Archive for the ‘ebi’ Category

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


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.

Read Full Post »

At the recent Genomic Standards Consortium (GSC) workshop, George Garrity led discussions to review and produce a final version of the MIGS/MIMS checklist that will be included in the MIGS paper to be published in Nature Biotechnology in February 2008.

The revised version of the MIGS/MIMS checklist, together with comments recorded during the GSC workshop, are available via the GSC wiki at:


The MIGS/MIMS checklist document is available directly at:


Nature Biotechnology Journal home page:


Nature Biotechnology invited the scientific community to comment on the MIGS paper prior to publication. The community consultation page http://www.nature.com/nbt/consult/index.ht includes a link to the version of the MIGS paper made available for the community consultation:

Towards richer descriptions of our collection of genomes and metagenomes: the “Minimum Information about a Genome Sequence” (MIGS) specification (PDF 45K)

Read Full Post »

Dawn Field and Susanna-Assunta Sansone guest edited a special issue of the journal OMICS on data standards as an output of the 2nd GSC workshop. There were 22 invited papers including 5 in the area of standardization of genomic data (See: Special_Issue_of_OMICS).
An overview of the issue and its goals is captured in the foreword: http://www.liebertonline.com/doi/pdfplus/10.1089/omi.2006.10.84
The entire issue was open source and many of the papers in the issue continue to be at the top of the most downloaded list: http://www.liebertonline.com/action/showMostReadArticles?journalCode=omi

Special issue of OMICS from the 5th GSC Workshop

Dawn Field 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. After guaging interest in this prior to the workshop, and in response to developments at the workshop, we are going to accept this invitation.We are now considering proposals from the participants of the 5th GSC workshop (and their colleagues) for contributions on several key topics of special interest to the GSC.

Further information:

GSC web site: http://gensc.org

Dawn Field : contact info

George Garrity : contact info

Susanna-Assunta Sansone : contact info

Eugene Kolker : contact info

Read Full Post »

Further to the 5th Genomic Standards Consortium (GSC) workshop, slides are available to download from the GSC wiki:

agenda and presentations

Read Full Post »

At the 5th Genomic Standards Consortium (GSC) workshop held at the EBI on 12-14th December 2007, discussions led to a proposal to standardise the description of 16S sequences using the GSC community-led standard called Minimum Information about a Genome Sequence/ Metagenome Sample (MIGS/MIMS).

MIGS/MIMS defines descriptors that can assist in the capture of a rich set of information about 16S sequences using a community-led standard.

Further information is available on the GSC wiki:


Read Full Post »