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 Spo; 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 Spo, 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

371 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 language	English
Journal	Nature Biotechnology
Volume	29
Issue number	5
Pages (from-to)	415-20
Number of pages	6
ISSN	1087-0156
DOIs	https://doi.org/10.1038/nbt.1823
Publication status	Published - May 2011

Keywords

Biological Markers
Checklist
Databases, Genetic
Environment
Genes, rRNA
Genetic Variation
Humans
Information Storage and Retrieval
Internet
Metagenomics
Programming Languages
Sequence Analysis, DNA
Software

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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), 415-20. https://doi.org/10.1038/nbt.1823

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, San Gil, I, 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, Spo, 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. 415-20. https://doi.org/10.1038/nbt.1823

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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.",

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doi = "10.1038/nbt.1823",

language = "English",

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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 - San Gil, Inigo

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 - Spo, 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

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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.

KW - Biological Markers

KW - Checklist

KW - Databases, Genetic

KW - Environment

KW - Genes, rRNA

KW - Genetic Variation

KW - Humans

KW - Information Storage and Retrieval

KW - Internet

KW - Metagenomics

KW - Programming Languages

KW - Sequence Analysis, DNA

KW - Software

U2 - 10.1038/nbt.1823

DO - 10.1038/nbt.1823

M3 - Journal article

C2 - 21552244

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

Abstract

Keywords

Access to Document

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