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Archive for the ‘genomic standards consortium’ Category

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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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

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

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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

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Further information:
Habitat-Lite

The GSC is interested in the description of ‘sample’ including the habitat. We are therefore exploring the creation of a limited list of terms for describing habitat.

Increasingly, short lists of habitat terms are being used to annotate databases and undertake a variety of analyses. These lists are continuously being developed a new because there is not yet a central place to put and compare lists.

We are:

1. collecting habitat lists in use within the GSC community
2. determining the overlaps in these lists
3. assessing whether it it feasible to ‘merge’ (unify) these lists into a single, short list, that might be widely adopted for its broad scope and suitable coverage of a wide range of samples (genomes, metagenomes, 16S, etc).

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Dawn Field, Susanna-Assunta Sansone and George Garrity have been asked by the OMICS Editor and Chief Eugene Kolker to produce a special issue of OMICS based on the 5th GSC Workshop.

A community consultation has now started with the posting of the first paper on the GSC wiki. special issue of OMICS Wiki page Authors are strongly encouraged to circulate their papers widely, including to members of the GSC.

Please provide feedback directly to the authors or Editors (Dawn Field, George Garrity, Susanna-Assunta Sansone).

Further information:

Genomic Standards Consortium: http://gensc.org

Earlier post: special issue of OMICS

special issue of OMICS Wiki page

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The GSC is helping to plan the first workshop for the Minimum Information for Biological and Biomedical Investigations (MIBBI) project, to be held on 2-3 April 2008, with funding from the UK research council, BBSRC.

The organizers are Chris Taylor (EBI), Susanna-Assunta Sansone (EBI) and Dawn Field (GSC, NERC Centre for Ecology and Hydrology).

About the MIBBI workshop

MIBBI workshop


About MIBBI

From http://mibbi.sourceforge.net/:

Throughout the biological and biomedical sciences prescriptive checklists specifying the key information to include when reporting experimental results are beginning to find favour with experimentalists, analysts, publishers and funders alike. However, such ‘minimum information’ (MI) checklists are usually developed independently, from within particular biologically- or technologically-delineated domains.

Consequently, the full range of checklists can be difficult to establish without intensive searching, and tracking their evolution is non-trivial; they are also inevitably partially-redundant one against another, and where they overlap arbitrary decisions on wording and substructuring make integration difficult.

This presents significant difficulties for the users of checklists; for example, in the area of systems biology, where data from multiple biological domains and technology platforms are routinely combined.

We offer a common portal to such MI checklists; to act as a ‘one-stop shop’ for those exploring the range of extant projects, foster collaborative development and ultimately promote gradual integration.


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