mSystems (Feb 2021)
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
Affiliations
- Pajau Vangay
- Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Josephine Burgin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Anjanette Johnston
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
- Kristen L. Beck
- IBM Almaden Research Center, San Jose, California, USA
- Daniel C. Berrios
- NASA Ames Research Center, Moffett Field, California, USA
- Kai Blumberg
- Biosystems Engineering Department, University of Arizona, Tucson, Arizona, USA
- Shane Canon
- Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Patrick Chain
- Los Alamos National Laboratory, Los Alamos, New Mexico, USA
- John-Marc Chandonia
- Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Danielle Christianson
- Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Sylvain V. Costes
- NASA Ames Research Center, Moffett Field, California, USA
- Joan Damerow
- Lawrence Berkeley National Laboratory, Berkeley, California, USA
- William D. Duncan
- Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Jose Pablo Dundore-Arias
- California State University, Monterey Bay, California, USA
- Kjiersten Fagnan
- Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Jonathan M. Galazka
- NASA Ames Research Center, Moffett Field, California, USA
- Sean M. Gibbons
- Institute for Systems Biology, Seattle, Washington, USA
- David Hays
- Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Judson Hervey
- Center for Bio/Molecular Science & Engineering, Naval Research Laboratory, Washington, DC, USA
- Bin Hu
- Los Alamos National Laboratory, Los Alamos, New Mexico, USA
- Bonnie L. Hurwitz
- Biosystems Engineering Department, University of Arizona, Tucson, Arizona, USA
- Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
- Marcin P. Joachimiak
- Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Linda Kinkel
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, USA
- Joshua Ladau
- Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Stanton L. Martin
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Lee Ann McCue
- Pacific Northwest National Laboratory, Richland, Washington, USA
- Kayd Miller
- Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Nigel Mouncey
- Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Chris Mungall
- Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Evangelos Pafilis
- Institute of Marine Biology Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Crete, Greece
- T. B. K. Reddy
- Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Lorna Richardson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Simon Roux
- Department of Energy Joint Genome Institute, Berkeley, California, USA
- Lynn M. Schriml
- University of Maryland School of Medicine, Institute for Genome Sciences, Baltimore, Maryland, USA
- Justin P. Shaffer
- Department of Pediatrics, School of Medicine, University of California, San Diego, California, USA
- Jagadish Chandrabose Sundaramurthi
- Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Luke R. Thompson
- Northern Gulf Institute, Mississippi State University, Mississippi State, Mississippi, USA
- Ruth E. Timme
- US Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland, USA
- Jie Zheng
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Elisha M. Wood-Charlson
- Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Emiley A. Eloe-Fadrosh
- Lawrence Berkeley National Laboratory, Berkeley, California, USA
- DOI
- https://doi.org/10.1128/mSystems.01194-20
- Journal volume & issue
-
Vol. 6,
no. 1
Abstract
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
