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

Computational and Predictive Biology

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

34 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
Article number	e01194-20
Journal	mSystems
Volume	6
Issue number	1
DOIs	https://doi.org/10.1128/MSYSTEMS.01194-20
State	Published - 2021

Funding

We thank the Toolbox Dialogue Initiative representatives Stephanie E. Vasko, Marisa A. Rinkus, and Chet McLeskey for leading activities at the start of the workshop to prepare participants for open, respectful dialogue (see https://microbiomedata.org/nmdc-ontology-workshop/ for a report on the activities). The NMDC is supported by the Genomic Science Program in the United States Department of Energy, Office of Science, Office of Biological and Environmental Research (BER) under contract numbers DE-AC02-05CH11231 (LBNL), 89233218CNA000001 (LANL), DE-AC05-00OR22725 (ORNL), and DE-AC05-76RL01830 (PNNL). S.V.C., D.C.B., and J.M.G. were funded by the Space Biology Program (Science Mission Directorate, Biological and Physical Sciences Division) of the National Aeronautics and Space Administration. J.H. was supported by internal Basic Research programs (Work Units 4888 and 1L73) at the U.S. Naval Research Laboratory. A.J. was supported by the Intramural Research Program of the National Library of Medicine, National Institutes of Health. The work of J.P.S. was supported by NIH-SD-IRACDA (5K12GM068524-17). S.M.G. was supported by a Washington Research Foundation Distinguished Investigator Award. The opinions and assertions contained herein are those of the authors and are not to be construed as those of the Department of Defense, U.S. Navy, military service at large, or the U.S. Government. The NMDC is supported by the Genomic Science Program in the United States Department of Energy, Office of Science, Office of Biological and Environmental Research (BER) under contract numbers DE-AC02-05CH11231 (LBNL), 89233218CNA000001 (LANL), DE-AC05-00OR22725 (ORNL), and DE-AC05-76RL01830 (PNNL). S.V.C., D.C.B., and J.M.G. were funded by the Space Biology Program (Science Mission Directorate, Biological and Physical Sciences Division) of the National Aeronautics and Space Administration. J.H. was supported by internal Basic Research programs (Work Units 4888 and 1L73) at the U.S. Naval Research Laboratory. A.J. was supported by the Intramural Research Program of the National Library of Medicine, National Institutes of Health. The work of J.P.S. was supported by NIH-SD-IRACDA (5K12GM068524-17). S.M.G. was supported by a Washington Research Foundation Distinguished Investigator Award. The National Microbiome Data Collaborative (NMDC) is a pilot initiative that was launched in July 2019 and is funded by the Department of Energy (DOE) Office of Science, Biological and Environmental Research Program, to support microbiome data exploration and discovery through a collaborative, integrative data science ecosystem (1). The NMDC team is building an open-source, integrated data science ecosystem that leverages existing data standards, data resources, and infrastructure in the micro-biome research space. The NMDC initiative embraces the FAIR (findable, accessible, interoperable, and reusable) data principles (2) by incorporating community-driven data standards and quality measures to enable data integration and access in its science gateway. Understanding the current landscape of data standards for the micro-biome research community is an important first step toward achieving the aims of the NMDC pilot initiative.

Funders	Funder number
Biological and Environmental Research program
Chet McLeskey
NIH-SD-IRACDA	5K12GM068524-17
National Institutes of Health
U.S. Department of Defense
U.S. Department of Energy
U.S. National Library of Medicine
National Aeronautics and Space Administration	1L73
Washington Research Foundation
Office of Science
Biological and Environmental Research	DE-AC02-05CH11231
Oak Ridge National Laboratory	DE-AC05-76RL01830
Lawrence Berkeley National Laboratory	89233218CNA000001
Los Alamos National Laboratory	DE-AC05-00OR22725
U.S. Navy
U.S. Naval Research Laboratory
Pacific Northwest National Laboratory

Keywords

Data standards
Metadata
Microbiome
Ontology

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10.1128/MSYSTEMS.01194-20

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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

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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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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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AU - Burgin, Josephine

AU - Johnston, Anjanette

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AU - Berrios, Daniel C.

AU - Blumberg, Kai

AU - Canon, Shane

AU - Chain, Patrick

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AU - Reddy, T. B.K.

AU - Richardson, Lorna

AU - Roux, Simon

AU - Shaffer, Justin P.

AU - Sundaramurthi, Jagadish Chandrabose

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

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