We are looking forward to seeing everyone this week starting with the GCDML technical workshop participants. We hope to get a lot done on Monday and Tuesday on GCDML before the main workshop starts.

The agendas for both meetings are now available on the web and have been ‘wikified’ to add live links and other relevant information so we can use them as a central source of information during the workshop.


The three day workshop is packed with short talks in the first two days to maximize exchange of information and the formulation of ideas, but there is also time for discussion. The third day, as always, is set aside for discussion and strategy development and is really when much of the lasting work gets done. We will split the morning into technical (GCDML) and strategic sessions and then rejoin to map out the next stage of the GSC roadmap.

As background to the workshop the GSC homepage has a new page to serve as a portal into all GSC projects.

GSC Projects

Links to the MIGS paper in Nat Biotech and the OMICS special issue including papers on the core GSC project are found on the home page.


GSC 6 and 7

The GSC 6 workshop will take place at the EBI Oct 15-17, 2008. There will be a GCDML satellite meeting the 13 and 14 of that week. Further details and an agenda have been posted into the GSC wiki.

GSC 6: http://gensc.org/gc_wiki/index.php/GSC_6

This meeting will be followed by GSC 7, which will be combined with the much larger Metagenomics 2008 meeting to be held in San Diego, the week of November 3rd.

GSC 7 at MG08: http://metagenomics.calit2.net/index.php

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.

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.

The Silva database is running a survey on which types of contextual data are most important for describing rRNA sequences.

The survey is quick to complete and can be found here: http://www.arb-silva.de/faqs/survey/

The results of this survey will be presented in a session on ribosomal RNA in the next GSC 6 meeting in Oct, 2007 at the EBI.

Further background on the survey is found in the emerging proposal for a “Minimum Information about an ENvironmental Sequence” (MIENS) guideline that takes into account MIGS/MIMS and modifies/extends it to describe rRNA sequences and related markers. This proposal is currently being developed in the GSC Wiki and feedback and contributions are welcomed from the wider community: http://gensc.org/gc_wiki/index.php/MIGS/MIMS_for_16S

The Ribosomal Database Project is running a user survey on habitat terms that are most important to users. Click on the RDP website and the quick survey will automatically launch in your browser: http://rdp.cme.msu.edu

The survey is part of the Habitat-Lite initiative within the Genomic Standards Consortium (GSC). Habitat-Lite is a small set of high-level terms for describing the habitat of biological samples, particular selected to cover genomes, metagenome, 16/18S sequences and related molecules. All Habitat-Lite terms are taken from the much larger Environment Ontology (http://environmentontology.org).

A paper on Habitat-Lite will appear as part of the special issue of OMICS to come from the 5th GSC workshop. A online version can be seen here: Pubmed

Thanks to the work of so many, the “Minimum Information about a Genome Sequence” (MIGS) perspective has finally appear in print in Nature Biotechnology. It contains the definitive version of the MIGS checklist as it applies to genome and metagenomes and provides the background for the development of the checklists and plans for its future implementation.

View it online for free here: http://www.nature.com/nbt/journal/v26/n5/full/nbt1360.html