Karsch-Mizrachi Ilene

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Karsch-Mizrachi
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Ilene
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  • 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
    The Genomic Standards Consortium
    (Public Library of Science, 2011-06-21) Field, Dawn ; Amaral-Zettler, Linda A. ; Cochrane, Guy R. ; Cole, James R. ; Dawyndt, Peter ; Garrity, George M. ; Gilbert, Jack A. ; Glockner, Frank Oliver ; Hirschman, Lynette ; Karsch-Mizrachi, Ilene ; Klenk, Hans-Peter ; Knight, Rob ; Kottmann, Renzo ; Kyrpides, Nikos C. ; Meyer, Folker ; San Gil, Inigo ; Sansone, Susanna-Assunta ; Schriml, Lynn M. ; Sterk, Peter ; Tatusova, Tatiana ; Ussery, David W. ; White, Owen ; Wooley, John
    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.
  • Preprint
    Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications
    ( 2011-01-04) Yilmaz, Pelin ; Kottmann, Renzo ; Field, Dawn ; Knight, Rob ; Cole, James R. ; Amaral-Zettler, Linda A. ; Gilbert, Jack A. ; Karsch-Mizrachi, Ilene ; Johnston, Anjanette ; Cochrane, Guy R. ; Vaughan, Robert ; Hunter, Christopher ; Park, Joonhong ; Morrison, Norman ; Rocca-Serra, Philippe ; Sterk, Peter ; Arumugam, Manimozhiyan ; Bailey, Mark ; Baumgartner, Laura ; Birren, Bruce W. ; Blaser, Martin J. ; Bonazzi, Vivien ; Booth, Tim ; Bork, Peer ; Bushman, Frederic D. ; Buttigieg, Pier Luigi ; Chain, Patrick S. G. ; Charlson, Emily ; Costello, Elizabeth K. ; Huot-Creasy, Heather ; Dawyndt, Peter ; DeSantis, Todd ; Fierer, Noah ; Fuhrman, Jed A. ; Gallery, Rachel E. ; Gevers, Dirk ; Gibbs, Richard A. ; San Gil, Inigo ; Gonzalez, Antonio ; Gordon, Jeffrey I. ; Guralnick, Robert P. ; Hankeln, Wolfgang ; Highlander, Sarah ; Hugenholtz, Philip ; Jansson, Janet K. ; Kau, Andrew L. ; Kelley, Scott T. ; Kennedy, Jerry ; Knights, Dan ; Koren, Omry ; Kuczynski, Justin ; Kyrpides, Nikos C. ; Larsen, Robert ; Lauber, Christian L. ; Legg, Teresa ; Ley, Ruth E. ; Lozupone, Catherine A. ; Ludwig, Wolfgang ; Lyons, Donna ; Maguire, Eamonn ; Methe, Barbara A. ; Meyer, Folker ; Muegge, Brian ; Nakielny, Sara ; Nelson, Karen E. ; Nemergut, Diana ; Neufeld, Josh D. ; Newbold, Lindsay K. ; Oliver, Anna E. ; Pace, Norman R. ; Palanisamy, Giriprakash ; Peplies, Jorg ; Petrosino, Joseph ; Proctor, Lita ; Pruesse, Elmar ; Quast, Christian ; Raes, Jeroen ; Ratnasingham, Sujeevan ; Ravel, Jacques ; Relman, David A. ; Assunta-Sansone, Susanna ; Schloss, Patrick D. ; Schriml, Lynn M. ; Sinha, Rohini ; Smith, Michelle I. ; Sodergren, Erica ; Spor, Ayme ; Stombaugh, Jesse ; Tiedje, James M. ; Ward, Doyle V. ; Weinstock, George M. ; Wendel, Doug ; White, Owen ; Whiteley, Andrew ; Wilke, Andreas ; Wortman, Jennifer R. ; Yatsunenko, Tanya ; Glockner, Frank Oliver
    Here we present a standard developed by the Genomic Standards Consortium (GSC) to describe 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 sequence whose origin is known and can therefore be used in combination with MIMARKS or 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 establish the minimum information about any (x) sequence (MIxS). Adoption of MIxS will enhance our ability to analyze natural genetic diversity across the Tree of Life as it is currently being documented by massive DNA sequencing efforts from myriad ecosystems in our ever-changing biosphere.
  • Article
    The genomic standards consortium : bringing standards to life for microbial ecology
    (Nature Publishing Group, 2011-04-07) Yilmaz, Pelin ; Gilbert, Jack A. ; Knight, Rob ; Amaral-Zettler, Linda A. ; Karsch-Mizrachi, Ilene ; Cochrane, Guy R. ; Nakamura, Yasukazu ; Sansone, Susanna-Assunta ; Glockner, Frank Oliver ; Field, Dawn
    Interest in sampling of diverse environments, combined with advances in high-throughput sequencing, vastly accelerates the pace at which new genomes and metagenomes are generated. For example, as of January 2011, 12 500 user-generated metagenomes have been submitted to the public MG-RAST Annotation server (http://metagenomics. nmpdr.org; Meyer et al., 2008), 490% of which were produced using high-throughput sequencing methodologies. We have entered into an era of ‘mega-sequencing projects’ that include the Genomic Encyclopaedia of Bacteria and Archaea project (http://www.jgi.doe.gov/programs/GEBA), the Microbial Earth Project (http://genome.jgi-psf. org/programs/bacteria-archaea/MEP/index.jsf), the Human Microbiome Project (http://nihroadmap.nih. gov/hmp), the Metagenomics of the Human Intestinal Tract consortium (http://www.metahit.eu), the Terragenome Initiative (http://www.terragenome. org), the Tara Oceans Expedition (http://oceans. taraexpeditions.org), the National Ecological Observatory Network (NEON-http://www.neoninc.org), the International Census of Marine Microbes (ICoMM-http://icomm.mbl.edu), Microbial Inventory Research Across Diverse Aquatic Long-Term Ecological Research Sites (http://amarallab.mbl. edu/mirada/mirada.html), the Earth Microbiome Project (http://www.earthmicrobiome.org) and other funded and unfunded projects, with many more visionary projects on the horizon.