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A reporting format for leaf-level gas exchange data and metadata
Ecological Informatics ( IF 5.8 ) Pub Date : 2021-01-24 , DOI: 10.1016/j.ecoinf.2021.101232
Kim S. Ely , Alistair Rogers , Deborah A. Agarwal , Elizabeth A. Ainsworth , Loren P. Albert , Ashehad Ali , Jeremiah Anderson , Michael J. Aspinwall , Chandra Bellasio , Carl Bernacchi , Steve Bonnage , Thomas N. Buckley , James Bunce , Angela C. Burnett , Florian A. Busch , Amanda Cavanagh , Lucas A. Cernusak , Robert Crystal-Ornelas , Joan Damerow , Kenneth J. Davidson , Martin G. De Kauwe , Michael C. Dietze , Tomas F. Domingues , Mirindi Eric Dusenge , David S. Ellsworth , John R. Evans , Paul P.G. Gauthier , Bruno O. Gimenez , Elizabeth P. Gordon , Christopher M. Gough , Aud H. Halbritter , David T. Hanson , Mary Heskel , J. Aaron Hogan , Jason R. Hupp , Kolby Jardine , Jens Kattge , Trevor Keenan , Johannes Kromdijk , Dushan P. Kumarathunge , Julien Lamour , Andrew D.B. Leakey , David S. LeBauer , Qianyu Li , Marjorie R. Lundgren , Nate McDowell , Katherine Meacham-Hensold , Belinda E. Medlyn , David J.P. Moore , Robinson Negrón-Juárez , Ülo Niinemets , Colin P. Osborne , Alexandria L. Pivovaroff , Hendrik Poorter , Sasha C. Reed , Youngryel Ryu , Alvaro Sanz-Saez , Stephanie C. Schmiege , Shawn P. Serbin , Thomas D. Sharkey , Martijn Slot , Nicholas G. Smith , Balasaheb V. Sonawane , Paul F. South , Daisy C. Souza , Joseph Ronald Stinziano , Ellen Stuart-Haëntjens , Samuel H. Taylor , Mauricio D. Tejera , Johan Uddling , Vigdis Vandvik , Charuleka Varadharajan , Anthony P. Walker , Berkley J. Walker , Jeffrey M. Warren , Danielle A. Way , Brett T. Wolfe , Jin Wu , Stan D. Wullschleger , Chonggang Xu , Zhengbing Yan , Dedi Yang

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.



中文翻译:

叶级气体交换数据和元数据的报告格式

叶级气体交换数据支持对植物碳和水通量的机械理解。这些通量告诉我们对生态系统功能的理解,是对陆地生物圈模型参数化的重要约束,对于理解植物对全球环境变化的响应是必不可少的,并且是改善作物产量的组成部分。使用气体分析仪收集这些数据可能在技术上既困难又费时,并且个别研究通常集中在小范围的物种,有限的时间段或有限的地理区域上。这些数据的高价值体现在许多重复使用和合成气体交换数据的出版物中,但是缺少元数据和数据报告约定使充分,有效地利用这些数据变得困难。在这里,我们提出了一种用于叶级气体交换数据和元数据的报告格式,以向数据提供者提供有关如何将数据存储在存储库中以最大程度地提高其可发现性,促进其有效重用以及为单个数据集增加价值的指导。对于数据用户,报告格式将更好地允许数据存储库优化数据搜索和提取,并且更容易将相似数据集成到统一的合成产品中。报告格式指定数据表变量命名和单位约定以及表征实验条件和协议的元数据。对于此报告格式的初始版本所关注的常见数据类型,即调查测量,暗呼吸,二氧化碳和光响应曲线以及从这些测量得出的参数,我们采取了进一步的步骤,定义所需的其他数据和元数据,以最大程度地重用这些数据类型。为了帮助数据提供者和数据存储库开发数据提取工具,我们提供了一个转换表,用于比较常见气体交换工具的输出。与数据收集者,数据用户,仪器制造商和数据科学家进行了广泛的协商,以确保报告格式满足社区的需求。此处介绍的报告格式旨在为将来的发展奠定基础,随着气体交换系统和测量方法的未来发展,它将结合更多的数据类型和变量。该报告格式已在美国能源部的ESS-DIVE数据存储库中发布,

更新日期:2021-01-31
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