Microbiome metadata standards: Report of the national microbiome data collaborative's workshop and follow-on activities

Pajau Vangay; Josephine Burgin; Anjanette Johnston; Kristen L. Beck; Daniel C. Berrios; Kai Blumberg; Shane Canon; Patrick Chain; John Marc Chandonia; Danielle Christianson; Sylvain V. Costes; Joan Damerow; William D. Duncan; Jose Pablo Dundore-Arias; Kjiersten Fagnan; Jonathan M. Galazka; Sean M. Gibbons; David Hays; Judson Hervey; Bin Hu; Bonnie L. Hurwitz; Pankaj Jaiswal; Marcin P. Joachimiak; Linda Kinkel; Joshua Ladau; Stanton L. Martin; Lee Ann McCue; Kayd Miller; Nigel Mouncey; Chris Mungall; Evangelos Pafilis; T. B.K. Reddy; Lorna Richardson; Simon Roux; Justin P. Shaffer; Jagadish Chandrabose Sundaramurthi; Luke R. Thompson; Ruth E. Timme; Jie Zheng; Elisha M. Wood-Charlson; Emiley A. Eloe-Fadrosh

doi:10.1128/MSYSTEMS.01194-20

Microbiome metadata standards: Report of the national microbiome data collaborative's workshop and follow-on activities

Pajau Vangay, Josephine Burgin, Anjanette Johnston, Kristen L. Beck, Daniel C. Berrios, Kai Blumberg, Shane Canon, Patrick Chain, John Marc Chandonia, Danielle Christianson, Sylvain V. Costes, Joan Damerow, William D. Duncan, Jose Pablo Dundore-Arias, Kjiersten Fagnan, Jonathan M. Galazka, Sean M. Gibbons, David Hays, Judson Hervey, Bin HuBonnie L. Hurwitz, Pankaj Jaiswal, Marcin P. Joachimiak, Linda Kinkel, Joshua Ladau, Stanton L. Martin, Lee Ann McCue, Kayd Miller, Nigel Mouncey, Chris Mungall, Evangelos Pafilis, T. B.K. Reddy, Lorna Richardson, Simon Roux, Justin P. Shaffer, Jagadish Chandrabose Sundaramurthi, Luke R. Thompson, Ruth E. Timme, Jie Zheng, Elisha M. Wood-Charlson, Emiley A. Eloe-Fadrosh

Plant Pathology

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

30 Scopus citations

Abstract

Microbiome samples are inherently defined by the environment in which they are found. Therefore, data that provide context and enable interpretation of measurements produced from biological samples, often referred to as metadata, are critical. Important contributions have been made in the development of community-driven metadata standards; however, these standards have not been uniformly embraced by the microbiome research community. To understand how these standards are being adopted, or the barriers to adoption, across research domains, institutions, and funding agencies, the National Microbiome Data Collaborative (NMDC) hosted a workshop in October 2019. This report provides a summary of discussions that took place throughout the workshop, as well as outcomes of the working groups initiated at the workshop.

Original language	English (US)
Article number	e01194-20
Journal	mSystems
Volume	6
Issue number	1
DOIs	https://doi.org/10.1128/MSYSTEMS.01194-20
State	Published - 2021

Bibliographical note

Publisher Copyright:
© 2021 American Society for Microbiology. All rights reserved.

Keywords

Data standards
Metadata
Microbiome
Ontology

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Vangay, P., Burgin, J., Johnston, A., Beck, K. L., Berrios, D. C., Blumberg, K., Canon, S., Chain, P., Chandonia, J. M., Christianson, D., Costes, S. V., Damerow, J., Duncan, W. D., Dundore-Arias, J. P., Fagnan, K., Galazka, J. M., Gibbons, S. M., Hays, D., Hervey, J., ... Eloe-Fadrosh, E. A. (2021). Microbiome metadata standards: Report of the national microbiome data collaborative's workshop and follow-on activities. mSystems, 6(1), Article e01194-20. https://doi.org/10.1128/MSYSTEMS.01194-20

Vangay, P, Burgin, J, Johnston, A, Beck, KL, Berrios, DC, Blumberg, K, Canon, S, Chain, P, Chandonia, JM, Christianson, D, Costes, SV, Damerow, J, Duncan, WD, Dundore-Arias, JP, Fagnan, K, Galazka, JM, Gibbons, SM, Hays, D, Hervey, J, Hu, B, Hurwitz, BL, Jaiswal, P, Joachimiak, MP, Kinkel, L, Ladau, J, Martin, SL, McCue, LA, Miller, K, Mouncey, N, Mungall, C, Pafilis, E, Reddy, TBK, Richardson, L, Roux, S, Shaffer, JP, Sundaramurthi, JC, Thompson, LR, Timme, RE, Zheng, J, Wood-Charlson, EM & Eloe-Fadrosh, EA 2021, 'Microbiome metadata standards: Report of the national microbiome data collaborative's workshop and follow-on activities', mSystems, vol. 6, no. 1, e01194-20. https://doi.org/10.1128/MSYSTEMS.01194-20

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abstract = "Microbiome samples are inherently defined by the environment in which they are found. Therefore, data that provide context and enable interpretation of measurements produced from biological samples, often referred to as metadata, are critical. Important contributions have been made in the development of community-driven metadata standards; however, these standards have not been uniformly embraced by the microbiome research community. To understand how these standards are being adopted, or the barriers to adoption, across research domains, institutions, and funding agencies, the National Microbiome Data Collaborative (NMDC) hosted a workshop in October 2019. This report provides a summary of discussions that took place throughout the workshop, as well as outcomes of the working groups initiated at the workshop.",

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Microbiome metadata standards: Report of the national microbiome data collaborative's workshop and follow-on activities

Abstract

Bibliographical note

Keywords

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