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

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 & 78 others 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 Elizabeth 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

Research output: Contribution to journalArticle

278 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)415-420
Number of pages6
JournalNature Biotechnology
Volume29
Issue number5
DOIs
StatePublished - May 2011
Externally publishedYes

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Genes
Specifications
Checklist
DNA Sequence Analysis
Ecosystems
Ecosystem
DNA
Genome

ASJC Scopus subject areas

  • Applied Microbiology and Biotechnology
  • Biotechnology
  • Molecular Medicine
  • Bioengineering
  • Biomedical Engineering

Cite this

Yilmaz, P., Kottmann, R., Field, D., Knight, R., Cole, J. R., Amaral-Zettler, L., ... Glöckner, F. O. (2011). Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nature Biotechnology, 29(5), 415-420. https://doi.org/10.1038/nbt.1823

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. / Yilmaz, Pelin; Kottmann, Renzo; Field, Dawn; Knight, Rob; Cole, James R.; Amaral-Zettler, Linda; Gilbert, Jack A.; Karsch-Mizrachi, Ilene; Johnston, Anjanette; Cochrane, Guy; 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 Elizabeth; Gevers, Dirk; Gibbs, Richard A.; Gil, Inigo San; Gonzalez, Antonio; Gordon, Jeffrey I.; Guralnick, Robert; Hankeln, Wolfgang; Highlander, Sarah; Hugenholtz, Philip; Jansson, Janet; Kau, Andrew L.; Kelley, Scott T.; Kennedy, Jerry; Knights, Dan; Koren, Omry; Kuczynski, Justin; Kyrpides, Nikos; Larsen, Robert; Lauber, Christian L.; Legg, Teresa; Ley, Ruth E.; Lozupone, Catherine A.; Ludwig, Wolfgang; Lyons, Donna; Maguire, Eamonn; Methé, 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, Jörg; 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; Sinha, Rohini; Smith, Michelle I.; Sodergren, Erica; Spor, Aymé; Stombaugh, Jesse; Tiedje, James M.; Ward, Doyle V.; Weinstock, George M.; Wendel, Doug; White, Owen; Whiteley, Andrew; Wilke, Andreas; Wortman, Jennifer R.; Yatsunenko, Tanya; Glöckner, Frank Oliver.

In: Nature Biotechnology, Vol. 29, No. 5, 05.2011, p. 415-420.

Research output: Contribution to journalArticle

Yilmaz, P, Kottmann, R, Field, D, Knight, R, Cole, JR, Amaral-Zettler, L, Gilbert, JA, Karsch-Mizrachi, I, Johnston, A, Cochrane, G, Vaughan, R, Hunter, C, Park, J, Morrison, N, Rocca-Serra, P, Sterk, P, Arumugam, M, Bailey, M, Baumgartner, L, Birren, BW, Blaser, MJ, Bonazzi, V, Booth, T, Bork, P, Bushman, FD, Buttigieg, PL, Chain, PSG, Charlson, E, Costello, EK, Huot-Creasy, H, Dawyndt, P, Desantis, T, Fierer, N, Fuhrman, JA, Gallery, RE, Gevers, D, Gibbs, RA, Gil, IS, Gonzalez, A, Gordon, JI, Guralnick, R, Hankeln, W, Highlander, S, Hugenholtz, P, Jansson, J, Kau, AL, Kelley, ST, Kennedy, J, Knights, D, Koren, O, Kuczynski, J, Kyrpides, N, Larsen, R, Lauber, CL, Legg, T, Ley, RE, Lozupone, CA, Ludwig, W, Lyons, D, Maguire, E, Methé, BA, Meyer, F, Muegge, B, Nakielny, S, Nelson, KE, Nemergut, D, Neufeld, JD, Newbold, LK, Oliver, AE, Pace, NR, Palanisamy, G, Peplies, J, Petrosino, J, Proctor, L, Pruesse, E, Quast, C, Raes, J, Ratnasingham, S, Ravel, J, Relman, DA, Assunta-Sansone, S, Schloss, PD, Schriml, L, Sinha, R, Smith, MI, Sodergren, E, Spor, A, Stombaugh, J, Tiedje, JM, Ward, DV, Weinstock, GM, Wendel, D, White, O, Whiteley, A, Wilke, A, Wortman, JR, Yatsunenko, T & Glöckner, FO 2011, 'Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications', Nature Biotechnology, vol. 29, no. 5, pp. 415-420. https://doi.org/10.1038/nbt.1823
Yilmaz, Pelin ; Kottmann, Renzo ; Field, Dawn ; Knight, Rob ; Cole, James R. ; Amaral-Zettler, Linda ; Gilbert, Jack A. ; Karsch-Mizrachi, Ilene ; Johnston, Anjanette ; Cochrane, Guy ; 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 Elizabeth ; Gevers, Dirk ; Gibbs, Richard A. ; Gil, Inigo San ; Gonzalez, Antonio ; Gordon, Jeffrey I. ; Guralnick, Robert ; Hankeln, Wolfgang ; Highlander, Sarah ; Hugenholtz, Philip ; Jansson, Janet ; Kau, Andrew L. ; Kelley, Scott T. ; Kennedy, Jerry ; Knights, Dan ; Koren, Omry ; Kuczynski, Justin ; Kyrpides, Nikos ; Larsen, Robert ; Lauber, Christian L. ; Legg, Teresa ; Ley, Ruth E. ; Lozupone, Catherine A. ; Ludwig, Wolfgang ; Lyons, Donna ; Maguire, Eamonn ; Methé, 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, Jörg ; 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 ; Sinha, Rohini ; Smith, Michelle I. ; Sodergren, Erica ; Spor, Aymé ; Stombaugh, Jesse ; Tiedje, James M. ; Ward, Doyle V. ; Weinstock, George M. ; Wendel, Doug ; White, Owen ; Whiteley, Andrew ; Wilke, Andreas ; Wortman, Jennifer R. ; Yatsunenko, Tanya ; Glöckner, Frank Oliver. / Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. In: Nature Biotechnology. 2011 ; Vol. 29, No. 5. pp. 415-420.
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AU - Yilmaz, Pelin

AU - Kottmann, Renzo

AU - Field, Dawn

AU - Knight, Rob

AU - Cole, James R.

AU - Amaral-Zettler, Linda

AU - Gilbert, Jack A.

AU - Karsch-Mizrachi, Ilene

AU - Johnston, Anjanette

AU - Cochrane, Guy

AU - Vaughan, Robert

AU - Hunter, Christopher

AU - Park, Joonhong

AU - Morrison, Norman

AU - Rocca-Serra, Philippe

AU - Sterk, Peter

AU - Arumugam, Manimozhiyan

AU - Bailey, Mark

AU - Baumgartner, Laura

AU - Birren, Bruce W.

AU - Blaser, Martin J.

AU - Bonazzi, Vivien

AU - Booth, Tim

AU - Bork, Peer

AU - Bushman, Frederic D.

AU - Buttigieg, Pier Luigi

AU - Chain, Patrick S G

AU - Charlson, Emily

AU - Costello, Elizabeth K.

AU - Huot-Creasy, Heather

AU - Dawyndt, Peter

AU - Desantis, Todd

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AU - Fuhrman, Jed A.

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AU - Lozupone, Catherine A.

AU - Ludwig, Wolfgang

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AU - Neufeld, Josh D.

AU - Newbold, Lindsay K.

AU - Oliver, Anna E.

AU - Pace, Norman R.

AU - Palanisamy, Giriprakash

AU - Peplies, Jörg

AU - Petrosino, Joseph

AU - Proctor, Lita

AU - Pruesse, Elmar

AU - Quast, Christian

AU - Raes, Jeroen

AU - Ratnasingham, Sujeevan

AU - Ravel, Jacques

AU - Relman, David A.

AU - Assunta-Sansone, Susanna

AU - Schloss, Patrick D.

AU - Schriml, Lynn

AU - Sinha, Rohini

AU - Smith, Michelle I.

AU - Sodergren, Erica

AU - Spor, Aymé

AU - Stombaugh, Jesse

AU - Tiedje, James M.

AU - Ward, Doyle V.

AU - Weinstock, George M.

AU - Wendel, Doug

AU - White, Owen

AU - Whiteley, Andrew

AU - Wilke, Andreas

AU - Wortman, Jennifer R.

AU - Yatsunenko, Tanya

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