Root system markup language: toward an unified root architecture description language

Lobet, Guillaume and Pound, Michael P. and Diener, Julian and Pradal, Christophe and Draye, Xavier and Godin, Christophe and Javaux, Mathieu and Leitner, Daniel and Meunier, Felicien and Nacry, Philippe and Pridmore, Tony P. and Schnepf, Andrea (2015) Root system markup language: toward an unified root architecture description language. Plant Physiology, 167 (3). pp. 617-627. ISSN 1532-2548

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Abstract

The number of image analysis tools supporting the extraction of architectural features of root systems has increased over the last years. These tools offer a handy set of complementary facilities, yet it is widely accepted that none of these software tool is able to extract in an efficient way growing array of static and dynamic features for different types of images and species.

We describe the Root System Markup Language (RSML) that has been designed to overcome two major challenges: (i) to enable portability of root architecture data between different software tools in an easy and interoperable manner allowing seamless collaborative work, and (ii) to provide a standard format upon which to base central repositories which will soon arise following the expanding worldwide root phenotyping effort.

RSML follows the XML standard to store 2D or 3D 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 scales, 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, C#) to enable researchers to integrate RSML files into popular research workflow.

Item Type: Article
Keywords: phenotyping root systems
Schools/Departments: University of Nottingham UK Campus > Faculty of Science > School of Biosciences
University of Nottingham UK Campus > Faculty of Science > School of Computer Science
Identification Number: https://doi.org/10.1104/pp.114.253625
Related URLs:
URLURL Type
http://www.plantphysiol.org/content/early/2015/01/22/pp.114.253625.1UNSPECIFIED
Depositing User: Pound, Michael
Date Deposited: 15 Jun 2016 13:01
Last Modified: 16 Sep 2016 09:01
URI: http://eprints.nottingham.ac.uk/id/eprint/34061

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