PhytoSYSTEMS, Université de Liège, 4000 Liege, Belgium (G.L.);Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Sutton Bonington LE12 5RD, United Kingdom (M.P.P.);Virtual Plants, Inria, Cirad, Institut National de la Recherche Agronomique, 34095 Montpellier, France (J.D., C.P., C.G.);Institut de Biologie Computationnelle, F-34095 Montpellier, France (C.P.);Earth and Life Institute, Université Catholique de Louvain, 1348 Louvain-la-Neuve, Belgium (X.D., M.J., F.M.);Institut für Bio- und Geowissenschaften: Agrosphäre, Forschungszentrum Jülich, D-52425 Julich, Germany (M.J., A.S.);Computational Science Center, University of Vienna, 1090 Vienna, Austria (D.L.);Biochemistry and Plant Molecular Physiology, Unité Mixte de Recherche 5004 Centre National de la Recherche Scientifique/Institut National de la Recherche Agronomique/SupAgro-M/UM2, Institut de Biologie Intégrative des Plantes, 34060 Montpellier cedex 1, France (P.N.); andSchool of Computer Science, University of Nottingham, Nottingham NG8 1BB, United Kingdom (T.P.P.).
PhytoSYSTEMS, Université de Liège, 4000 Liege, Belgium (G.L.);Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Sutton Bonington LE12 5RD, United Kingdom (M.P.P.);Virtual Plants, Inria, Cirad, Institut National de la Recherche Agronomique, 34095 Montpellier, France (J.D., C.P., C.G.);Institut de Biologie Computationnelle, F-34095 Montpellier, France (C.P.);Earth and Life Institute, Université Catholique de Louvain, 1348 Louvain-la-Neuve, Belgium (X.D., M.J., F.M.);Institut für Bio- und Geowissenschaften: Agrosphäre, Forschungszentrum Jülich, D-52425 Julich, Germany (M.J., A.S.);Computational Science Center, University of Vienna, 1090 Vienna, Austria (D.L.);Biochemistry and Plant Molecular Physiology, Unité Mixte de Recherche 5004 Centre National de la Recherche Scientifique/Institut National de la Recherche Agronomique/SupAgro-M/UM2, Institut de Biologie Intégrative des Plantes, 34060 Montpellier cedex 1, France (P.N.); andSchool of Computer Science, University of Nottingham, Nottingham NG8 1BB, United Kingdom (T.P.P.)
Plant Physiol. 2015 Mar;167(3):617-27. doi: 10.1104/pp.114.253625. Epub 2015 Jan 22.
The number of image analysis tools supporting the extraction of architectural features of root systems has increased in recent years. These tools offer a handy set of complementary facilities, yet it is widely accepted that none of these software tools is able to extract in an efficient way the growing array of static and dynamic features for different types of images and species. We describe the Root System Markup Language (RSML), which has been designed to overcome two major challenges: (1) to enable portability of root architecture data between different software tools in an easy and interoperable manner, allowing seamless collaborative work; and (2) to provide a standard format upon which to base central repositories that will soon arise following the expanding worldwide root phenotyping effort. RSML follows the XML standard to store two- or three-dimensional image metadata, plant and root properties and geometries, continuous functions along individual root paths, and a suite of annotations at the image, plant, or root scale at one or several time points. Plant ontologies are used to describe botanical entities that are relevant at the scale of root system architecture. An XML schema describes the features and constraints of RSML, and open-source packages have been developed in several languages (R, Excel, Java, Python, and C#) to enable researchers to integrate RSML files into popular research workflow.
近年来，支持提取根系结构特征的图像分析工具的数量有所增加。这些工具提供了一套方便的互补设施，但人们普遍认为，这些软件工具都不能有效地提取不同类型图像和物种的不断增加的静态和动态特征。我们描述了根系标记语言 (RSML)，它旨在克服两个主要挑战：(1) 以一种简单且可互操作的方式在不同的软件工具之间实现根系结构数据的可移植性，从而实现无缝协作；(2) 提供一个标准格式，为即将出现的全球范围的根系表型分析工作提供中央存储库。RSML 遵循 XML 标准存储二维或三维图像元数据、植物和根系属性和几何形状、沿单个根系路径的连续函数以及在一个或多个时间点在图像、植物或根系尺度上的一套注释。植物本体用于描述与根系结构尺度相关的植物实体。XML 模式描述了 RSML 的特征和约束，并且已经用几种语言（R、Excel、Java、Python 和 C#）开发了开源包，以使研究人员能够将 RSML 文件集成到流行的研究工作流程中。
