Special issue of OMICS from the Genomic Standards Consortium (GSC)

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.

Putting Molecules on the Map

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.

Silva runs contextual data survey for rRNA sequences

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

RDP runs Habitat survey

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

MIGS paper published in Nature Biotechnology

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

GSC at Microbial Commons International Workshop

CONFERENCE ANNOUNCEMENT: MICROBIAL COMMONS

Designing the Microbial Research Commons:
learning from institutional policies
and collaborative network technologies

12-13 June 2008

Het Pand, Ghent, Belgium

http://www.microbialcommons.org

Dear colleague,

As part of an international undertaking and collaboration between Science
Commons, the StrainInfo.net bioportal, the Genomic Standards Consortium,
Bioversity International and the US national committees of CODATA, IUMS
and IUBS, an international conference on the building of an integrated
infrastructure in microbial research dealing with issues such as
bioinformatics, intellectual property rights, material transfer agreements,
text mining and integration with genomics databases will be organised on
June 12-13 2008 at “Het Pand” Conference Centre in Ghent, Belgium. This
conference is open to all involved in microbial research, microbial
resources, industrial microbiology, publishing and policy making.

Conference website: http://www.microbialcommons.org

Contact us: MicrobialCommons@lists.UGent.be

The microbial commons conference is organized back to back with the
annual meeting of the European Culture Collections’ Organisation (ECCO),
June 10-11 2008.

ECCO website: http://www.eccosite.org/

Feedback requested from GSC on MINSEQE

As an output of discussions at the recent MGED-organized UHTS standardization workshop, a new MI checklist is being developed. Participants at the workshop included representatives from the GSC, SRF, the short read trace archives, major sequencing centres, large projects like ENCODE, vendors, funders and researchers generating data.

The checklist is called the “Minimum Information about a high throughput Nucleotide SeQuencing Experiment” (MINSEQE) and is available for feedback here:  http://uhts.lbl.gov/

GSC vote: Genomic Rosetta Stone and LinkOut implementation

There is currently a vote open to GSC members, with a closing date of 2nd April 2008 23.00GMT.

The vote concerns the implementation of the Genomic Rosetta Stone utilising NCBI LinkOut. To state your preferred option please visit:

http://gensc.org/gc_wiki/index.php/Vote.001:_GRS_LinkOut_Implementation

GSC FAQ available to give a quick overview of all GSC activities

The GSC FAQ is now available, and provides a quick overview of all GSC activities.

Members of GSC working to complete example MIGS/MIMS report in ISA-Tab format

The RSBI working group has proposed an “Investigation Study Assay” paradigm for the modularization of minimum information checklists to accomodate reporting of multi-omic studies. This “ISA” construct is now also recognized by MIBBI.

The GSC’s MIGS checklist was specifically revised to also reflect the ISA structure to help in its modularization - some fields describe the whole Investigation, some the Study and some the Assay (in this case sequencing by any method including ultra high-throughput methods).

Further information:

http://gensc.org/gc_wiki/index.php/ISA-Tab