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Archive for January, 2008

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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The Microarray and Gene Expression (MGED) Society, is calling for an effort to develop standards for exchanging ultra-high throughput sequencing (UHTS) data.

Dawn Field will be attending the workshop to represent the GSC.

Guy Cochrane will be there to represent the EBI Short Read Trace Archive.

Susanna-Assunta Sansone, a member of the MGED Board, will also be there.

UPDATED: Oct 8: the resulting proposal is now found at the MGED MINSEQE working group homepage

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Further to discussions at the Asia Pacific Bioinformatics Conference 2008 (APBC2008), Vineet K. Sharma is the newest member of the Genomic Standards Consortium (GSC).

Vineet’s work concerns computational analysis of metagenomic data and novel genome analysis. Vineet’s group sequences metagenomic samples from human and other organism’s metabiomes. Vineet will be involved in the further development of the GSC data standard, GCDML, that includes descriptors for metagenomic samples.

Further Information

GCDML

Genomic Contextual Data Markup Language incorporates the MIGS/MIMS specification and provides an extended data capture and exchange mechanism for integrating a wide range of information relevant to the in depth description of genomes and metagenomes.

Vineet K. Sharma

home page

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A poster will be presented at the Asia Pacific Bioinformatics Conference 2008 describing GenCat and the Genome Catalogue, two products of the Genomic Standards Consortium (GSC). If you are attending APBC 2008 and are interested in the work of the GSC, please contact Tanya Gray at tgra at ceh.ac.uk.

About the GSC:

The Genomic Standards Consortium (GSC) formed in 2005 with the aim to promote methods to standardize the description of genomes and the exchange and integration of genomics data.

The GSC is an open-membership international working body. 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.

For more information, please visit http://gensc.org

Products

The GSC has released a number of products:

MIGS/MIMS
Minimum Information about a Genome Sequence/Metagenome Sequence specification. Provides an extensions to the minimum information already captured by primary nucleotide databases (DDBJ/EMBL/Genbank) (Field et al, 2007).

GCDML
Genomic Contextual Data Markup Language that incorporates the MIGS/MIMS specification and provides an extended data capture and exchange mechanism for integrating a wide range of information relevant to the in depth description of genomes and metagenomes.

Genome Catalogue
A repository of genome reports that are compliant with the MIGS/MIMS specification. The Genome Catalogue is based on the GenCat software.

GenCat
A generic XML data catalogue tool that supports the development of data standards by providing a data repository and input forms auto-generated from successive XML schema files (used to define a data standard). (http://gencat.sf.net)

APBC 2008

http://sunflower.kuicr.kyoto-u.ac.jp/apbc2008/

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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:

http://gensc.org/gc_wiki/index.php/MIGS_Checklist_Proofs

The MIGS/MIMS checklist document is available directly at:

http://gensc.sourceforge.net/docs/migsmims/

Nature Biotechnology Journal home page:

http://www.nature.com/nbt/index.html

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)

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