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Root system markup language: Toward a unified root architecture description language

Meunier, Félicien; Lobet, Guillaume; Pound, Michael P.; Diener, Julian; Pradal, Christophe; Draye, Xavier; Godin, Christophe; Javaux, Mathieu; Leitner, Daniel; Meunier, Felicien; Nacry, Philippe; Pridmore, Tony P.; Schnepf, Andrea

Authors

Félicien Meunier

Guillaume Lobet

Julian Diener

Christophe Pradal

Xavier Draye

Christophe Godin

Mathieu Javaux

Daniel Leitner

Felicien Meunier

Philippe Nacry

TONY PRIDMORE tony.pridmore@nottingham.ac.uk
Professor of Computer Science

Andrea Schnepf



Abstract

© 2015 American Society of Plant Biologists. All rights reserved. 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 opensource packages have been developed in several languages (R, Excel, Java, Python, and C#) to enable researchers to integrate RSML files into popular research workflow.

Journal Article Type Article
Publication Date Jan 22, 2015
Journal Plant Physiology
Print ISSN 0032-0889
Electronic ISSN 1532-2548
Publisher American Society of Plant Biologists
Peer Reviewed Peer Reviewed
Volume 167
Issue 3
Pages 617-627
APA6 Citation Meunier, F., Diener, J., Lobet, G., Pound, M. P., Diener, J., Pradal, C., …Schnepf, A. (2015). Root system markup language: Toward a unified root architecture description language. Plant Physiology, 167(3), 617-627. https://doi.org/10.1104/pp.114.253625
DOI https://doi.org/10.1104/pp.114.253625
Keywords phenotyping root systems
Publisher URL http://www.plantphysiol.org/content/167/3/617
Related Public URLs http://www.plantphysiol.org/content/early/2015/01/22/pp.114.253625.1
Copyright Statement Copyright information regarding this work can be found at the following address: http://eprints.nottingh.../end_user_agreement.pdf

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Copyright Statement
Copyright information regarding this work can be found at the following address: http://eprints.nottingham.ac.uk/end_user_agreement.pdf





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