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

Ely, Kim S and Rogers, Alistair and Agarwal, Deborah A and Ainsworth, Elizabeth A and Albert, Loren P and Ali, Ashehad and Anderson, Jeremiah and Aspinwall, Michael J and Bellasio, Chandra and Bernacchi, Carl and Bonnage, Steve and Buckley, Thomas N and Bunce, James and Burnett, Angela C and Busch, Florian A and Cavanagh, Amanda and Cernusak, Lucas A and Crystal-Ornelas, Robert and Damerow, Joan and Davidson, Kenneth J and De Kauwe, Martin G and Dietze, Michael C and Domingues, Tomas F and Dusenge, Mirindi Eric and Ellsworth, David S and Evans, John R and Gauthier, Paul PG and Gimenez, Bruno O and Gordon, Elizabeth P and Gough, Christopher M and Halbritter, Aud H and Hanson, David T and Heskel, Mary and Hogan, J Aaron and Hupp, Jason R and Jardine, Kolby and Kattge, Jens and Keenan, Trevor and Kromdijk, Johannes and Kumarathunge, Dushan P and Lamour, Julien and Leakey, Andrew DB and LeBauer, David S and Li, Qianyu and Lundgren, Marjorie R and McDowell, Nate and Meacham-Hensold, Katherine and Medlyn, Belinda E and Moore, David JP and Negrón-Juárez, Robinson and Niinemets, Ülo and Osborne, Colin P and Pivovaroff, Alexandria L and Poorter, Hendrik and Reed, Sasha C and Ryu, Youngryel and Sanz-Saez, Alvaro and Schmiege, Stephanie C and Serbin, Shawn P and Sharkey, Thomas D and Slot, Martijn and Smith, Nicholas G and Sonawane, Balasaheb V and South, Paul F and Souza, Daisy C and Stinziano, Joseph Ronald and Stuart-Haëntjens, Ellen and Taylor, Samuel H and Tejera, Mauricio D and Uddling, Johan and Vandvik, Vigdis and Varadharajan, Charuleka and Walker, Anthony P and Walker, Berkley J and Warren, Jeffrey M and Way, Danielle A and Wolfe, Brett T and Wu, Jin and Wullschleger, Stan D and Xu, Chonggang and Yan, Zhengbing and Yang, Dedi (2021) 'A reporting format for leaf-level gas exchange data and metadata.' Ecological Informatics, 61. ISSN 1574-9541

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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 Type: Article
Uncontrolled Keywords: Photosynthesis; Carbon dioxide; Irradiance; Data reporting format; Metadata; Data standard
Divisions: Faculty of Science and Health > Life Sciences, School of
Depositing User: Elements
Date Deposited: 03 Sep 2021 13:32
Last Modified: 03 Sep 2021 13:32
URI: http://repository.essex.ac.uk/id/eprint/31046

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