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1.
Glass E Meyer F Gilbert JA Field D Hunter S Kottmann R Kyrpides N Sansone S Schriml L Sterk P White O Wooley J 《Standards in genomic sciences》2010,3(3):225-231
This report summarizes the proceedings of the 10th workshop of the Genomic Standards Consortium (GSC), held at Argonne National Laboratory, IL, USA. It was the second GSC workshop to have open registration and attracted over 60 participants who worked together to progress the full range of projects ongoing within the GSC. Overall, the primary focus of the workshop was on advancing the M5 platform for next-generation collaborative computational infrastructures. Other key outcomes included the formation of a GSC working group focused on MIGS/MIMS/MIENS compliance using the ISA software suite and the formal launch of the GSC Developer Working Group. Further information about the GSC and its range of activities can be found at http://gensc.org/. 相似文献
2.
Neil Davies Dawn Field Linda Amaral-Zettler Katharine Barker Mesude Bicak Sarah Bourlat Jonathan Coddington John Deck Alexei Drummond Jack A. Gilbert Frank Oliver Gl?ckner Renzo Kottmann Chris Meyer Norman Morrison Matthias Obst Robert Robbins Lynn Schriml Peter Sterk Steven Stones-Havas 《Standards in genomic sciences》2014,9(3):1236-1250
This report summarizes the proceedings of the 14th workshop of the Genomic Standards Consortium (GSC) held at the University of Oxford in September 2012. The primary goal of the workshop was to work towards the launch of the Genomic Observatories (GOs) Network under the GSC. For the first time, it brought together potential GOs sites, GSC members, and a range of interested partner organizations. It thus represented the first meeting of the GOs Network (GOs1). Key outcomes include the formation of a core group of “champions” ready to take the GOs Network forward, as well as the formation of working groups. The workshop also served as the first meeting of a wide range of participants in the Ocean Sampling Day (OSD) initiative, a first GOs action. Three projects with complementary interests – COST Action ES1103, MG4U and Micro B3 – organized joint sessions at the workshop. A two-day GSC Hackathon followed the main three days of meetings. 相似文献
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Hirschman L Sterk P Field D Wooley J Cochrane G Gilbert J Kolker E Kyrpides N Meyer F Mizrachi I Nakamura Y Sansone SA Schriml L Tatusova T White O Yilmaz P 《Standards in genomic sciences》2010,2(3):357-360
This report summarizes the M3 Workshop held at the January 2010 Pacific Symposium on Biocomputing. The workshop, organized by Genomic Standards Consortium members, included five contributed talks, a series of short presentations from stakeholders in the genomics standards community, a poster session, and, in the evening, an open discussion session to review current projects and examine future directions for the GSC and its stakeholders. 相似文献
4.
Field D Sterk P Kyrpides N Kottmann R Glöckner FO Hirschman L Garrity GM Wooley J Gilna P 《Standards in genomic sciences》2009,1(1):68-71
This report summarizes the proceedings of the 6th and 7th workshops of the Genomic Standards Consortium (GSC), held back-to-back in 2008. GSC 6 focused on furthering the activities of GSC working groups, GSC 7 focused on outreach to the wider community. GSC 6 was held October 10-14, 2008 at the European Bioinformatics Institute, Cambridge, United Kingdom and included a two-day workshop focused on the refinement of the Genomic Contextual Data Markup Language (GCDML). GSC 7 was held as the opening day of the International Congress on Metagenomics 2008 in San Diego California. Major achievements of these combined meetings included an agreement from the International Nucleotide Sequence Database Consortium (INSDC) to create a "MIGS" keyword for capturing "Minimum Information about a Genome Sequence" compliant information within INSDC (DDBJ/EMBL /Genbank) records, launch of GCDML 1.0, MIGS compliance of the first set of "Genomic Encyclopedia of Bacteria and Archaea" project genomes, approval of a proposal to extend MIGS to 16S rRNA sequences within a "Minimum Information about an Environmental Sequence", finalization of plans for the GSC eJournal, "Standards in Genomic Sciences" (SIGS), and the formation of a GSC Board. Subsequently, the GSC has been awarded a Research Co-ordination Network (RCN4GSC) grant from the National Science Foundation, held the first SIGS workshop and launched the journal. The GSC will also be hosting outreach workshops at both ISMB 2009 and PSB 2010 focused on "Metagenomics, Metadata and MetaAnalysis" (M(3)). Further information about the GSC and its range of activities can be found at http://gensc.org, including videos of all the presentations at GSC 7. 相似文献
5.
Kyrpides N Field D Sterk P Kottmann R Glöckner FO Hirschman L Garrity GM Cochrane G Wooley J 《Standards in genomic sciences》2010,3(1):93-96
This report summarizes the proceedings of the 8th meeting of the Genomic Standards Consortium held at the Department of Energy Joint Genome Institute in Walnut Creek, CA, USA on September 9-11, 2009. This three-day workshop marked the maturing of Genomic Standards Consortium from an informal gathering of researchers interested in developing standards in the field of genomic and metagenomics to an established community with a defined governance mechanism, its own open access journal, and a family of established standards for describing genomes, metagenomes and marker studies (i.e. ribosomal RNA gene surveys). There will be increased efforts within the GSC to reach out to the wider scientific community via a range of new projects. Further information about the GSC and its activities can be found at http://gensc.org/. 相似文献
6.
Field D Glöckner FO Garrity GM Gray T Sterk P Cochrane G Vaughan R Kolker E Kottmann R Kyrpides N Angiuoli S Dawyndt P Guralnick R Goldstein P Hall N Hirschman L Kravitz S Lister AL Markowitz V Thomson N Whetzel T 《Omics : a journal of integrative biology》2008,12(2):101-108
This meeting report summarizes the proceedings of the "eGenomics: Cataloguing our Complete Genome Collection IV" workshop held June 6-8, 2007, at the National Institute for Environmental eScience (NIEeS), Cambridge, United Kingdom. This fourth workshop of the Genomic Standards Consortium (GSC) was a mix of short presentations, strategy discussions, and technical sessions. Speakers provided progress reports on the development of the "Minimum Information about a Genome Sequence" (MIGS) specification and the closely integrated "Minimum Information about a Metagenome Sequence" (MIMS) specification. The key outcome of the workshop was consensus on the next version of the MIGS/MIMS specification (v1.2). This drove further definition and restructuring of the MIGS/MIMS XML schema (syntax). With respect to semantics, a term vetting group was established to ensure that terms are properly defined and submitted to the appropriate ontology projects. Perhaps the single most important outcome of the workshop was a proposal to move beyond the concept of "minimum" to create a far richer XML schema that would define a "Genomic Contextual Data Markup Language" (GCDML) suitable for wider semantic integration across databases. GCDML will contain not only curated information (e.g., compliant with MIGS/MIMS), but also be extended to include a variety of data processing and calculations. Further information about the Genomic Standards Consortium and its range of activities can be found at http://gensc.org. 相似文献
7.
Field D Friedberg I Sterk P Kottmann R Glöckner FO Hirschman L Garrity GM Cochrane G Wooley J Gilbert J 《Standards in genomic sciences》2009,1(3):278-282
This report summarizes the proceedings of the "Metagenomics, Metadata and Meta-analysis" (M3) Special Interest Group (SIG) meeting held at the Intelligent Systems for Molecular Biology 2009 conference. The Genomic Standards Consortium (GSC) hosted this meeting to explore the bottlenecks and emerging solutions for obtaining biological insights through large-scale comparative analysis of metagenomic datasets. The M3 SIG included 16 talks, half of which were selected from submitted abstracts, a poster session and a panel discussion involving members of the GSC Board. This report summarizes this one-day SIG, attempts to identify shared themes and recapitulates community recommendations for the future of this field. The GSC will also host an M3 workshop at the Pacific Symposium on Biocomputing (PSB) in January 2010. Further information about the GSC and its range of activities can be found at http://gensc.org/. 相似文献
8.
Field D Garrity GM Sansone SA Sterk P Gray T Kyrpides N Hirschman L Glöckner FO Kottmann R Angiuoli S White O Dawyndt P Thomson N Gil IS Morrison N Tatusova T Mizrachi I Vaughan R Cochrane G Kagan L Murphy S Schriml L;Genomic Standards Consortium 《Omics : a journal of integrative biology》2008,12(2):109-113
9.
This article summarizes the proceedings of the "eGenomics: Cataloguing our Complete Genome Collection II" workshop held November 10-11, 2005, at the European Bioinformatics Institute. This exploratory workshop, organized by members of the Genomic Standards Consortium (GSC), brought together researchers from the genomic, functional OMICS, and computational biology communities to discuss standardization activities across a range of projects. The workshop proceedings and outcomes are set to help guide the development of the GSC's Minimal Information about a Genome Sequence (MIGS) specification. 相似文献
10.
Field D Sansone S Delong EF Sterk P Friedberg I Kottmann R Hirschman L Garrity G Cochrane G Wooley J Meyer F Hunter S White O 《Standards in genomic sciences》2010,3(3):232-234
This report summarizes the proceedings of the first day of the Metagenomics, Metadata and MetaAnalysis (M3) workshop held at the Intelligent Systems for Molecular Biology 2010 conference. The second day, which was dedicated to the inaugural meeting of the BioSharing initiative is presented in a separate report. The Genomic Standards Consortium (GSC) hosted the first day of this Special Interest Group (SIG) at ISMB to continue exploring the bottlenecks and emerging solutions for obtaining biological insights through large-scale comparative analysis of metagenomic datasets. The M3 SIG included invited and selected talks and a panel discussion at the end of the day involving the plenary speakers. Further information about the GSC and its range of activities can be found at http://gensc.org. Information about the newly established BioSharing effort can be found at http://biosharing.org/. 相似文献
11.
Gilbert JA Meyer F Knight R Field D Kyrpides N Yilmaz P Wooley J 《Standards in genomic sciences》2010,3(3):235-239
This report summarizes the proceedings of the Metagenomics, Metadata, Metaanalysis, Models and Metainfrastructure (M5) Roundtable at the 13th International Society for Microbial Ecology Meeting in Seattle, WA, USA August 22-27, 2010. The Genomic Standards Consortium (GSC) hosted this meeting as a community engagement exercise to describe the GSC to the microbial ecology community during this important international meeting. The roundtable included five talks given by members of the GSC, and was followed by audience participation in the form of a roundtable discussion. This report summarizes this event. Further information on the GSC and its range of activities can be found at http://www.gensc.org. 相似文献
12.
Gil IS Sheldon W Schmidt T Servilla M Aguilar R Gries C Gray T Field D Cole J Pan JY Palanisamy G Henshaw D O'Brien M Kinkel L McMahon K Kottmann R Amaral-Zettler L Hobbie J Goldstein P Guralnick RP Brunt J Michener WK 《Omics : a journal of integrative biology》2008,12(2):151-156
The Genomic Standards Consortium (GSC) invited a representative of the Long-Term Ecological Research (LTER) to its fifth workshop to present the Ecological Metadata Language (EML) metadata standard and its relationship to the Minimum Information about a Genome/Metagenome Sequence (MIGS/MIMS) and its implementation, the Genomic Contextual Data Markup Language (GCDML). The LTER is one of the top National Science Foundation (NSF) programs in biology since 1980, representing diverse ecosystems and creating long-term, interdisciplinary research, synthesis of information, and theory. The adoption of EML as the LTER network standard has been key to build network synthesis architectures based on high-quality standardized metadata. EML is the NSF-recognized metadata standard for LTER, and EML is a criteria used to review the LTER program progress. At the workshop, a potential crosswalk between the GCDML and EML was explored. Also, collaboration between the LTER and GSC developers was proposed to join efforts toward a common metadata cataloging designer's tool. The community adoption success of a metadata standard depends, among other factors, on the tools and trainings developed to use the standard. LTER's experience in embracing EML may help GSC to achieve similar success. A possible collaboration between LTER and GSC to provide training opportunities for GCDML and the associated tools is being explored. Finally, LTER is investigating EML enhancements to better accommodate genomics data, possibly integrating the GCDML schema into EML. All these action items have been accepted by the LTER contingent, and further collaboration between the GSC and LTER is expected. 相似文献
13.
Dawn Field Peter Sterk Renzo Kottmann J. Wim De Smet Linda Amaral-Zettler Guy Cochrane James R. Cole Neil Davies Peter Dawyndt George M. Garrity Jack A. Gilbert Frank Oliver Gl?ckner Lynette Hirschman Hans-Peter Klenk Rob Knight Nikos Kyrpides Folker Meyer Ilene Karsch-Mizrachi Norman Morrison Robert Robbins Inigo San Gil Susanna Sansone Lynn Schriml Tatiana Tatusova Dave Ussery Pelin Yilmaz Owen White John Wooley Gregory Caporaso 《Standards in genomic sciences》2014,9(3):599-601
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15.
éamonn ó Tuama John Deck Gabriel Dr?ge Markus D?ring Dawn Field Renzo Kottmann Juncai Ma Hiroshi Mori Norman Morrison Peter Sterk Hideaki Sugawara John Wieczorek Linhuan Wu Pelin Yilmaz 《Standards in genomic sciences》2012,7(1):166-170
The Global Biodiversity Information Facility and the Genomic Standards Consortium convened a joint workshop at the University of Oxford, 27-29 February 2012, with a small group of experts from Europe, USA, China and Japan, to continue the alignment of the Darwin Core with the MIxS and related genomics standards. Several reference mappings were produced as well as test expressions of MIxS in RDF. The use and management of controlled vocabulary terms was considered in relation to both GBIF and the GSC, and tools for working with terms were reviewed. Extensions for publishing genomic biodiversity data to the GBIF network via a Darwin Core Archive were prototyped and work begun on preparing translations of the Darwin Core to Japanese and Chinese. Five genomic repositories were identified for engagement to begin the process of testing the publishing of genomic data to the GBIF network commencing with the SILVA rRNA database. 相似文献
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17.
Through a newly established Research Coordination Network for the Genomic Standards Consortium (RCN4GSC), the GSC will continue its leadership in establishing and integrating genomic standards through community-based efforts. These efforts, undertaken in the context of genomic and metagenomic research aim to ensure the electronic capture of all genomic data and to facilitate the achievement of a community consensus around collecting and managing relevant contextual information connected to the sequence data. The GSC operates as an open, inclusive organization, welcoming inspired biologists with a commitment to community service. Within the collaborative framework of the ongoing, international activities of the GSC, the RCN will expand the range of research domains engaged in these standardization efforts and sustain scientific networking to encourage active participation by the broader community. The RCN4GSC, funded for five years by the US National Science Foundation, will primarily support outcome-focused working meetings and the exchange of early-career scientists between GSC research groups in order to advance key standards contributions such as GCDML. Focusing on the timely delivery of the extant GSC core projects, the RCN will also extend the pioneering efforts of the GSC to engage researchers active in developing ecological, environmental and biodiversity data standards. As the initial goals of the GSC are increasingly achieved, promoting the comprehensive use of effective standards will be essential to ensure the effective use of sequence and associated data, to provide access for all biologists to all of the information, and to create interdisciplinary opportunities for discovery. The RCN will facilitate these implementation activities through participation in major scientific conferences and presentations on scientific advances enabled by community usage of genomic standards. 相似文献
18.
Yilmaz P Kottmann R Field D Knight R Cole JR Amaral-Zettler L Gilbert JA Karsch-Mizrachi I Johnston A Cochrane G Vaughan R Hunter C Park J Morrison N Rocca-Serra P Sterk P Arumugam M Bailey M Baumgartner L Birren BW Blaser MJ Bonazzi V Booth T Bork P Bushman FD Buttigieg PL Chain PS Charlson E Costello EK Huot-Creasy H Dawyndt P DeSantis T Fierer N Fuhrman JA Gallery RE Gevers D Gibbs RA San Gil I Gonzalez A Gordon JI Guralnick R Hankeln W Highlander S Hugenholtz P Jansson J Kau AL Kelley ST 《Nature biotechnology》2011,29(5):415-420
Here we present a standard developed by the Genomic Standards Consortium (GSC) for reporting marker gene sequences--the minimum information about a marker gene sequence (MIMARKS). We also introduce a system for describing the environment from which a biological sample originates. The 'environmental packages' apply to any genome sequence of known origin and can be used in combination with MIMARKS and other GSC checklists. Finally, to establish a unified standard for describing sequence data and to provide a single point of entry for the scientific community to access and learn about GSC checklists, we present the minimum information about any (x) sequence (MIxS). Adoption of MIxS will enhance our ability to analyze natural genetic diversity documented by massive DNA sequencing efforts from myriad ecosystems in our ever-changing biosphere. 相似文献
19.
Van Brabant B Gray T Verslyppe B Kyrpides N Dietrich K Glöckner FO Cole J Farris R Schriml LM De Vos P De Baets B Field D Dawyndt P;Genomic Standards Consortium 《Omics : a journal of integrative biology》2008,12(2):123-127
Given the growing wealth of downstream information, the integration of molecular and non-molecular data on a given organism has become a major challenge. For micro-organisms, this information now includes a growing collection of sequenced genes and complete genomes, and for communities of organisms it includes metagenomes. Integration of the data is facilitated by the existence of authoritative, community-recognized, consensus identifiers that may form the heart of so-called information knuckles. The Genomic Standards Consortium (GSC) is building a mapping of identifiers across a group of federated databases with the aim to improve navigation across these resources and to enable the integration of their information in the near future. In particular, this is possible because of the existence of INSDC Genome Project Identifiers (GPIDs) and accession numbers, and the ability of the community to define new consensus identifiers such as the culture identifiers used in the StrainInfo.net bioportal. Here we outline (1) the general design of the Genomic Rosetta Stone project, (2) introduce example linkages between key databases (that cover information about genomes, 16S rRNA gene sequences, and microbial biological resource centers), and (3) make an open call for participation in this project providing a vision for its future use. 相似文献
20.
Field D Amaral-Zettler L Cochrane G Cole JR Dawyndt P Garrity GM Gilbert J Glöckner FO Hirschman L Karsch-Mizrachi I Klenk HP Knight R Kottmann R Kyrpides N Meyer F San Gil I Sansone SA Schriml LM Sterk P Tatusova T Ussery DW White O Wooley J 《PLoS biology》2011,9(6):e1001088
A vast and rich body of information has grown up as a result of the world's enthusiasm for 'omics technologies. Finding ways to describe and make available this information that maximise its usefulness has become a major effort across the 'omics world. At the heart of this effort is the Genomic Standards Consortium (GSC), an open-membership organization that drives community-based standardization activities, Here we provide a short history of the GSC, provide an overview of its range of current activities, and make a call for the scientific community to join forces to improve the quality and quantity of contextual information about our public collections of genomes, metagenomes, and marker gene sequences. 相似文献