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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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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

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The latest release of GenCat is available to download from the project SourceForge SVN repository:

gencat release-1.1

GenCat uses the latest technology including Orbeon Forms, eXist, AJAX, XForms and XML Pipeline Language (XPL/XPROC), and provides a generic XML data catalogue with input forms generated on-the-fly from XML schema files, to capture schema-compliant XML instances.

GenCat has been implemented as the Genome Catalogue, an online repository from the Genomic Standards Consortium (GSC) containing MIGS/MIMS-compliant reports.

For further information:

GSC web site: http://gensc.org

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

agenda and presentations

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The 5th GSC Workshop is underway. The workshop will run from 12-14th December, and is hosted at the EBI in Hinxton. The GSC wiki will be updated during the workshop. For further information visit

http://gensc.org/gc_wiki/index.php/5th_GSC_Workshop

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Minimum Information about a Genome Sequence/ Minimum Information about a Metagenomic Sequence/Sample

Some pointers to resources to retrieve, visualize and explore the MIGS/MIMS specification:

Introduction to MIGS/MIMS

GSC Wiki page describing MIGS/MIMS

MIGS/MIMS XML Schema web service

The MIGS/MIMS XML schema can be downloaded via a URL-based web service. The web service API is described in the GSC wiki.

MIGS/MIMS XML Schema CSV file

The same web service allows the XML schema to be downloaded as a comma separated text file (csv) that can be imported into a spreadsheet application, including Google Docs.

GSC Wiki page describing web service to download MIGS XML schema and CSV file

MIGS XML schema download

The following link also allows the XML schema file to be downloaded:

Download latest MIGS XML schema file

 

MIGS/MIMS graph visualization

Graph visualization of latest MIGS schema (Java applet)


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