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Archive for the ‘MIGS/MIMS’ Category

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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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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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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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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