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Archive for the ‘genome’ Category

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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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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The GSC will present a poster at the Genomics and Society meeting, to be held in London on 25-26th October 2007.

The event will feature lectures, debates, workshops and exhibitions, on the past, present and future roles of genomics in society. More information on the meeting is available on the dedicated web site: http://www.genomicsandsociety.org/

If you plan to attend the meeting, please send a note to curator@ceh.ac.uk.

 

genomics and society network logo

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The Genomic Standards Consortium held a Birds of a Feather meeting at ISMB/ECCB 2007.

There were three presentations, and a discussion led by Robert Stevens. Presentation slides can be downloaded from the GSC wiki:

Presentation Slides

* Tatiana Tatusov slides

* Dawn Field slides

* Lynette Hirschman slides

We mostly discussed how to achieve wider community involvement. In particular we discussed the fact that a group of us worked quite extensively at ISMB on the development of an ontology for the georeferencing of biological samples and records.

Environmental Ontology workshop

Related to this, the GSC is co-sponsor of an Environmental Ontology (EnvO) workshop to be held on August 29-31 2007 where the ontology obo file (called geo.obo) will be further reviewed. The agenda for the EnvO meeting is available on the GSC wiki and further details will be publishing shortly.

http://darwin.nerc-oxford.ac.uk/gc_wiki/index.php/EnvO_Workshop

Geo.obo file from Michael Ashburner

Michael Ashburner sent out an email on June 29th 2007 regarding the geo.obo file. A copy of the email and file attachments have been uploaded to the GSC wiki.

http://darwin.nerc-oxford.ac.uk/gc_wiki/index.php/Michael_ashburner_email

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