Microbiome Metadata Standards: Report of the National Microbiome Data Collaboratives Workshop and Follow-On Activities,mSystems

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Microbiome Metadata Standards: Report of the National Microbiome Data Collaboratives Workshop and Follow-On Activities
mSystems ( IF 5.0 ) Pub Date : 2021-02-23 , DOI: 10.1128/msystems.01194-20
Pajau Vangay ₁ , Josephine Burgin ₂ , Anjanette Johnston ₃ , Kristen L Beck ₄ , Daniel C Berrios ₅ , Kai Blumberg ₆ , Shane Canon ₁ , Patrick Chain ₇ , John-Marc Chandonia ₁ , Danielle Christianson ₁ , Sylvain V Costes ₅ , Joan Damerow ₁ , William D Duncan ₁ , Jose Pablo Dundore-Arias ₈ , Kjiersten Fagnan ₁ , Jonathan M Galazka ₅ , Sean M Gibbons _{9,

10} , David Hays ₁ , Judson Hervey ₁₁ , Bin Hu ₇ , Bonnie L Hurwitz ₆ , Pankaj Jaiswal ₁₂ , Marcin P Joachimiak ₁ , Linda Kinkel ₁₃ , Joshua Ladau ₁ , Stanton L Martin ₁₄ , Lee Ann McCue ₁₅ , Kayd Miller ₁ , Nigel Mouncey ₁ , Chris Mungall ₁ , Evangelos Pafilis ₁₆ , T B K Reddy ₁ , Lorna Richardson ₂ , Simon Roux ₁₇ , Lynn M. Schriml ₁₈ , Justin P Shaffer ₁₉ , Jagadish Chandrabose Sundaramurthi ₁ , Luke R Thompson _{20,

21} , Ruth E Timme ₂₂ , Jie Zheng ₂₃ , Elisha M Wood-Charlson ₁ , Emiley A Eloe-Fadrosh ₂₄

Affiliation

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

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.

中文翻译：

微生物组元数据标准：国家微生物组数据协作研讨会和后续活动的报告

微生物组样本本质上是由它们所在的环境定义的。因此，提供上下文并能够解释从生物样本产生的测量结果的数据（通常称为元数据）至关重要。在开发社区驱动的元数据标准方面做出了重要贡献；然而，微生物组研究界并未统一接受这些标准。为了了解这些标准是如何在研究领域、机构和资助机构中被采用的，或者采用的障碍，国家微生物组数据协作组织 (NMDC) 于 2019 年 10 月举办了一次研讨会。本报告总结了所发生的讨论在整个研讨会期间，以及研讨会发起的工作组的成果。

更新日期：2021-02-23

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