A reporting format for leaf-level gas exchange data and metadata

Ely, Kim S., Rogers, Alistair, Agarwal, Deborah A., Ainsworth, Elizabeth A., Albert, Loren P., Ali, Ashehad, Anderson, Jeremiah, Aspinwall, Michael J., Bellasio, Chandra, Bernacchi, Carl, Bonnage, Steve, Buckley, Thomas N., Bunce, James, Burnett, Angela C., Busch, Florian A., Cavanagh, Amanda, Cernusak, Lucas A., Crystal-Ornelas, Robert, Damerow, Joan, Davidson, Kenneth J., De Kauwe, Martin G., Dietze, Michael C, Domingues, Tomas F., Dusenge, Mirindi Eric, Ellsworth, David S., Evans, John R., Gauthier, Paul P.G., Gimenez, Bruno O., Gordon, Elizabeth P., Gough, Christopher M., Halbritter, Aud H., Hanson, David T., Heskel, Mary, Hogan, J. Aaron, Hupp, Jason R., Jardine, Kolby, Kattge, Jens, Keenan, Trevor, Kromdijk, Johannes, Kumarathunge, Dushan P., Lamour, Julien, Leakey, Andrew D.B., LeBauer, David S., Li, Qianyu, Lundgren, Marjorie R., McDowell, Nate, Meacham-Hensold, Katherine, Medlyn, Belinda E., Moore, David J.P., Negrón-Juárez, Robinson, Niinemets, Ülo, Osborne, Colin P., Pivovaroff, Alexandria L., Poorter, Hendrik, Reed, Sasha C., Ryu, Youngryel, Sanz-Saez, Alvaro, Schmiege, Stephanie C., Serbin, Shawn P., Sharkey, Thomas D., Slot, Martijn, Smith, Nicholas G., Sonawane, Balasaheb V., South, Paul F., Souza, Daisy C., Stinziano, Joseph Ronald, Stuart-Haëntjens, Ellen, Taylor, Samuel H., Tejera, Mauricio D., Uddling, Johan, Vandvik, Vigdis, Varadharajan, Charuleka, Walker, Anthony P., Walker, Berkley J., Warren, Jeffrey M., Way, Danielle A., Wolfe, Brett T., Wu, Jin, Wullschleger, Stan D., Xu, Chonggang, Yan, Zhengbing, and Yang, Dedi (2021) A reporting format for leaf-level gas exchange data and metadata. Ecological Informatics, 61. 101232.

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Abstract

Leaf-level gas exchange data support the mechanistic understanding of plant fluxes of carbon and water. These fluxes inform our understanding of ecosystem function, are an important constraint on parameterization of terrestrial biosphere models, are necessary to understand the response of plants to global environmental change, and are integral to efforts to improve crop production. Collection of these data using gas analyzers can be both technically challenging and time consuming, and individual studies generally focus on a small range of species, restricted time periods, or limited geographic regions. The high value of these data is exemplified by the many publications that reuse and synthesize gas exchange data, however the lack of metadata and data reporting conventions make full and efficient use of these data difficult. Here we propose a reporting format for leaf-level gas exchange data and metadata to provide guidance to data contributors on how to store data in repositories to maximize their discoverability, facilitate their efficient reuse, and add value to individual datasets. For data users, the reporting format will better allow data repositories to optimize data search and extraction, and more readily integrate similar data into harmonized synthesis products. The reporting format specifies data table variable naming and unit conventions, as well as metadata characterizing experimental conditions and protocols. For common data types that were the focus of this initial version of the reporting format, i.e., survey measurements, dark respiration, carbon dioxide and light response curves, and parameters derived from those measurements, we took a further step of defining required additional data and metadata that would maximize the potential reuse of those data types. To aid data contributors and the development of data ingest tools by data repositories we provided a translation table comparing the outputs of common gas exchange instruments. Extensive consultation with data collectors, data users, instrument manufacturers, and data scientists was undertaken in order to ensure that the reporting format met community needs. The reporting format presented here is intended to form a foundation for future development that will incorporate additional data types and variables as gas exchange systems and measurement approaches advance in the future. The reporting format is published in the U.S. Department of Energy's ESS-DIVE data repository, with documentation and future development efforts being maintained in a version control system.

Item ID: 66905
Item Type: Article (Research - C1)
ISSN: 1878-0512
Keywords: Carbon dioxide, Data reporting format, Data standard, Irradiance, Metadata, Photosynthesis
Copyright Information: © 2021 The Authors. ublished by Elsevier B.V. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
Funders: Office of Biological and Environmental Research (OBER), United States Department of Energy (US-DE), National Institute of Food and Agriculture (NIFA), Biotechnology and Biological Sciences Research Council (BBSRC), U.S. Department of Agriculture (USDA), US Department of Defense (DOD), USGS Ecosystems Mission Area
Projects and Grants: OBER Environmental Systems Science Data Infrastructure for a Virtual Ecosystem (ESS-DIVE), OBER Next Generation Ecosystem Experiments -Arctic (NGEE-Arctic) and -Tropics (NGEE-Tropics), OBER Next Generation Ecosystem Experiments -Tropics (NGEE-Tropics), US-DE contract No. DE-SC0012704, US-DE contract No. DE-AC02-05CH11231, US-DE contract No. DE-AC05-00OR22725, NIFA Alabama Agricultural Experiment Station and the Hatch program, US-DE Grant DE-FG02-91ER20021, BBSRC Grant BB/T007583/1, USDA Award 2019-67013-29161, DOD RC18-1322
Date Deposited: 10 Aug 2021 00:09
FoR Codes: 31 BIOLOGICAL SCIENCES > 3108 Plant biology > 310806 Plant physiology @ 100%
SEO Codes: 28 EXPANDING KNOWLEDGE > 2801 Expanding knowledge > 280102 Expanding knowledge in the biological sciences @ 100%
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