Linda Amaral-Zettler

Publications of Linda Amaral-Zettler

• The Genomic Standards Consortium.

  Authors: Dawn Field, Linda Amaral-Zettler, Guy Cochrane, James R Cole, Peter Dawyndt, George M Garrity, Jack Gilbert, Frank Oliver Glöckner, Lynette Hirschman, Ilene Karsch-Mizrachi [......] Nikos Kyrpides, Folker Meyer, Inigo San Gil, Susanna-Assunta Sansone, Lynn M Schriml, Peter Sterk, Tatiana Tatusova, David W Ussery, Owen White, John Wooley

  PLoS biology. 06/2011; 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 itsA 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.

• Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications.

  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 [......] 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

  Nature biotechnology. 05/2011; 29(5):415-20.

  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 aHere 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.

• The genomic standards consortium: bringing standards to life for microbial ecology.

  Authors: Pelin Yilmaz, Jack A Gilbert, Rob Knight, Linda Amaral-Zettler, Ilene Karsch-Mizrachi, Guy Cochrane, Yasukazu Nakamura, Susanna-Assunta Sansone, Frank Oliver Glöckner, Dawn Field

  The ISME journal. 04/2011; 5(10):1565-7.

• Proceedings of the international workshop on Ribosomal RNA technology, April 7-9, 2008, Bremen, Germany.

  Authors: Linda Amaral-Zettler, Jörg Peplies, Alban Ramette, Bernhard Fuchs, Wolfgang Ludwig, Frank Oliver Glöckner

  Systematic and applied microbiology. 10/2008; 31(4):258-68.

  Thirty years have passed since Carl Woese proposed three primary domains of life based on the phylogenetic analysis of ribosomal RNA (rRNA) genes. Adopted by researchers worldwide, rRNA has becomeThirty years have passed since Carl Woese proposed three primary domains of life based on the phylogenetic analysis of ribosomal RNA (rRNA) genes. Adopted by researchers worldwide, rRNA has become the "gold-standard" for molecular taxonomy, biodiversity analysis and the identification of microorganisms. The more than 700,000 rRNA sequences in public databases constitute an unprecedented hallmark of the richness of microbial biodiversity on earth. The International Workshop on Ribosomal RNA Technology convened on April 7-9, 2008 in Bremen, Germany (http://www.arb-silva.de/rrna-workshop) to summarize the current status of the field and strategize on the best ways of proceeding on both biological and technological fronts. In five sessions, 26 leading international speakers and approximately 120 participants representing diverse disciplines discussed new technological approaches to address three basic ecological questions: "Who is out there?" "How many are there?" and "What are they doing?".

• Defining Linkages between the GSC and NSF's LTER Program: How the Ecological Metadata Language (EML) Relates to GCDML and Other Outcomes.

  Authors: Inigo San Gil, Wade Sheldon, Tom Schmidt, Mark Servilla, Raul Aguilar, Corinna Gries, Tanya Gray, Dawn Field, James Cole, Jerry Yun Pan [......] Margaret O'Brien, Linda Kinkel, Katherine McMahon, Renzo Kottman, Linda Amaral-Zettler, John Hobbie, Philip Goldstein, Robert P Guralnick, James Brunt, William K Michener

  Omics : a journal of integrative biology. 05/2008;

  Abstract 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) metadataAbstract 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.

• Working Together to Put Molecules on the Map

  Authors: Dawn Field, Norman Morrison, Frank Oliver Glȵckner, Renzo Kottmann, Guy Cochrane, Robert Vaughan, George Garrity, Jim Cole, Lynette Hirschman, Lynn Schriml [......] David E Schindel, Scott E. Miller, Paul D N Hebert, Sujeevan Ratnasingham, Robert Hanner, Linda Amaral-Zettler, Mitchell Sogin, Michael Ashburner, Suzanna Lewis, Barry Smith

• The “Minimum Information about an ENvironmental Sequence” (MIENS) specification

  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 [......] Aymé Spor, Jesse Stombaugh, James M Tiedje, Doyle V Ward, George M Weinstock, Doug Wendel, Owen White, Andreas Wilke, Jennifer Wortmann, Frank Oliver Glöckner

  Nature Precedings.

  We present the Genomic Standards Consortium’s (GSC) “Minimum Information about an ENvironmental Sequence” (MIENS) standard for describing marker genes. Adoption of MIENS will enhance our ability toWe present the Genomic Standards Consortium’s (GSC) “Minimum Information about an ENvironmental Sequence” (MIENS) standard for describing marker genes. Adoption of MIENS 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.