencing technologies has led to the number and pace of genomic and metagenomic sequencing projects growing rapidly. Common standards such as MIGS are therefore increasingly vital to scientific progress, as groups from around the world look to share their data.
According to lead author and founding member of the GSC, Dr. Dawn Field, of the UK Centre for Ecology & Hydrology, “MIGS is relatively easy to complete compared to other MI standards that are emerging. There is great enthusiasm in the community for this project and we are already collecting MIGS-compliant reports. We are a highly collaborative group and open to new participants joining the GSC at any time”.
Prof. George M. Garrity, Michigan State University, USA, a co-author on the paper commented that “The MIGS specification comprises light-weight standard set descriptors that are applicable to all genome and metagenome sequences. The addition of this key information greatly enhances the value of the growing body of sequence data by making it more generally accessible and interoperable, at minimal cost to annotators and data curators”
The GSC started this project to remedy the lack of descriptive information currently attached to genome and metagenome sequences in public databases. This is particularly true for environmental samples, which are amassing at an astounding pace.
Co-author Prof. Dr. Frank Oliver Gloeckner, Max Planck Institute for Marine Microbiology, Germany said "We have worked now for more than seven years in the field of marine environmental (meta)genomics. The MIGS specifications and standards will be a major step forward in discovering the secrets hidden in the genes of our environmental microorganisms".
Additional information
The full paper reference is Field, D. et al. 2008. The minimum information about a genome sequence (MIGS) specification. Nature Biotechnology, 26, 541 – 547. Published online: 8 May 2008 | doi:10.1038/nbt1360
The 2006 impact factor for Nature Biotechnology is 22.7, according to the ISI Journal Citation Reports. This places Nature Biotechnology (external link) first among primary research journals in the field of biotechnology.
The Genomic Standards Consortium is an initiative working towards richer descriptions of our collection of genomes and metagenomes. Established in September 2005, this international community includes representatives from a range of major sequencing and bioinformatics centres (including NCBI, EMBL, DDBJ, JCVI, JGI, EBI, Sanger, FIG) and research institutions.
More information about the Genomic Standards Consortium including contact details can be found here.
Details of MIGS
MIGS describes the genomes of eukaryotes, bacteria, archaea, plasmids, organelles, viruses and the communities of genomes found in metagenomic samples. The GSC expects MIGS to be stable enough to be used now but is open to further modification, for example as sequencing technologies change.
The MIGS specification enables description of the range of possible genomes and metagenomes using core descriptors such as origin of the nucleic acid, its source environment, date and time of sampling, and sample and sequence processing.
Specifically, the MIGS guideline describes each project as an Investigation split into a study and an assay. Under study, information can be reported about the environment of the sample (i.e. geographic location and habitat) and the details of the origin of the nucleic acid sequence. The assay section of the guideline contains a description of the use of a single sequencing technology, or a combination of technologies.
The GSC is currently working on an implementation of the MIGS specification in the form of the ‘Genomic Contextual Data Markup Language’ (GCDML). In contrast to minimum reporting, this expanded set of descriptors should facilitate ‘maximal’ reporting of information. GCDML has already been adopted by the Gordon and Betty Moore Foundation.
