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PMID: 21552244 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

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

Nature biotechnology ·Vol. 29 ·No. 5 ·2011-05-00 ·Pages 415-20

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 PS, 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

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.

MeSH Terms

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

Chemicals

Biomarkers

Authors & Affiliations

98 authors, click to expand affiliations / ORCID

Yilmaz Pelin

Microbial Genomics and Bioinformatics Group, Max Planck Institute for Marine Microbiology, Bremen, Germany.

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 E

Gevers Dirk

Gibbs Richard A

San Gil Inigo

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

Spo 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

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Article Info

Journal

Nature biotechnology

Abbr.

Nat Biotechnol

ISSN

1546-1696

DOI

10.1038/nbt.1823

Published

2011-05-00

Pages

415-20

Language

English

Region

United States

NLM ID

9604648

PMCID

PMC3367316

Subset

Grants

NIDDK NIH HHS · UH2 DK083981 · United States

Howard Hughes Medical Institute · United States

NHGRI NIH HHS · U54 HG003273 · United States

NIDDK NIH HHS · K01 DK090285 · United States

NHLBI NIH HHS · U01 HL098957 · United States

NHGRI NIH HHS · R01 HG005975-02 · United States

NHGRI NIH HHS · R01 HG005975 · United States

NIAID NIH HHS · P30 AI045008 · United States

External Links

PubMed source DOI: 10.1038/nbt.1823 PMC Full Text View journal details

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