towards a richer set of information to describe our complete genome collection

GSC Publications

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[edit] GSC Publication in Press

[edit] Special issue of OMICS from the 5th GSC workshop

A second special issue of OMICS based on the 5th GSC workshop is also at the proof stage (see OMICS special issue for an overview). It will include the 4th and 5th GSC workshop reports, the first ISA-Tab workshop report, and roadmap papers on GCDML, Genomic Rosetta Stone, Habitat-Lite, an SOP central repository and EML/GCDML.

[edit] GSC Publications in Print

[edit] The MIGS Publication

The “Minimum Information about a Genome Sequence” (MIGS) perspective has finally appeared in print in Nature Biotechnology see HTML Fulltext and PDF version. It contains the definitive version of the MIGS checklist as it applies to genome and metagenomes and provides the background for the development of the checklists and plans for its future implementation. The MIGS publication went through a Nature Biotech community consultation that concluded April 19th, 2007.

PubMed Citation

[edit] 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.

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


  • 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 (2005) 6: 363-368.

PDF Journal


[edit] Special Issue of OMICS on data standards June 2006

As a result of the 2nd GSC workshop a special issue of OMICS appeared on data standards guest edited by Dawn Field and Susanna Sansone. It contained 22 invited pieces from the standards community, including new checklist descriptions. The issue can be found here:

OMICS special issue on Data Standards: http://www.liebertonline.com/toc/omi/10/2


Papers from the special issue of OMICS on data standards that emerged from the 2nd GSC workshop:


  • 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 Journal PubMed


Related papers in the same OMICS issue: 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


[edit] 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


[edit] 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


[edit] Papers citing MIGS/MIMS and the GSC

  • Raes J, Foerstner KU, Bork P. Get the most out of your metagenome: computational analysis of environmental

sequence data. Curr Opin Microbiol. 2007 Oct;10(5):490-498. Epub 2007 Oct 23. PubMed

Comment:
The authors propose MINIMESS, a minimal standard for metagenomics data analysis and cite GSC/MIMS. The link between MIMS and MINIMESS is discussed in the article (Box 1, page 496).


  • Markowitz VM, Ivanova N, Palaniappan K, Szeto E, Korzeniewski F, Lykidis A, Anderson I, Mavromatis K, Kunin V, Garcia Martin H, Dubchak I, Hugenholtz P, Kyrpides NC. An experimental metagenome data management and analysis system. Bioinformatics. 2006 Jul 15;22(20):2580.

PubMed


  • Liolios K, Mavromatis K, Tavernarakis N, Kyrpides NC. The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res. 2007 Nov 2; [Epub ahead of print]

PubMed


  • Wassenaar TM, Gamieldien J, Shatkin J, et al. The importance of virulence prediction and gene networks in microbial risk assessment.HUMAN AND ECOLOGICAL RISK ASSESSMENT 13 (2): 254-268 MAR-APR 2007 (PMID:?)


  • Morrison N, Bearden D, Bundy JG, et al. Standard reporting requirements for biological samples in metabolomics experiments: environmental context METABOLOMICS 3 (3): 203-210 SEP 2007 (PMID:?)


  • Adrian Tett, Andrew J Spiers, Lisa C Crossman, Duane Ager, Lena Ciric, J Maxwell Dow, John C Fry, David Harris, Andrew Lilley, Anna Oliver, Julian Parkhill, Michael A Quail, Paul B Rainey, Nigel J Saunders, Kathy Seeger, Lori A S Snyder, Rob Squares, Christopher M Thomas, Sarah L Turner, Xue-Xian Zhang, Dawn Field and Mark J Bailey. Sequence-based analysis of pQBR103; a representative of a unique, transfer-proficient mega plasmid resident in the microbial community of sugar beet. The ISME Journal (2007) 1, 331-340.

http://www.nature.com/ismej/journal/v1/n4/abs/ismej200747a.html


  • Rekha Seshadri, Saul A. Kravitz, Larry Smarr, Paul Gilna, Marvin Frazier 2007 CAMERA: A Community Resource for Metagenomics. Plos Biology

http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0050075.


[edit] Related papers

Papers discussing the need for meta-data standards in genomics


  • Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett CM, Knight R, Gordon JI. The human microbiome project. Nature. 2007 Oct 18;449(7164):804-10.

PubMed

Comment:
The section "Depositing and distributing data" of the paper discusses the need for a flexible, simple and open format for depositing metadata in the context of the human microbiome project.


[edit] GSC in the Media

  • Bionity.com: Genomic Standards for the Future: Setting the Guidelines May 22 2008 English and German
  • LabOnline: International guidelines for genome databases May 14 2008
  • Lead story in GenomeWeb: Genomic Standards Consortium Issues Guidelines May 13 2008
  • News Medical.net: Scientists publish guidelines for the improved description of genomes and metagenomes - May 13 2008
  • MIGS paper mentioned as Congoo news item: The minimum information about a genome sequence (MIGS) specification May 9 2008
  • MIGS publication press release by CEH: International Group of scientists publishes guidelines for the improved description of Genomes and Metagenomes - May 9 2008
  • MINSEQE and MIGS in BioInform: Workshop Spawns New ‘Minimum Information’ Guide for Next-Gen Sequencing Experiments - April 11, 2008
  • MINSEQE and MIGS in In Sequence Teams Develop New ‘Minimum Information’ Guidelines for High-Throughput Sequencing - April 15, 2008
  • SRF and MIGS in Bioinform:As Next-Gen Sequencers, Metagenomics Create Glut of Genomic Data, New Standards Emerge - March 2007
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