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; 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

doi:10.1038/nbt.1823

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. BirrenMartin 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

Environmental Sciences Division

Research output: Contribution to journal › Review article › peer-review

542 Scopus citations

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 language	English
Pages (from-to)	415-420
Number of pages	6
Journal	Nature Biotechnology
Volume	29
Issue number	5
DOIs	https://doi.org/10.1038/nbt.1823
State	Published - May 2011

Funding

Funders	Funder number
National Human Genome Research Institute	U54HG003273

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10.1038/nbt.1823

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Yilmaz, P., Kottmann, R., Field, D., Knight, R., Cole, J. R., Amaral-Zettler, L., Gilbert, J. A., 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., ... 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

@article{471b8edf1cc64bea8374672a231e1fa6,

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

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.",

author = "Pelin Yilmaz and Renzo Kottmann and Dawn Field and Rob Knight and Cole, {James R.} and Linda Amaral-Zettler and Gilbert, {Jack A.} and Ilene Karsch-Mizrachi and Anjanette Johnston and Guy Cochrane and Robert Vaughan and Christopher Hunter and Joonhong Park and Norman Morrison and Philippe Rocca-Serra and Peter Sterk and Manimozhiyan Arumugam and Mark Bailey and Laura Baumgartner and Birren, {Bruce W.} and Blaser, {Martin J.} and Vivien Bonazzi and Tim Booth and Peer Bork and Bushman, {Frederic D.} and Buttigieg, {Pier Luigi} and Chain, {Patrick S.G.} and Emily Charlson and Costello, {Elizabeth K.} and Heather Huot-Creasy and Peter Dawyndt and Todd Desantis and Noah Fierer and Fuhrman, {Jed A.} and Gallery, {Rachel E.} and Dirk Gevers and Gibbs, {Richard A.} and Gil, {Inigo San} and Antonio Gonzalez and Gordon, {Jeffrey I.} and Robert Guralnick and Wolfgang Hankeln and Sarah Highlander and Philip Hugenholtz and Janet Jansson and Kau, {Andrew L.} and Kelley, {Scott T.} and Jerry Kennedy and Dan Knights and Omry Koren and Justin Kuczynski and Nikos Kyrpides and Robert Larsen and Lauber, {Christian L.} and Teresa Legg and Ley, {Ruth E.} and Lozupone, {Catherine A.} and Wolfgang Ludwig and Donna Lyons and Eamonn Maguire and Meth{\'e}, {Barbara A.} and Folker Meyer and Brian Muegge and Sara Nakielny and Nelson, {Karen E.} and Diana Nemergut and Neufeld, {Josh D.} and Newbold, {Lindsay K.} and Oliver, {Anna E.} and Pace, {Norman R.} and Giriprakash Palanisamy and J{\"o}rg Peplies and Joseph Petrosino and Lita Proctor and Elmar Pruesse and Christian Quast and Jeroen Raes and Sujeevan Ratnasingham and Jacques Ravel and Relman, {David A.} and Susanna Assunta-Sansone and Schloss, {Patrick D.} and Lynn Schriml and Rohini Sinha and Smith, {Michelle I.} and Erica Sodergren and Aym{\'e} Spor and Jesse Stombaugh and Tiedje, {James M.} and Ward, {Doyle V.} and Weinstock, {George M.} and Doug Wendel and Owen White and Andrew Whiteley and Andreas Wilke and Wortman, {Jennifer R.} and Tanya Yatsunenko and Gl{\"o}ckner, {Frank Oliver}",

year = "2011",

month = may,

doi = "10.1038/nbt.1823",

language = "English",

volume = "29",

pages = "415--420",

journal = "Nature Biotechnology",

issn = "1087-0156",

publisher = "Nature Research",

number = "5",

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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

TY - JOUR

T1 - Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications

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

AU - Fierer, Noah

AU - Fuhrman, Jed A.

AU - Gallery, Rachel E.

AU - Gevers, Dirk

AU - Gibbs, Richard A.

AU - Gil, Inigo San

AU - Gonzalez, Antonio

AU - Gordon, Jeffrey I.

AU - Guralnick, Robert

AU - Hankeln, Wolfgang

AU - Highlander, Sarah

AU - Hugenholtz, Philip

AU - Jansson, Janet

AU - Kau, Andrew L.

AU - Kelley, Scott T.

AU - Kennedy, Jerry

AU - Knights, Dan

AU - Koren, Omry

AU - Kuczynski, Justin

AU - Kyrpides, Nikos

AU - Larsen, Robert

AU - Lauber, Christian L.

AU - Legg, Teresa

AU - Ley, Ruth E.

AU - Lozupone, Catherine A.

AU - Ludwig, Wolfgang

AU - Lyons, Donna

AU - Maguire, Eamonn

AU - Methé, Barbara A.

AU - Meyer, Folker

AU - Muegge, Brian

AU - Nakielny, Sara

AU - Nelson, Karen E.

AU - Nemergut, Diana

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

AU - Glöckner, Frank Oliver

PY - 2011/5

Y1 - 2011/5

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=79955749319&partnerID=8YFLogxK

U2 - 10.1038/nbt.1823

DO - 10.1038/nbt.1823

M3 - Review article

C2 - 21552244

AN - SCOPUS:79955749319

SN - 1087-0156

VL - 29

SP - 415

EP - 420

JO - Nature Biotechnology

JF - Nature Biotechnology

IS - 5

ER -

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

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