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; Lynn M. Schriml; 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

mSystems. 2021 Feb 23;6(1):e01194-20. doi: 10.1128/mSystems.01194-20.

Authors

Pajau Vangay¹, Josephine Burgin², Anjanette Johnston³, Kristen L Beck⁴, Daniel C Berrios⁵, Kai Blumberg⁶, Shane Canon¹, Patrick Chain⁷, John-Marc Chandonia¹, Danielle Christianson¹, Sylvain V Costes⁵, Joan Damerow¹, William D Duncan¹, Jose Pablo Dundore-Arias⁸, Kjiersten Fagnan¹, Jonathan M Galazka⁵, Sean M Gibbons^{9

10}, David Hays¹, Judson Hervey¹¹, Bin Hu⁷, Bonnie L Hurwitz⁶, Pankaj Jaiswal¹², Marcin P Joachimiak¹, Linda Kinkel¹³, Joshua Ladau¹, Stanton L Martin¹⁴, Lee Ann McCue¹⁵, Kayd Miller¹, Nigel Mouncey¹, Chris Mungall¹, Evangelos Pafilis¹⁶, T B K Reddy¹, Lorna Richardson², Simon Roux¹⁷, Lynn M. Schriml¹⁸, Justin P Shaffer¹⁹, Jagadish Chandrabose Sundaramurthi¹, Luke R Thompson^{20

21}, Ruth E Timme²², Jie Zheng²³, Elisha M Wood-Charlson¹, Emiley A Eloe-Fadrosh²⁴

Affiliations

¹ Lawrence Berkeley National Laboratory, Berkeley, California, USA.
² European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
³ National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA.
⁴ IBM Almaden Research Center, San Jose, California, USA.
⁵ NASA Ames Research Center, Moffett Field, California, USA.
⁶ Biosystems Engineering Department, University of Arizona, Tucson, Arizona, USA.
⁷ Los Alamos National Laboratory, Los Alamos, New Mexico, USA.
⁸ California State University, Monterey Bay, California, USA.
⁹ Institute for Systems Biology, Seattle, Washington, USA.
¹⁰ Department of Bioengineering, University of Washington, Seattle, Washington, USA.
¹¹ Center for Bio/Molecular Science & Engineering, Naval Research Laboratory, Washington, DC, USA.
¹² Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA.
¹³ Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, USA.
¹⁴ Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.
¹⁵ Pacific Northwest National Laboratory, Richland, Washington, USA.
¹⁶ Institute of Marine Biology Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Crete, Greece.
¹⁷ Department of Energy Joint Genome Institute, Berkeley, California, USA.
¹⁸ University of Maryland School of Medicine, Institute for Genome Sciences, Baltimore, Maryland, USA
¹⁹ Department of Pediatrics, School of Medicine, University of California, San Diego, California, USA.
²⁰ Northern Gulf Institute, Mississippi State University, Mississippi State, Mississippi, USA.
²¹ Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, Miami, Florida, USA.
²² US Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland, USA.
²³ Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
²⁴ Lawrence Berkeley National Laboratory, Berkeley, California, USA [email protected].

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.

Keywords: data standards; metadata; microbiome; ontology.

Grants and funding

K12 GM068524/GM/NIGMS NIH HHS/United States