Literature DB >> 18464787

The minimum information about a genome sequence (MIGS) specification.

Dawn Field1, George Garrity, Tanya Gray, Norman Morrison, Jeremy Selengut, Peter Sterk, Tatiana Tatusova, Nicholas Thomson, Michael J Allen, Samuel V Angiuoli, Michael Ashburner, Nelson Axelrod, Sandra Baldauf, Stuart Ballard, Jeffrey Boore, Guy Cochrane, James Cole, Peter Dawyndt, Paul De Vos, Claude DePamphilis, Robert Edwards, Nadeem Faruque, Robert Feldman, Jack Gilbert, Paul Gilna, Frank Oliver Glöckner, Philip Goldstein, Robert Guralnick, Dan Haft, David Hancock, Henning Hermjakob, Christiane Hertz-Fowler, Phil Hugenholtz, Ian Joint, Leonid Kagan, Matthew Kane, Jessie Kennedy, George Kowalchuk, Renzo Kottmann, Eugene Kolker, Saul Kravitz, Nikos Kyrpides, Jim Leebens-Mack, Suzanna E Lewis, Kelvin Li, Allyson L Lister, Phillip Lord, Natalia Maltsev, Victor Markowitz, Jennifer Martiny, Barbara Methe, Ilene Mizrachi, Richard Moxon, Karen Nelson, Julian Parkhill, Lita Proctor, Owen White, Susanna-Assunta Sansone, Andrew Spiers, Robert Stevens, Paul Swift, Chris Taylor, Yoshio Tateno, Adrian Tett, Sarah Turner, David Ussery, Bob Vaughan, Naomi Ward, Trish Whetzel, Ingio San Gil, Gareth Wilson, Anil Wipat.   

Abstract

With the quantity of genomic data increasing at an exponential rate, it is imperative that these data be captured electronically, in a standard format. Standardization activities must proceed within the auspices of open-access and international working bodies. To tackle the issues surrounding the development of better descriptions of genomic investigations, we have formed the Genomic Standards Consortium (GSC). Here, we introduce the minimum information about a genome sequence (MIGS) specification with the intent of promoting participation in its development and discussing the resources that will be required to develop improved mechanisms of metadata capture and exchange. As part of its wider goals, the GSC also supports improving the 'transparency' of the information contained in existing genomic databases.

Entities:  

Mesh:

Year:  2008        PMID: 18464787      PMCID: PMC2409278          DOI: 10.1038/nbt1360

Source DB:  PubMed          Journal:  Nat Biotechnol        ISSN: 1087-0156            Impact factor:   54.908


  26 in total

1.  Sequenced strains must be saved from extinction.

Authors:  N Ward; J Eisen; C Fraser; E Stackebrandt
Journal:  Nature       Date:  2001-11-08       Impact factor: 49.962

2.  Bacterial whole-genome sequences: minimal information and strain availability.

Authors:  Tom Coenye; Peter Vandamme
Journal:  Microbiology (Reading)       Date:  2004-07       Impact factor: 2.777

3.  Genome Properties: a system for the investigation of prokaryotic genetic content for microbiology, genome annotation and comparative genomics.

Authors:  Daniel H Haft; Jeremy D Selengut; Lauren M Brinkac; Nikhat Zafar; Owen White
Journal:  Bioinformatics       Date:  2004-09-03       Impact factor: 6.937

Review 4.  Development of FuGO: an ontology for functional genomics investigations.

Authors:  Patricia L Whetzel; Ryan R Brinkman; Helen C Causton; Liju Fan; Dawn Field; Jennifer Fostel; Gilberto Fragoso; Tanya Gray; Mervi Heiskanen; Tina Hernandez-Boussard; Norman Morrison; Helen Parkinson; Philippe Rocca-Serra; Susanna-Assunta Sansone; Daniel Schober; Barry Smith; Robert Stevens; Christian J Stoeckert; Chris Taylor; Joe White; Andrew Wood
Journal:  OMICS       Date:  2006

Review 5.  Get the most out of your metagenome: computational analysis of environmental sequence data.

Authors:  Jeroen Raes; Konrad Ulrich Foerstner; Peer Bork
Journal:  Curr Opin Microbiol       Date:  2007-10-23       Impact factor: 7.934

6.  The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes.

Authors:  Ross Overbeek; Tadhg Begley; Ralph M Butler; Jomuna V Choudhuri; Han-Yu Chuang; Matthew Cohoon; Valérie de Crécy-Lagard; Naryttza Diaz; Terry Disz; Robert Edwards; Michael Fonstein; Ed D Frank; Svetlana Gerdes; Elizabeth M Glass; Alexander Goesmann; Andrew Hanson; Dirk Iwata-Reuyl; Roy Jensen; Neema Jamshidi; Lutz Krause; Michael Kubal; Niels Larsen; Burkhard Linke; Alice C McHardy; Folker Meyer; Heiko Neuweger; Gary Olsen; Robert Olson; Andrei Osterman; Vasiliy Portnoy; Gordon D Pusch; Dmitry A Rodionov; Christian Rückert; Jason Steiner; Rick Stevens; Ines Thiele; Olga Vassieva; Yuzhen Ye; Olga Zagnitko; Veronika Vonstein
Journal:  Nucleic Acids Res       Date:  2005-10-07       Impact factor: 16.971

7.  Megx.net--database resources for marine ecological genomics.

Authors:  Thierry Lombardot; Renzo Kottmann; Hauke Pfeffer; Michael Richter; Hanno Teeling; Christian Quast; Frank Oliver Glöckner
Journal:  Nucleic Acids Res       Date:  2006-01-01       Impact factor: 16.971

8.  The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific.

Authors:  Douglas B Rusch; Aaron L Halpern; Granger Sutton; Karla B Heidelberg; Shannon Williamson; Shibu Yooseph; Dongying Wu; Jonathan A Eisen; Jeff M Hoffman; Karin Remington; Karen Beeson; Bao Tran; Hamilton Smith; Holly Baden-Tillson; Clare Stewart; Joyce Thorpe; Jason Freeman; Cynthia Andrews-Pfannkoch; Joseph E Venter; Kelvin Li; Saul Kravitz; John F Heidelberg; Terry Utterback; Yu-Hui Rogers; Luisa I Falcón; Valeria Souza; Germán Bonilla-Rosso; Luis E Eguiarte; David M Karl; Shubha Sathyendranath; Trevor Platt; Eldredge Bermingham; Victor Gallardo; Giselle Tamayo-Castillo; Michael R Ferrari; Robert L Strausberg; Kenneth Nealson; Robert Friedman; Marvin Frazier; J Craig Venter
Journal:  PLoS Biol       Date:  2007-03       Impact factor: 8.029

9.  IMG/M: a data management and analysis system for metagenomes.

Authors:  Victor M Markowitz; Natalia N Ivanova; Ernest Szeto; Krishna Palaniappan; Ken Chu; Daniel Dalevi; I-Min A Chen; Yuri Grechkin; Inna Dubchak; Iain Anderson; Athanasios Lykidis; Konstantinos Mavromatis; Philip Hugenholtz; Nikos C Kyrpides
Journal:  Nucleic Acids Res       Date:  2007-10-11       Impact factor: 16.971

10.  The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata.

Authors:  Konstantinos Liolios; Konstantinos Mavromatis; Nektarios Tavernarakis; Nikos C Kyrpides
Journal:  Nucleic Acids Res       Date:  2007-11-02       Impact factor: 16.971

View more
  819 in total

1.  A global network of coexisting microbes from environmental and whole-genome sequence data.

Authors:  Samuel Chaffron; Hubert Rehrauer; Jakob Pernthaler; Christian von Mering
Journal:  Genome Res       Date:  2010-05-10       Impact factor: 9.043

2.  Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology.

Authors:  Peter D Karp; Mario Latendresse; Suzanne M Paley; Markus Krummenacker; Quang D Ong; Richard Billington; Anamika Kothari; Daniel Weaver; Thomas Lee; Pallavi Subhraveti; Aaron Spaulding; Carol Fulcher; Ingrid M Keseler; Ron Caspi
Journal:  Brief Bioinform       Date:  2015-10-10       Impact factor: 11.622

3.  The genome of Pseudomonas fluorescens strain R124 demonstrates phenotypic adaptation to the mineral environment.

Authors:  Michael D Barton; Michael Petronio; Juan G Giarrizzo; Bethany V Bowling; Hazel A Barton
Journal:  J Bacteriol       Date:  2013-08-30       Impact factor: 3.490

Review 4.  The microbial ocean from genomes to biomes.

Authors:  Edward F DeLong
Journal:  Nature       Date:  2009-05-14       Impact factor: 49.962

Review 5.  A bioinformatician's guide to metagenomics.

Authors:  Victor Kunin; Alex Copeland; Alla Lapidus; Konstantinos Mavromatis; Philip Hugenholtz
Journal:  Microbiol Mol Biol Rev       Date:  2008-12       Impact factor: 11.056

Review 6.  Application of 'next-generation' sequencing technologies to microbial genetics.

Authors:  Daniel MacLean; Jonathan D G Jones; David J Studholme
Journal:  Nat Rev Microbiol       Date:  2009-04       Impact factor: 60.633

7.  Mostly, your results matter to others.

Authors: 
Journal:  Nat Genet       Date:  2009-02       Impact factor: 38.330

8.  Considerations When Designing a Microbiome Study: Implications for Nursing Science.

Authors:  Katherine A Maki; Ana F Diallo; Mark B Lockwood; Alexis T Franks; Stefan J Green; Paule V Joseph
Journal:  Biol Res Nurs       Date:  2018-11-08       Impact factor: 2.522

9.  Fifteen years of microbial genomics: meeting the challenges and fulfilling the dream.

Authors:  Nikos C Kyrpides
Journal:  Nat Biotechnol       Date:  2009-07       Impact factor: 54.908

10.  Minimum Information about a Biosynthetic Gene cluster.

Authors:  Marnix H Medema; Renzo Kottmann; Pelin Yilmaz; Matthew Cummings; John B Biggins; Kai Blin; Irene de Bruijn; Yit Heng Chooi; Jan Claesen; R Cameron Coates; Pablo Cruz-Morales; Srikanth Duddela; Stephanie Düsterhus; Daniel J Edwards; David P Fewer; Neha Garg; Christoph Geiger; Juan Pablo Gomez-Escribano; Anja Greule; Michalis Hadjithomas; Anthony S Haines; Eric J N Helfrich; Matthew L Hillwig; Keishi Ishida; Adam C Jones; Carla S Jones; Katrin Jungmann; Carsten Kegler; Hyun Uk Kim; Peter Kötter; Daniel Krug; Joleen Masschelein; Alexey V Melnik; Simone M Mantovani; Emily A Monroe; Marcus Moore; Nathan Moss; Hans-Wilhelm Nützmann; Guohui Pan; Amrita Pati; Daniel Petras; F Jerry Reen; Federico Rosconi; Zhe Rui; Zhenhua Tian; Nicholas J Tobias; Yuta Tsunematsu; Philipp Wiemann; Elizabeth Wyckoff; Xiaohui Yan; Grace Yim; Fengan Yu; Yunchang Xie; Bertrand Aigle; Alexander K Apel; Carl J Balibar; Emily P Balskus; Francisco Barona-Gómez; Andreas Bechthold; Helge B Bode; Rainer Borriss; Sean F Brady; Axel A Brakhage; Patrick Caffrey; Yi-Qiang Cheng; Jon Clardy; Russell J Cox; René De Mot; Stefano Donadio; Mohamed S Donia; Wilfred A van der Donk; Pieter C Dorrestein; Sean Doyle; Arnold J M Driessen; Monika Ehling-Schulz; Karl-Dieter Entian; Michael A Fischbach; Lena Gerwick; William H Gerwick; Harald Gross; Bertolt Gust; Christian Hertweck; Monica Höfte; Susan E Jensen; Jianhua Ju; Leonard Katz; Leonard Kaysser; Jonathan L Klassen; Nancy P Keller; Jan Kormanec; Oscar P Kuipers; Tomohisa Kuzuyama; Nikos C Kyrpides; Hyung-Jin Kwon; Sylvie Lautru; Rob Lavigne; Chia Y Lee; Bai Linquan; Xinyu Liu; Wen Liu; Andriy Luzhetskyy; Taifo Mahmud; Yvonne Mast; Carmen Méndez; Mikko Metsä-Ketelä; Jason Micklefield; Douglas A Mitchell; Bradley S Moore; Leonilde M Moreira; Rolf Müller; Brett A Neilan; Markus Nett; Jens Nielsen; Fergal O'Gara; Hideaki Oikawa; Anne Osbourn; Marcia S Osburne; Bohdan Ostash; Shelley M Payne; Jean-Luc Pernodet; Miroslav Petricek; Jörn Piel; Olivier Ploux; Jos M Raaijmakers; José A Salas; Esther K Schmitt; Barry Scott; Ryan F Seipke; Ben Shen; David H Sherman; Kaarina Sivonen; Michael J Smanski; Margherita Sosio; Evi Stegmann; Roderich D Süssmuth; Kapil Tahlan; Christopher M Thomas; Yi Tang; Andrew W Truman; Muriel Viaud; Jonathan D Walton; Christopher T Walsh; Tilmann Weber; Gilles P van Wezel; Barrie Wilkinson; Joanne M Willey; Wolfgang Wohlleben; Gerard D Wright; Nadine Ziemert; Changsheng Zhang; Sergey B Zotchev; Rainer Breitling; Eriko Takano; Frank Oliver Glöckner
Journal:  Nat Chem Biol       Date:  2015-09       Impact factor: 15.040

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.