Genomic Standards Consortium
Encyclopedia
The Genomic Standards Consortium (GSC) is an initiative working towards richer descriptions of our collection of genomes, metagenomes
and marker genes. 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. The goal of the GSC is to promote mechanisms for standardizing the description of (meta)genomes, including the exchange and integration of (meta)genomic data. The number and pace of genomic and metagenomic sequencing projects will only increase as the use of ultra-high-throughput methods becomes common place and standards are vital to scientific progress and data sharing.
.
Metagenomics
Metagenomics is the study of metagenomes, genetic material recovered directly from environmental samples. The broad field may also be referred to as environmental genomics, ecogenomics or community genomics. Traditional microbiology and microbial genome sequencing rely upon cultivated clonal cultures...
and marker genes. Established in September 2005, this international community includes representatives from a range of major sequencing
DNA sequencing
DNA sequencing includes several methods and technologies that are used for determining the order of the nucleotide bases—adenine, guanine, cytosine, and thymine—in a molecule of DNA....
and bioinformatics
Bioinformatics
Bioinformatics is the application of computer science and information technology to the field of biology and medicine. Bioinformatics deals with algorithms, databases and information systems, web technologies, artificial intelligence and soft computing, information and computation theory, software...
centres (including NCBI
National Center for Biotechnology Information
The National Center for Biotechnology Information is part of the United States National Library of Medicine , a branch of the National Institutes of Health. The NCBI is located in Bethesda, Maryland and was founded in 1988 through legislation sponsored by Senator Claude Pepper...
, EMBL, DDBJ, JCVI
J. Craig Venter Institute
The J. Craig Venter Institute is a non-profit genomics research institute founded by J. Craig Venter, Ph.D. in October 2006. The Institute was the result of consolidating four organizations: the Center for the Advancement of Genomics, The Institute for Genomic Research, the Institute for...
, JGI
Joint Genome Institute
The U.S. Department of Energy Joint Genome Institute was created in 1997 to unite the expertise and resources in genome mapping, DNA sequencing, technology development, and information sciences pioneered at the DOE genome centers at Lawrence Berkeley National Laboratory , Lawrence Livermore...
, EBI
European Bioinformatics Institute
The European Bioinformatics Institute is a centre for research and services in bioinformatics, and is part of European Molecular Biology Laboratory...
, Sanger, FIG) and research institutions. The goal of the GSC is to promote mechanisms for standardizing the description of (meta)genomes, including the exchange and integration of (meta)genomic data. The number and pace of genomic and metagenomic sequencing projects will only increase as the use of ultra-high-throughput methods becomes common place and standards are vital to scientific progress and data sharing.
Mission
Community-driven standards have the best chance of success if developed within the auspices of international working groups. Participants in the GSC include biologists, computer scientists, those building genomic databases and conducting large-scale comparative genomic analyses, and those with experience of building community-based standards. The mission of the GSC is to work with the wider community towards:- the implementation of a new genomic standards
- methods of capturing and exchanging metadata
- harmonization of metadata collection and analysis efforts across the wider genomics community
MIGS/MIMS/MIMARKS and other projects
The GSC has published a “Minimum Information about a (Meta)Genome Sequence” specification and has now completed a "Minimum Information about an ENvironmental Sequence" specification. MIGS/MIMS/MIMARKS provides an extension of the minimum information already captured by the primary nucleotide databases (DDBJ/EMBL/Genbank). The development of any checklist must be an open and iterative process that involves a balanced group of participants. Further, this development process must be supported by providing mechanisms for achieving compliance if a checklist is to be adopted as a tool for the standardization of a particular area of knowledge. Work towards this goal has spawned a set of interlocking projects that are described in more detail here: GSC projects. These include The Genomic Contextual Data Markup Language (GCDML), Genomic Rosetta Stone (GRS), Habitat-Lite. Newer projects include the M5 project.Linkages to other groups
The GSC is interested in making and building links with other communities. As stated above, the GSC is engaged in ontology development within the OBO Foundry. The GSC is also a founding member community of the Minimum Information about a Biomedical or Biological Investigation (MIBBI), an umbrella community for supporting and co-ordinating the development of checklists describing Minimum Information StandardsMinimum Information Standards
Minimum Information standards or reporting guidelines specify the minimum amount of meta data and data required to meet a specific aim or aims. Usually the aim is to provide enough meta data and data to enable the unambiguous reproduction and interpretation of an experiment...
.