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Archive for June, 2008

The Genomic Standards Consortium (GSC) has produced a second special issue of OMICS. The first, published in 2006, brought together 20 invited papers from a diversity of standards communities, many of which are still in the most read list of OMICS papers. This special issue focuses exclusively on the efforts of the GSC as defined at the 5th GSC workshop held at the European Bioinformatics Institute (EBI) in December 2007. All papers in both issues are available online as free content and can be accessed without a subscription.

Community-driven standards activities are becoming increasingly important given the deluge of data being generated across the life-sciences, and in particular in the area of ‘omics. This is nowhere more true than in the field of genomics, especially given the explosion of metagenomic studies and the development of ultra high-throughput sequencing technologies.

The mission of the GSC is to improve the descriptions of genomes and metagenomes in the public domain and promote data sharing and exchange. Following the publication of its “Minimum Information about a Genome Sequence” guideline in May 2008, the GSC is now focusing on a set of projects that are designed to make MIGS an operational standard. Read the papers in this special issue to learn more about the Genomic Contextual Data Markup Language (GCDML) which implements MIGS in XML, the Genomic Rosetta Stone project, a mapping of genomic identifiers, and Habitat-Lite, a high-level, short list of terms selected from the Environment Ontology (EnvO). These, and other activities, are summarized in the proceedings of the 5th GSC workshop report also found in this issue. Combined, all of these projects are steps towards realizing the vision of creating a comprehensive and easily accessible store of information about our complete genome and metagenome collection.

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At the heart of the MIGS specification is a call for all genomes and metagenomes to be reported with geographic location (lat/long). We were therefore very pleased to see a Nature Editorial calling for ALL biological samples to be tagged with lat/long. The GSC responded with a Nature Correspondence to underscore our collaborative interest in seeing all molecules (in particular genomes, metagenomes and phylogenetic markers like 16S/18S ribosomal RNA genes) placed into a geospatial framework. Location of isolation is increasingly of relevance as an informative piece of contextual data for the interpretation of collections of sequences. In addition to the GSC, the Correspondence was signed by the INSDC, CBOL, ICoMM, and EnvO

The original Editorial can be found here: http://www.nature.com/nature/journal/v453/n7191/full/453002a.html

Our response is here (see bottom of article for all signatories including the GSC): http://www.nature.com/nature/journal/v453/n7198/full/453978b.html

Both pieces are available as free content and can be accessed without a subscription to Nature.

The full list of Signatories on the Correspondence can be seen here.

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