Meeting Report from the Genomic Standards Consortium (GSC) Workshop 9

Davidsen, Tanja; Madupu, Ramana; Sterk, Peter; Field, Dawn; Garrity, George; Gilbert, Jack; Glöckner, Frank Oliver; Hirschman, Lynette; Kolker, Eugene; Kottmann, Renzo; Kyrpides, Nikos; Meyer, Folker; Morrison, Norman; Schriml, Lynn; Tatusova, Tatiana; Wooley, John

doi:10.4056/sigs.1353455

Title: Meeting Report from the Genomic Standards Consortium (GSC) Workshop 9

Journal Article · Fri Dec 31 00:00:00 EST 2010 · Standards in Genomic Sciences

DOI:https://doi.org/10.4056/sigs.1353455· OSTI ID:1629410

Davidsen, Tanja ^[1]; Madupu, Ramana ^[1]; Sterk, Peter ^[2]; Field, Dawn ^[3]; Garrity, George ^[4]; Gilbert, Jack ^[5]; Glöckner, Frank Oliver ^[6]; Hirschman, Lynette ^[7]; Kolker, Eugene ^[8]; Kottmann, Renzo ^[6]; Kyrpides, Nikos ^[9]; Meyer, Folker ^[10]; Morrison, Norman ^[11]; Schriml, Lynn ^[12]; Tatusova, Tatiana ^[13]; Wooley, John ^[14]

J. Craig Venter Inst., Inc., Rockville, MD (United States)
NERC Center for Ecology and Hydrology, Oxford (United Kingdom); Wellcome Trust Sanger Inst., Hinxton (United States)
NERC Center for Ecology and Hydrology, Oxford (United Kingdom)
Michigan State Univ., East Lansing, MI (United States). Dept. of Microbiology and Molecular Genetics
Plymouth Marine Laboratory (PML), Plymouth (United Kingdom); Argonne National Lab. (ANL), Argonne, IL (United States)
Max Planck Institute for Marine Microbiology, Bremen (Germany). Microbial Genomics Group; Jacobs Univ. Bremen (Germany)
The MITRE Corporation, Bedford, MA (United States). Information Technology Center
Seattle Children’s Hospital, Seattle, WA (United States)
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
Argonne National Lab. (ANL), Argonne, IL (United States)
Univ. of Manchester (United Kingdom). School of Computer Science
University of Maryland School of Medicine, Baltimore, MD (United States)
National Institutes of Health (NIH), Bethesda, MD (United States). National Library of Medicine (NLM)
Univ. of California San Diego, La Jolla, CA (United States)

This report summarizes the proceedings of the 9th workshop of the Genomic Standards Consortium (GSC), held at the J. Craig Venter Institute, Rockville, MD, USA. It was the first GSC workshop to have open registration and attracted over 90 participants. This workshop featured sessions that provided overviews of the full range of ongoing GSC projects. It included sessions on Standards in Genomic Sciences, the open access journal of the GSC, building standards for genome annotation, the M5 platform for next-generation collaborative computational infrastructures, building ties with the biodiversity research community and two discussion panels with government and industry participants. Progress was made on all fronts, and major outcomes included the completion of the MIENS specification for publication and the formation of the Biodiversity working group.

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Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division; National Science Foundation (NSF); Natural Environment Research Council (NERC)

Grant/Contract Number:: RCN4GSC; DBI-0840989; IIS 0844419; E/D01252X/1

OSTI ID:: 1629410

Journal Information:: Standards in Genomic Sciences, Vol. 3, Issue 3; Conference: 9.Workshop of the Genomic Standards Consortium (GSC 9), Rockville, MD (United States), 28-30 Apr 2010; ISSN 1944-3277

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

References (13)

The minimum information about a genome sequence (MIGS) specification Field, Dawn; Garrity, George; Gray, Tanya Nature Biotechnology, Vol. 26, Issue 5 https://doi.org/10.1038/nbt1360	journal	May 2008
MetaBar - a tool for consistent contextual data acquisition and standards compliant submission Hankeln, Wolfgang; Buttigieg, Pier Luigi; Fink, Dennis BMC Bioinformatics, Vol. 11, Issue 1 https://doi.org/10.1186/1471-2105-11-358	journal	January 2010
The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata Liolios, Konstantinos; Chen, I-Min A.; Mavromatis, Konstantinos Nucleic Acids Research, Vol. 38, Issue suppl_1 https://doi.org/10.1093/nar/gkp848	journal	November 2009
The Ribosomal Database Project: improved alignments and new tools for rRNA analysis Cole, J. R.; Wang, Q.; Cardenas, E. Nucleic Acids Research, Vol. 37, Issue Database https://doi.org/10.1093/nar/gkn879	journal	January 2009
eGenomics: Cataloguing our Complete Genome Collection Field, Dawn; Garrity, George; Morrison, Norman Comparative and Functional Genomics, Vol. 6, Issue 7-8 https://doi.org/10.1002/cfg.494	journal	January 2005
Laying the Foundation for a Genomic Rosetta Stone: Creating Information Hubs through the Use of Consensus Identifiers Van Brabant, Bart; Gray, Tanya; Verslyppe, Bert OMICS: A Journal of Integrative Biology, Vol. 12, Issue 2 https://doi.org/10.1089/omi.2008.0020	journal	June 2008
CAMERA: A Community Resource for Metagenomics Seshadri, Rekha; Kravitz, Saul A.; Smarr, Larry PLoS Biology, Vol. 5, Issue 3 https://doi.org/10.1371/journal.pbio.0050075	journal	March 2007
The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes Meyer, F.; Paarmann, D.; D'Souza, M. BMC Bioinformatics, Vol. 9, Issue 1 https://doi.org/10.1186/1471-2105-9-386	journal	September 2008
ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level Rocca-Serra, P.; Brandizi, M.; Maguire, E. Bioinformatics, Vol. 26, Issue 18 https://doi.org/10.1093/bioinformatics/btq415	journal	August 2010
Meeting Report: Metagenomics, Metadata and Meta-analysis; (M3) Special Interest Group at ISMB 2009 Field, Dawn; Friedberg, Iddo; Sterk, Peter Standards in Genomic Sciences, Vol. 1, Issue 3 https://doi.org/10.4056/sigs.641096	journal	December 2009
The “Minimum Information about an ENvironmental Sequence” (MIENS) specification Glöckner, Frank Oliver; Yilmaz, Pelin; Kottmann, Renzo Nature Precedings https://doi.org/10.1038/npre.2010.5252.2	journal	November 2010
A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea Wu, Dongying; Hugenholtz, Philip; Mavromatis, Konstantinos Nature, Vol. 462, Issue 7276 https://doi.org/10.1038/nature08656	journal	December 2009
A Standard MIGS/MIMS Compliant XML Schema: Toward the Development of the Genomic Contextual Data Markup Language (GCDML) Kottmann, Renzo; Gray, Tanya; Murphy, Sean OMICS: A Journal of Integrative Biology, Vol. 12, Issue 2 https://doi.org/10.1089/omi.2008.0a10	journal	June 2008

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The first special issue of Standards in Genomic Sciences from the Genomic Standards Consortium Field, Dawn; Kottmann, Renzo; Sterk, Peter Standards in Genomic Sciences, Vol. 3, Issue 3 https://doi.org/10.4056/sigs.1493697	journal	January 2010

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