Robbins Robert J.

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Robbins
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Robert J.
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  • Article
    Meeting report : GBIF hackathon-workshop on Darwin Core and sample data (22-24 May 2013)
    (Genomic Standards Consortium, 2014) Wieczorek, John ; Banki, Olaf ; Blum, Stan D. ; Deck, John ; Doring, Markus ; Droge, Gabriele ; Endresen, Dag ; Goldstein, Philip ; Leary, Patrick R. ; Krishtalka, Leonard ; O'Tuama, Eamonn ; Robbins, Robert J. ; Robertson, Tim ; Yilmaz, Pelin
    The workshop-hackathon was convened by the Global Biodiversity Information Facility (GBIF) at its secretariat in Copenhagen over 22-24 May 2013 with additional support from several projects (RCN4GSC, EAGER, VertNet, BiSciCol, GGBN, and Micro B3). It assembled a team of experts to address the challenge of adapting the Darwin Core standard for a wide variety of sample data. Topics addressed in the workshop included 1) a review of outstanding issues in the Darwin Core standard, 2) issues relating to publishing of biodiversity data through Darwin Core Archives, 3) use of Darwin Core Archives for publishing sample and monitoring data, 4) the case for modifying the Darwin Core Text Guide specification to support many-to-many relations, and 5) the generalization of the Darwin Core Archive to a “Biodiversity Data Archive”. A wide variety of use cases were assembled and discussed in order to inform further developments.
  • Article
    Genomic Standards Consortium projects
    (Genomic Standards Consortium, 2014) Field, Dawn ; Sterk, Peter ; Kottmann, Renzo ; De Smet, Wim ; Amaral-Zettler, Linda A. ; Cochrane, Guy R. ; James, Cole R. ; Davies, Neil ; Dawyndt, Peter ; Garrity, George M. ; Gilbert, Jack A. ; Glockner, Frank Oliver ; Hirschman, Lynette ; Klenk, Hans-Peter ; Knight, Rob ; Kyrpides, Nikos C. ; Meyer, Folker ; Karsch-Mizrachi, Ilene ; Morrison, Norman ; Robbins, Robert J. ; San Gil, Inigo ; Sansone, Susanna-Assunta ; Schriml, Lynn M. ; Tatusova, Tatiana ; Ussery, David W. ; Yilmaz, Pelin ; White, Owen ; Wooley, John ; Caporaso, J. Gregory
    The Genomic Standards Consortium (GSC) is an open-membership community working towards the development, implementation and harmonization of standards in the field of genomics. The mission of the GSC is to improve digital descriptions of genomes, metagenomes and gene marker sequences. The GSC started in late 2005 with the defined task of establishing what is now termed the “Minimum Information about any Sequence” (MIxS) standard [1,2]. As an outgrowth of the activities surrounding the creation and implementation of the MixS standard there are now 18 projects within the GSC [3]. These efforts cover an ever widening range of standardization activities. Given the growth of projects and to promote transparency, participation and adoption the GSC has developed a “GSC Project Description Template”. A complete set of GSC Project Descriptions and the template are available on the GSC website. The GSC has an open policy of participation and continues to welcome new efforts. Any projects that facilitate the standard descriptions and exchange of data are potential candidates for inclusion under the GSC umbrella. Areas that expand the scope of the GSC are encouraged. Through these collective activities we hope to help foster the growth of the ‘bioinformatics standards’ community. For more information on the GSC and its range of projects, please see http://gensc.org/.
  • Article
    RCN4GSC Workshop Report : managing data at the interface of biodiversity and (meta)genomics, March 2011
    (Genomic Standards Consortium, 2012-07-28) Robbins, Robert J. ; Amaral-Zettler, Linda A. ; Bik, Holly M. ; Blum, Stan D. ; Edwards, James ; Field, Dawn ; Garrity, George M. ; Gilbert, Jack A. ; Kottmann, Renzo ; Krishtalka, Leonard ; Lapp, Hilmar ; Lawrence, Carolyn ; Morrison, Norman ; O Tuama, Eamonn ; Parr, Cynthia Sims ; San Gil, Inigo ; Schindel, David ; Schriml, Lynn M. ; Vieglas, David ; Wooley, John
    Building on the planning efforts of the RCN4GSC project, a workshop was convened in San Diego to bring together experts from genomics and metagenomics, biodiversity, ecology, and bioinformatics with the charge to identify potential for positive interactions and progress, especially building on successes at establishing data standards by the GSC and by the biodiversity and ecological communities. Until recently, the contribution of microbial life to the biomass and biodiversity of the biosphere was largely overlooked (because it was resistant to systematic study). Now, emerging genomic and metagenomic tools are making investigation possible. Initial research findings suggest that major advances are in the offing. Although different research communities share some overlapping concepts and traditions, they differ significantly in sampling approaches, vocabularies and workflows. Likewise, their definitions of ‘fitness for use’ for data differ significantly, as this concept stems from the specific research questions of most importance in the different fields. Nevertheless, there is little doubt that there is much to be gained from greater coordination and integration. As a first step toward interoperability of the information systems used by the different communities, participants agreed to conduct a case study on two of the leading data standards from the two formerly disparate fields: (a) GSC’s standard checklists for genomics and metagenomics and (b) TDWG’s Darwin Core standard, used primarily in taxonomy and systematic biology.
  • Article
    Report of the 14th Genomic Standards Consortium Meeting, Oxford, UK, September 17-21, 2012
    (Genomic Standards Consortium, 2014) Davies, Neil ; Field, Dawn ; Amaral-Zettler, Linda A. ; Bicak, Mesude ; Bourlat, Sarah ; Coddington, Jonathan ; Deck, John ; Drummond, Alexei ; Gilbert, Jack A. ; Glockner, Frank Oliver ; Kottmann, Renzo ; Meyer, Chris ; Morrison, Norman ; Obst, Matthias ; Robbins, Robert J. ; Schriml, Lynn M. ; Sterk, Peter ; Stones-Havas, Steven
    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 workshop’s primary goal 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.