Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2011-05-06

AUTHORS

Pelin Yilmaz, Renzo Kottmann, Dawn Field, Rob Knight, James R Cole, Linda Amaral-Zettler, Jack A Gilbert, Ilene Karsch-Mizrachi, Anjanette Johnston, Guy Cochrane, Robert Vaughan, Christopher Hunter, Joonhong Park, Norman Morrison, Philippe Rocca-Serra, Peter Sterk, Manimozhiyan Arumugam, Mark Bailey, Laura Baumgartner, Bruce W Birren, Martin J Blaser, Vivien Bonazzi, Tim Booth, Peer Bork, Frederic D Bushman, Pier Luigi Buttigieg, Patrick S G Chain, Emily Charlson, Elizabeth K Costello, Heather Huot-Creasy, Peter Dawyndt, Todd DeSantis, Noah Fierer, Jed A Fuhrman, Rachel E Gallery, Dirk Gevers, Richard A Gibbs, Inigo San Gil, Antonio Gonzalez, Jeffrey I Gordon, Robert Guralnick, Wolfgang Hankeln, Sarah Highlander, Philip Hugenholtz, Janet Jansson, Andrew L Kau, Scott T Kelley, Jerry Kennedy, Dan Knights, Omry Koren, Justin Kuczynski, Nikos Kyrpides, Robert Larsen, Christian L Lauber, Teresa Legg, Ruth E Ley, Catherine A Lozupone, Wolfgang Ludwig, Donna Lyons, Eamonn Maguire, Barbara A Methé, Folker Meyer, Brian Muegge, Sara Nakielny, Karen E Nelson, Diana Nemergut, Josh D Neufeld, Lindsay K Newbold, Anna E Oliver, Norman R Pace, Giriprakash Palanisamy, Jörg Peplies, Joseph Petrosino, Lita Proctor, Elmar Pruesse, Christian Quast, Jeroen Raes, Sujeevan Ratnasingham, Jacques Ravel, David A Relman, Susanna Assunta-Sansone, Patrick D Schloss, Lynn Schriml, Rohini Sinha, Michelle I Smith, Erica Sodergren, Aymé Spor, Jesse Stombaugh, James M Tiedje, Doyle V Ward, George M Weinstock, Doug Wendel, Owen White, Andrew Whiteley, Andreas Wilke, Jennifer R Wortman, Tanya Yatsunenko, Frank Oliver Glöckner

ABSTRACT

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. More... »

PAGES

415-420

Journal

TITLE

Nature Biotechnology

ISSUE

5

VOLUME

29

Author Affiliations

  • Jacobs University Bremen gGmbH, Bremen, Germany
  • Microbial Genomics and Bioinformatics Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
  • Natural Environment Research Council Environmental Bioinformatics Centre, Wallington CEH, Oxford, UK.
  • Howard Hughes Medical Institute, San Francisco, California, USA
  • Center for Microbial Ecology, Michigan State University, East Lansing, Michigan, USA
  • The Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts, USA
  • Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, USA
  • National Center for Biotechnology Information (NCBI), National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
  • European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
  • WCU Center for Green Metagenomics, School of Civil and Environmental Engineering, Yonsei University, Seoul, Republic of Korea
  • School of Computer Science, University of Manchester, Manchester, UK
  • Oxford e-Research Centre, University of Oxford, Oxford, UK
  • Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
  • Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado, USA
  • Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, USA
  • Department of Medicine and the Department of Microbiology, New York University Langone Medical Center, New York, New York, USA
  • National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
  • Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA
  • Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
  • Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado, USA
  • Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
  • Department of Applied Mathematics and Computer Science, Ghent University, Ghent, Belgium
  • Center for Environmental Biotechnology, Lawrence Berkeley National Laboratory, Berkeley, California, USA
  • Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, USA
  • Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
  • National Ecological Observatory Network, Boulder, Colorado, USA
  • Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
  • Department of Biology, University of New Mexico, LTER Network Office, Albuquerque, New Mexico, USA
  • Department of Computer Science, University of Colorado, Boulder, Colorado, USA
  • Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
  • University of Colorado Museum of Natural History, University of Colorado, Boulder, Colorado, USA
  • Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
  • Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
  • Earth Science Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
  • Department of Biology, San Diego State University, San Diego, California, USA
  • Department of Microbiology, Cornell University, Ithaca, New York, USA
  • DOE Joint Genome Institute, Walnut Creek, California, USA
  • Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, Colorado, USA
  • Lehrstuhl für Mikrobiologie, Technische Universität München, Freising, Germany
  • J. Craig Venter Institute, Rockville, Maryland, USA
  • Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA
  • Department of Environmental Sciences, University of Colorado, Boulder, Colorado, USA
  • Department of Biology, University of Waterloo, Ontario, Canada
  • Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
  • Ribocon GmbH, Bremen, Germany
  • VIB - Vrije Universiteit Brussel, Brussels, Belgium
  • Canadian Centre for DNA Barcoding, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
  • Veterans Affairs Palo Alto Health Care System, Palo Alto, California, USA
  • Department of Microbiology and Immunology, Ann Arbor, Michigan, USA
  • Department of Genetics, The Genome Center, Washington University in St. Louis School of Medicine, St. Louis, Missouri, USA
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/nbt.1823

    DOI

    http://dx.doi.org/10.1038/nbt.1823

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1005906569

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/21552244


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