Enabling reusability of plant phenomic datasets with MIAPPE 1.1.

François Tardieu, Markus Oppermann, Richard Ostler, Hendrik Poorter, Ricardo Ramı Rez-Gonzalez, Živa Ramšak, Jochen C Reif, Philippe Rocca-Serra, Susanna-Assunta Sansone, Uwe Scholz, Célia Michotey, Cristobal Uauy, Björn Usadel, Richard G F Visser, Stephan Weise, Paul J Kersey, Célia M Miguel, Anne-Françoise Adam-Blondon, Cyril Pommier, Hanna Ćwiek-Kupczyńska, Daniel Faria, Daniel Arend, Elizabeth Arnaud, Ioannis N Athanasiadis, Inês Chaves, Frederik Coppens, Guillaume Cornut, Bruno V Costa, Evangelia A Papoutsoglou, Bert Droesbeke, Richard Finkers, Kristina Gruden, Astrid Junker, Graham J King, Paweł Krajewski, Matthias Lange, Marie-Angélique Laporte

Journal: The New phytologist 2021;227(1):260-273

PMID: 32171029

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Abstract

Enabling data reuse and knowledge discovery is increasingly critical in modern science, and requires an effort towards standardising data publication practices. This is particularly challenging in the plant phenotyping domain, due to its complexity and heterogeneity. We have produced the MIAPPE 1.1 release, which enhances the existing MIAPPE standard in coverage, to support perennial plants, in structure, through an explicit data model, and in clarity, through definitions and examples. We evaluated MIAPPE 1.1 by using it to express several heterogeneous phenotyping experiments in a range of different formats, to demonstrate its applicability and the interoperability between the various implementations. Furthermore, the extended coverage is demonstrated by the fact that one of the datasets could not have been described under MIAPPE 1.0. MIAPPE 1.1 marks a major step towards enabling plant phenotyping data reusability, thanks to its extended coverage, and especially the formalisation of its data model, which facilitates its implementation in different formats. Community feedback has been critical to this development, and will be a key part of ensuring adoption of the standard.

Address: Plant Breeding, Wageningen University & Research, PO Box 386, Wageningen, 6700AJ, the Netherlands.; BioData.pt, Instituto Gulbenkian de Ciência, 2780-156, Oeiras, Portugal.; INESC-ID, 1000-029, Lisboa, Portugal.; Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany.; Bioversity International, Parc Scientifique Agropolis II, Montpellier Cedex 5, 34397, France.; Geo-Information Science and Remote Sensing Laboratory, Wageningen University, Droevendaalsesteeg 3, Wageningen, 6708PB, the Netherlands.; Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA) Avenida da República, 2780-157, Oeiras, Portugal.; Instituto de Biologia Experimental e Tecnológica (iBET), 2780-157, Oeiras, Portugal.; Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, 9052, Belgium.; VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, 9052, Belgium.; Université Paris-Saclay, INRAE, URGI, Versailles, 78026, France.; BioISI - Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Lisboa, 1749-016, Portugal.; Institute of Plant Genetics, Polish Academy of Sciences, ul. Strzeszyńska 34, 60-479, Poznań, Poland.; Department of Biotechnology and Systems Biology, National Institute of Biology, SI1000, Ljubljana, Slovenia.; Southern Cross Plant Science, Southern Cross University, Lismore, NSW 2577, Australia.; Computational and Analytical Sciences, Rothamsted Research, Harpenden, AL5 2JQ, UK.; Plant Sciences (IBG-2), Forschungszentrum Jülich GmbH, D-52425, Jülich, Germany.; Department of Biological Sciences, Macquarie University, North Ryde, NSW 2109, Australia.; Department of Crop Genetics, John Innes Centre, Norwich Research Park, Colney, Norwich, NR4 7UH, UK.; Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, Oxford, OX1 3QG, UK.; INRA, Laboratoire d'Ecophysiologie des Plantes sous Stress Environnementaux, UMR759, Montpellier, 34060, France.; Institute for Biology I, BioSC, RWTH Aachen University, Worringer Weg 3, 52074, Aachen, Germany.; Royal Botanic Gardens, Kew, Richmond, TW9 3AE, UK.

DOI: 10.1111/nph.16544

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MeSH Terms: Phenomics, Plants