Treffer: Root system markup language: toward a unified root architecture description language.
Title:
Root system markup language: toward a unified root architecture description language.
Authors:
Lobet G; 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.)., Pound MP; 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.)., Diener J; 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.)., Pradal C; 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.)., Draye X; 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.) xavier.draye@uclouvain.be., Godin C; 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.)., Javaux M; 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.)., Leitner D; 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.)., Meunier F; 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.)., Nacry 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.)., Pridmore TP; 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.)., Schnepf A; 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.).
Source:
Plant physiology [Plant Physiol] 2015 Mar; Vol. 167 (3), pp. 617-27. Date of Electronic Publication: 2015 Jan 22.
Publication Type:
Journal Article; Research Support, Non-U.S. Gov't
Language:
English
Journal Info:
Publisher: American Society of Plant Biologists Country of Publication: United States NLM ID: 0401224 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1532-2548 (Electronic) Linking ISSN: 00320889 NLM ISO Abbreviation: Plant Physiol Subsets: MEDLINE
Imprint Name(s):
Publication: : [Rockville, MD] : American Society of Plant Biologists
Original Publication: Lancaster, Pa., American Society of Plant Physiologists.
Original Publication: Lancaster, Pa., American Society of Plant Physiologists.
MeSH Terms:
References:
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Plant Physiol. 2014 Oct;166(2):470-86. (PMID: 25187526)
Plant Physiol. 2013 Aug;162(4):1802-14. (PMID: 23766367)
Plant Physiol. 2013 Sep;163(1):161-79. (PMID: 23852440)
Funct Plant Biol. 2008 Dec;35(10):751-760. (PMID: 32688829)
Plant J. 2009 Mar;57(5):945-56. (PMID: 19000163)
Front Plant Sci. 2013 Nov 05;4:442. (PMID: 24204374)
Plant Physiol. 2011 Jul;156(3):1190-201. (PMID: 21628631)
Comp Funct Genomics. 2002;3(2):137-42. (PMID: 18628842)
J Theor Biol. 2001 Oct 21;212(4):481-520. (PMID: 11597182)
Plant Methods. 2013 Oct 09;9(1):38. (PMID: 24107223)
Plant Physiol. 2012 Feb;158(2):561-9. (PMID: 22190339)
Nat Cell Biol. 2012 Oct;14(10):991-8. (PMID: 22983115)
Nucleic Acids Res. 2013 Jan;41(Database issue):D987-90. (PMID: 23193272)
Plant Physiol. 2014 Jan;164(1):24-35. (PMID: 24218493)
Plant Physiol. 2010 Mar;152(3):1148-57. (PMID: 20107024)
Plant Cell. 2014 Apr 1;26(4):1480-1496. (PMID: 24692421)
Plant Physiol. 2011 Sep;157(1):29-39. (PMID: 21771915)
Plant Physiol. 2011 Jun;156(2):455-65. (PMID: 21454799)
Plant Cell Environ. 2013 Feb;36(2):454-66. (PMID: 22860896)
BMC Plant Biol. 2012 Jul 26;12:116. (PMID: 22834569)
Plant Methods. 2013 Mar 20;9(1):8. (PMID: 23514198)
Plant Physiol. 1995 Sep;109(1):7-13. (PMID: 12228579)
PLoS One. 2014 Sep 24;9(9):e108255. (PMID: 25251072)
Front Plant Sci. 2012 May 30;3:76. (PMID: 22670147)
New Phytol. 2005 Jun;166(3):705-8. (PMID: 15869632)
Plant Physiol. 2014 Apr;164(4):1619-27. (PMID: 24515834)
Ann Bot. 2007 Mar;99(3):375-407. (PMID: 17218346)
J Theor Biol. 1998 Mar 7;191(1):1-46. (PMID: 9593655)
Ann Bot. 2014 Sep;114(4):795-812. (PMID: 24925323)
Plant Physiol. 2009 Aug;150(4):1784-95. (PMID: 19515787)
Nucleic Acids Res. 2008 Jan;36(Database issue):D449-54. (PMID: 18194960)
J Exp Bot. 2010 May;61(8):2145-55. (PMID: 20453027)
Plant Physiol. 2005 Oct;139(2):960-8. (PMID: 16183852)
Neuron. 2013 Mar 20;77(6):1017-38. (PMID: 23522039)
Plant Physiol. 2014 Oct;166(2):470-86. (PMID: 25187526)
Plant Physiol. 2013 Aug;162(4):1802-14. (PMID: 23766367)
Plant Physiol. 2013 Sep;163(1):161-79. (PMID: 23852440)
Funct Plant Biol. 2008 Dec;35(10):751-760. (PMID: 32688829)
Plant J. 2009 Mar;57(5):945-56. (PMID: 19000163)
Front Plant Sci. 2013 Nov 05;4:442. (PMID: 24204374)
Plant Physiol. 2011 Jul;156(3):1190-201. (PMID: 21628631)
Comp Funct Genomics. 2002;3(2):137-42. (PMID: 18628842)
J Theor Biol. 2001 Oct 21;212(4):481-520. (PMID: 11597182)
Plant Methods. 2013 Oct 09;9(1):38. (PMID: 24107223)
Plant Physiol. 2012 Feb;158(2):561-9. (PMID: 22190339)
Nat Cell Biol. 2012 Oct;14(10):991-8. (PMID: 22983115)
Nucleic Acids Res. 2013 Jan;41(Database issue):D987-90. (PMID: 23193272)
Plant Physiol. 2014 Jan;164(1):24-35. (PMID: 24218493)
Plant Physiol. 2010 Mar;152(3):1148-57. (PMID: 20107024)
Plant Cell. 2014 Apr 1;26(4):1480-1496. (PMID: 24692421)
Plant Physiol. 2011 Sep;157(1):29-39. (PMID: 21771915)
Plant Physiol. 2011 Jun;156(2):455-65. (PMID: 21454799)
Plant Cell Environ. 2013 Feb;36(2):454-66. (PMID: 22860896)
BMC Plant Biol. 2012 Jul 26;12:116. (PMID: 22834569)
Plant Methods. 2013 Mar 20;9(1):8. (PMID: 23514198)
Entry Date(s):
Date Created: 20150124 Date Completed: 20160123 Latest Revision: 20240322
Update Code:
20250114
PubMed Central ID:
PMC4348768
DOI:
10.1104/pp.114.253625
PMID:
25614065
Database:
MEDLINE
Weitere Informationen
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.
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