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The Genomic Standards Consortium will be hosting a Birds of a Feather meeting at ISMB/ECCB 2007.

Date: Monday 23rd July 2007
Time: 12.15pm – 1.30pm
Room: see noticeboards

An open invitation :-
Meet members of the Genomic Standards Consortium
Learn about the activities of the Genomic Standards Consortium
Find out how to participate in the work of the Genomic Standards Consortium
Join in an open discussion

Meeting agenda:

* 12.30 – 12.40 : Introduction by Tatiana Tatusov
* 12.40 – 12.50 : Dawn Field – Overview of Genomic Standards Consortium (GSC) Activities
* 12.50 – 13.00 : Robert Stevens – Harnessing Ontologies to Describe Genomes
* 13.00 – 13.10 : Lynette Hirschman – Mining Metadata for Metagenomics
* 13.10 – 13.30 : Open Discussion

http://gensc.sf.net

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A meeting report summarizing the proceedings of the “eGenomics: Cataloguing our Complete Genome Collection III” workshop held September 11–13, 2006, at the National Institute for Environmental eScience (NIEeS), Cambridge, United Kingdom, is now available:

download meeting report

Comparative and Functional Genomics
Volume 2007 (2007), Article ID 47304, 7 pages
doi:10.1155/2007/47304

Meeting Report

eGenomics: Cataloguing Our Complete Genome Collection III

Dawn Field, George Garrity, Tanya Gray, Jeremy Selengut, Peter Sterk, Nick Thomson, Tatiana Tatusova, Guy Cochrane, Frank Oliver Glöckner, Renzo Kottmann, Allyson L. Lister, Yoshio Tateno, and Robert Vaughan

This 3rd workshop of the Genomic Standards Consortium was divided into two parts. The first half of the three-day workshop was dedicated to reviewing the genomic diversity of our current and future genome and metagenome collection, and exploring linkages to a series of existing projects through formal presentations. The second half was dedicated to strategic discussions. Outcomes of the workshop include a revised “Minimum Information about a Genome Sequence” (MIGS) specification (v1.1), consensus on a variety of features to be added to the Genome Catalogue (GCat), agreement by several researchers to adopt MIGS for imminent genome publications, and an agreement by the EBI and NCBI to input their genome collections into GCat for the purpose of quantifying the amount of optional data already available (e.g., for geographic location coordinates) and working towards a single, global list of all public genomes and metagenomes.

http://www.hindawi.com/GetArticle.aspx?doi=10.1155/2007/47304

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Presentation slides from the 4th GSC Workshop held on 6-8th June 2007 at NIEeS in Cambridge, are now available from the NIEeS archive

NIEeS

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The 4th Genomic Standards Consortium Workshop will be held next week, 6-8th June, 2007 at the National Institute for Environmental e-Science (NIEeS), Cambridge.

As at previous workshops there will be a mix of talks and discussion sessions, although this year the talks will be shorter and more focused on progress made towards GSC goals. There will be 6 sessions covering key topics of interest to the GSC.

There will be a special focus on progress to date, the development of MIMS, future implementation of MIGS/MIMS, CVs and ontologies for describing genomes and metagenomes, the need for a single, global list of genomes and metagenomes and the role of the GSC’s proposed Genomic Rosetta Stone.

The latest agenda is available on the GSC wiki. Workshop homepage on NIEeSweb site

Date: 6-8 June, 2007

Venue: National Institute for Environmental e-Science, Cambridge, UK

Organizers: Dawn Field, Tatiana Tatusova, Tanya Gray, George Garrity, and Frank Oliver Glöckner

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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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The latest release of the Genomic Standards Consortium Genome Catalogue is now available:

http://gensc.sf.net

Features are described in the
GSC wiki

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The current GSC publication list:

The MIGS manuscript: The Nature Biotech community consultation concluded April 19th, 2007. Decision by NBT pending.

Nature Biotech

GSC Meeting Reports

  • Dawn Field, George Garrity, Tanya Gray, Jeremy Selengut, Peter Sterk, Nick Thomson, Tatiana Tatusova, Guy Cochrane, Frank Oliver Glockner, Renzo Kottmann, Allyson L. Lister, Yoshio Tateno, and Robert Vaughan. (2007) Meeting Report: eGenomics: Cataloguing Our Complete Genome Collection III. Comparative and Functional Genomics: A journal of integrative biology (2006) June, Vol. 10, No. 2: 100 -104.

PDF – Uncorrected proof Journal PubMed

  • Field D, Morrison N, Selengut J, Sterk P. Meeting Report: eGenomics: Cataloguing Our Complete Genome Collection II. OMICS: A journal of integrative biology (2006) June, Vol. 10, No. 2: 100 -104.

PDF Journal PubMed

  • Field D, Garrity G, Morrison N, Selengut J, Sterk P, Thomson N, Tatusova T. Meeting Report: eGenomics: Cataloguing our Complete Genome Collection. Comparative and Functional Genomics (2006) 6: 363-368.

PDF Journal

 

Special Issue of OMICS

Papers from the special issue of OMICS (http://www.liebertonline.com/toc/omi/10/2) on data standards that emerged from the 2nd and 1st GSC workshops:

  • Field D, Sansone S-A. A special issue on Omic data standards. OMICS: A journal of integrative biology (2006) June, Vol. 10, No. 2: 84 -93

PDF Journal PubMed

  • Morrison N, Cochrane G, Faruque N, Tatusova T, Tateno Y, Hancock D, and Field D. The concept of Sample in Omics Technology. OMICS: A journal of integrative biology (2006) June, Vol. 10, No. 2: 127 -137 .

PDF PubMed

OMICS Journal

Related papers: standardization of genomic databases

  • Jeffrey L. Boore. Requirements and Standards for Organelle Genome Databases. OMICS: A Journal of Integrative Biology (2006) June, Vol. 10, No. 2 : 119 -126.

PDF Journal PubMed

  • Guy Cochrane, Kirsty Bates, Rolf Apweiler, Yoshio Tateno, Jun Mashima, Takehide Kosuge, Ilene Karsch Mizrachi, Susan Schafer, Michael Fetchko. Evidence Standards in Experimental and Inferential INSDC Third Party Annotation Data. OMICS: A Journal of Integrative Biology (2006) June, 2006, Vol. 10, No. 2: 105-113.

PDF Journal PubMed

  • Peter Sterk, Paul J. Kersey, Rolf Apweiler. Genome Reviews: Standardizing Content and Representation of Information about Complete Genomes OMICS: A Journal of Integrative Biology (2006) June, 2006, Vol. 10, No. 2: 114-118.

PDF Journal PubMed

 

Development of Ontologies relevant to the description of genomes and metagenomes

  • Whetzel P.L, Brinkman R.R, Causton H.C, Fan L, Field D, Fostel J, Fragaso G, Gray T, Heiskanen M, Hernandez-Boussard T, Morrison N, Parkinson H, Rocca-Serra P, Sansone S-A, Schober D, Smith B, Stevens R, Stoeckert Jnr C.J, Taylor C, White J, Wood A, and the FuGO Working Group. Development of FuGO: An Ontology for Functional Genomics Investigations. OMICS: A journal of integrative biology (2006) June, Vol. 10, No. 2: 199 -204.

PDF Journal PubMed

Initial Proposal for MIGS

  • Field D, & Hughes J. Cataloguing our current genome collection. Microbiology (2005) 151, 1016-1019.

PDF Journal PubMed

  • The review paper that led to the above call for MIGS: Martiny, J.B.H. and D. Field. Ecological perspectives on the sequenced genome collection. (2005) Ecology Letters 8: 1334-1345.

PDF Journal

See the GSC wiki for the latest publications list: http://darwin.nerc-oxford.ac.uk/gc_wiki/index.php/GSC_Publications

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