The GSC 8 meeting was hosted at the Joint Genome Institute Sept 9-11, 2009. It was preceded by an ISA-Tab-GCDML workshop. The agenda can be see here on the GSC 8 meeting homepage.

The first report to appear on the meeting is in Bioinform:

The JGI is also producing a article and will post all talks as videos online soon.

Some of the GSC-8 photos are online at the JGI website.

A formal meeting report is being written by the organizers and will appear in the GSC’s journal Standards in the Genomic Sciences.

The GSC is launching an open-access online journal to support its mission. The “Standards in Genomic Sciences” (SIGS) journal will provide a forum for publishing genome and metagenome notes structured according to the GSC’s MIGS/MIMS specification. It will also support the community by providing a venue for the publication of a wide range of articles that are standards-compliant and standards supportive. For example, this will include the publication of Standard Operating Procedures (SOPs) such as those describing the annotation pipelines of the major sequencing centres. Submissions on a range of topics now welcomed. For more information, please see the links below.

SIGS: website
SIGS: Editorial Board
About SIGS

Another MIGS-compliant report has been published as a Supplementary an article – see Reference 137 and the table S1 listed in the Materials and Methods.

“Adaptations to Submarine Hydrothermal Environments Exemplified by the Genome of Nautilia profundicola”

See the full paper here.

The Terragenome project has launched a survey to capture the most popular descriptors for describing microbial studies of soils.

Take the survey here: Soil Metadata Survey for Microbial Studies

Background taken from the survey website:

The purpose of this survey is to determine what data about soil is believed to be important to accompany microbial molecular data entered into major databases, e.g GenBank, EMBL, RDP. The value of this metadata is to enable a search of the data for particular features and for determining relationships among soil features and molecular data over more global data sets. We are surveying the soil biology community to gain this assessment and then will work with the Genomic Standards Consortium (GSC) and the Environmental Ontology Consortium to ensure that soil data will be properly considered along with the metadata from other environments.

–from Jim Tiedje, Michigan State University, as an initiative
of the Genomic Standards Consortium and the new
International Soil Metagenome Consortium (Terragenome)

The GSC proposal to host a SIG this year at ISMB 2009 in Sweden has been successful. Further details will follow soon but the one day meeting will be held Saturday June 27th before the start of the main ISMB / ECCB 2009 meeting in Stockholm.

The official title of the SIG is “Metagenomics, Metadata and Metaanalysis (M3)“. There will a set of invited speakers along with a call for papers and posters.

Some further background about the spirit of the meeting below. The “M3″ Hompage will appear here in time

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ISMB SIG: Metagenomics, Metadata and Metaanalysis (M3), June 27th, Stockholm

There are now thousands of genomes and metagenomes available for study (see the Genomes Online Database. Interest in improved sampling of diverse environments (e.g. ocean, soil, sediment, and a range of hosts) combined with advances in the development and application of ultra-high throughput sequence methodologies is set to vastly accelerate the pace at which new metagenomes are generated. For example, in 2007, the Global Ocean Survey published scientific analyses of 41 metagenomes, and as of October 2008, the submission of user-generated metagenomes to the public MG-Rast Annotation server surpassed 1300. We have also entered an era of ‘mega-sequencing projects’ that now include funded projects like the Genomic Encyclopedia of Bacteria and Archaea (GEBA) project and the Human Microbiome Initiative (e.g. HMP), with many more visionary projects on the horizon.

While genomes represent the full genetic (DNA) complement of a single organism, metagenomes represent the DNA of an entire community of organisms. Metagenomes are partial samples of complex and largely unknown communities that can only be poorly assembled. Genome and metagenomes are now also being complemented with studies of metatranscriptomes (community transcript profiles) and metaproteomes (community protein profiles). The comparative study of these datasets, including multi-omic data sets from the same community, bring with them the need for new computational approaches.
These data hold the promise of unparalleled insights into fundamental questions across a range of fields including evolution, ecology, environment biology, health and medicine. Advances stem from improved understandings of the combinations, abundances and functions of the organisms in these communities and their genes and pathways. We are just starting to exploit these technologies to understand the microbial world and have only scratched the surface in terms of sampling natural microbial diversity in terms of space and time.

This SIG will explore the latest concepts, algorithms, tools, informatics pipelines, databases and standards being developed to cope with the analysis of vast quantities of metagenomic data. Through a series of invited and contributed talks, a panel discussion, and flash talks associated with a poster session, we aim to highlight scientific advances in the field and identify core computational challenges facing the wider community.

We aim to bring together researchers collecting samples for metagenomic analysis with those building the computational infrastructure required to fully exploit them with those thinking about the implementation of standards. In particular, we aim to encourage the participation of researchers already using metadata to detect patterns of biological interest. For example, those that are detecting trends in collections of genomes or metagenomes based on habitat or geographic location, or by analogy for microbiome studies by host or anatomical location, or studies that integrate substantial environmental, phenotypic, or epidemiology data.

This SIG will be hosted by the Genomic Standards Consortium (GSC). It will place emphasis on understanding the community’s needs for the complementary standards required to drive metagenomic science forward and support comparative studies. A SIG report will be published in the GSC’s online, open access journal “Standards in Genomic Sciences”. Contributed submissions based on talks and posters that describe studies that demonstrate the power of using curated (e.g. habitat or host) and measured (e.g. geographic location, salinity, temperature, or pH) contextual data in comparative metagenomic studies of large numbers of samples are encouraged. Likewise, papers describing new approaches, tools, databases, standards, ontologies or substantial new sets of curated metadata that aid in the integration and inter-operablility of disparate datasets are welcomed.

The Metagenomics 2008 meeting was a great venue for the GSC 7 meeting. The entire meeting, including the first day dedicated to GSC activities, was presented as a Webcast. This Web Cast has now been archived and all the talks can be viewed here: http://metagenomics.calit2.net/webcast.php

Information about all GSC projects is now being collated on a single page in the GSC Wiki. Please log in during the workshop and help update pages relevant to you and your project(s). The GSC core projects are MIGS/MIMS, the Genome Catalogue, GCDML, GRS, Habitat-Lite and the GSC eJournal and SOP central repository. In addition, the GSC projects page includes descriptions of the larger community efforts in which the GSC participates as a community (MIBBI, MINSEQE, EnvO, OBI, ISATAB).

GSC Projects

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.

AGENDA and LOGISTICS

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.

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.