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Perspective | Applied and Environmental Science

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
Vanni Bucci, Editor
Pajau Vangay
aLawrence Berkeley National Laboratory, Berkeley, California, USA
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Josephine Burgin
bEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
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Anjanette Johnston
cNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
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Kristen L. Beck
dIBM Almaden Research Center, San Jose, California, USA
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Daniel C. Berrios
eNASA Ames Research Center, Moffett Field, California, USA
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Kai Blumberg
fBiosystems Engineering Department, University of Arizona, Tucson, Arizona, USA
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Shane Canon
aLawrence Berkeley National Laboratory, Berkeley, California, USA
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Patrick Chain
gLos Alamos National Laboratory, Los Alamos, New Mexico, USA
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John-Marc Chandonia
aLawrence Berkeley National Laboratory, Berkeley, California, USA
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Danielle Christianson
aLawrence Berkeley National Laboratory, Berkeley, California, USA
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Sylvain V. Costes
eNASA Ames Research Center, Moffett Field, California, USA
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Joan Damerow
aLawrence Berkeley National Laboratory, Berkeley, California, USA
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William D. Duncan
aLawrence Berkeley National Laboratory, Berkeley, California, USA
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Jose Pablo Dundore-Arias
hCalifornia State University, Monterey Bay, California, USA
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Kjiersten Fagnan
aLawrence Berkeley National Laboratory, Berkeley, California, USA
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Jonathan M. Galazka
eNASA Ames Research Center, Moffett Field, California, USA
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Sean M. Gibbons
iInstitute for Systems Biology, Seattle, Washington, USA
jDepartment of Bioengineering, University of Washington, Seattle, Washington, USA
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David Hays
aLawrence Berkeley National Laboratory, Berkeley, California, USA
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Judson Hervey
kCenter for Bio/Molecular Science & Engineering, Naval Research Laboratory, Washington, DC, USA
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Bin Hu
gLos Alamos National Laboratory, Los Alamos, New Mexico, USA
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Bonnie L. Hurwitz
fBiosystems Engineering Department, University of Arizona, Tucson, Arizona, USA
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Pankaj Jaiswal
lDepartment of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
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Marcin P. Joachimiak
aLawrence Berkeley National Laboratory, Berkeley, California, USA
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Linda Kinkel
mDepartment of Plant Pathology, University of Minnesota, St. Paul, Minnesota, USA
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Joshua Ladau
aLawrence Berkeley National Laboratory, Berkeley, California, USA
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Stanton L. Martin
nOak Ridge National Laboratory, Oak Ridge, Tennessee, USA
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Lee Ann McCue
oPacific Northwest National Laboratory, Richland, Washington, USA
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Kayd Miller
aLawrence Berkeley National Laboratory, Berkeley, California, USA
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Nigel Mouncey
aLawrence Berkeley National Laboratory, Berkeley, California, USA
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Chris Mungall
aLawrence Berkeley National Laboratory, Berkeley, California, USA
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Evangelos Pafilis
pInstitute of Marine Biology Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Crete, Greece
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T. B. K. Reddy
aLawrence Berkeley National Laboratory, Berkeley, California, USA
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Lorna Richardson
bEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
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Simon Roux
qDepartment of Energy Joint Genome Institute, Berkeley, California, USA
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Justin P. Shaffer
rDepartment of Pediatrics, School of Medicine, University of California, San Diego, California, USA
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Jagadish Chandrabose Sundaramurthi
aLawrence Berkeley National Laboratory, Berkeley, California, USA
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Luke R. Thompson
sNorthern Gulf Institute, Mississippi State University, Mississippi State, Mississippi, USA
tOcean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, Miami, Florida, USA
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Ruth E. Timme
uUS Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland, USA
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Jie Zheng
vDepartment of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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Elisha M. Wood-Charlson
aLawrence Berkeley National Laboratory, Berkeley, California, USA
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Emiley A. Eloe-Fadrosh
aLawrence Berkeley National Laboratory, Berkeley, California, USA
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Vanni Bucci
University of Massachusetts Medical School
Roles: Editor
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DOI: 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.

This is a work of the U.S. Government and is not subject to copyright protection in the United States. Foreign copyrights may apply.

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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
mSystems Feb 2021, 6 (1) e01194-20; DOI: 10.1128/mSystems.01194-20

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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
mSystems Feb 2021, 6 (1) e01194-20; DOI: 10.1128/mSystems.01194-20
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  • Article
    • ABSTRACT
    • PERSPECTIVE
    • ADDRESSING BARRIERS IN MICROBIOME DATA STANDARDS
    • OUTCOMES FROM THE WORKING GROUPS
    • ACKNOWLEDGMENTS
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KEYWORDS

data standards
metadata
microbiome
ontology

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