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      Measures for interoperability of phenotypic data: minimum information requirements and formatting

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          Abstract

          Background

          Plant phenotypic data shrouds a wealth of information which, when accurately analysed and linked to other data types, brings to light the knowledge about the mechanisms of life. As phenotyping is a field of research comprising manifold, diverse and time-consuming experiments, the findings can be fostered by reusing and combining existing datasets. Their correct interpretation, and thus replicability, comparability and interoperability, is possible provided that the collected observations are equipped with an adequate set of metadata. So far there have been no common standards governing phenotypic data description, which hampered data exchange and reuse.

          Results

          In this paper we propose the guidelines for proper handling of the information about plant phenotyping experiments, in terms of both the recommended content of the description and its formatting. We provide a document called “Minimum Information About a Plant Phenotyping Experiment”, which specifies what information about each experiment should be given, and a Phenotyping Configuration for the ISA-Tab format, which allows to practically organise this information within a dataset. We provide examples of ISA-Tab-formatted phenotypic data, and a general description of a few systems where the recommendations have been implemented.

          Conclusions

          Acceptance of the rules described in this paper by the plant phenotyping community will help to achieve findable, accessible, interoperable and reusable data.

          Electronic supplementary material

          The online version of this article (doi:10.1186/s13007-016-0144-4) contains supplementary material, which is available to authorized users.

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          Most cited references17

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          A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB

          Background Sharing of microarray data within the research community has been greatly facilitated by the development of the disclosure and communication standards MIAME and MAGE-ML by the MGED Society. However, the complexity of the MAGE-ML format has made its use impractical for laboratories lacking dedicated bioinformatics support. Results We propose a simple tab-delimited, spreadsheet-based format, MAGE-TAB, which will become a part of the MAGE microarray data standard and can be used for annotating and communicating microarray data in a MIAME compliant fashion. Conclusion MAGE-TAB will enable laboratories without bioinformatics experience or support to manage, exchange and submit well-annotated microarray data in a standard format using a spreadsheet. The MAGE-TAB format is self-contained, and does not require an understanding of MAGE-ML or XML.
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            Towards recommendations for metadata and data handling in plant phenotyping.

            Recent methodological developments in plant phenotyping, as well as the growing importance of its applications in plant science and breeding, are resulting in a fast accumulation of multidimensional data. There is great potential for expediting both discovery and application if these data are made publicly available for analysis. However, collection and storage of phenotypic observations is not yet sufficiently governed by standards that would ensure interoperability among data providers and precisely link specific phenotypes and associated genomic sequence information. This lack of standards is mainly a result of a large variability of phenotyping protocols, the multitude of phenotypic traits that are measured, and the dependence of these traits on the environment. This paper discusses the current situation of standardization in the area of phenomics, points out the problems and shortages, and presents the areas that would benefit from improvement in this field. In addition, the foundations of the work that could revise the situation are proposed, and practical solutions developed by the authors are introduced.
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              The art of growing plants for experimental purposes: a practical guide for the plant biologist

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                Author and article information

                Contributors
                hcwi@igr.poznan.pl
                altmann@ipk-gatersleben.de
                arendd@ipk-gatersleben.de
                e.arnaud@cgiar.org
                dijun.chen@uni-potsdam.de
                guillaume.cornut@versailles.inra.fr
                f.fiorani@fz-juelich.de
                wojciech.frohmberg@cs.put.poznan.pl
                junkera@ipk-gatersleben.de
                christian.klukas@lemnatec.de
                lange@ipk-gatersleben.de
                mazurek@man.poznan.pl
                a.nafissi@fz-juelich.de
                pascal.neveu@supagro.inra.fr
                jan.van-oeveren@keygene.com
                cyril.pommier@versailles.inra.fr
                h.poorter@fz-juelich.de
                philippe.rocca-serra@oerc.ox.ac.uk
                susanna-assunta.sansone@oerc.ox.ac.uk
                scholz@ipk-gatersleben.de
                marco.van-schriek@keygene.com
                uemit.seren@gmi.oeaw.ac.at
                usadel@bio1.rwth-aachen.de
                weise@ipk-gatersleben.de
                pkersey@ebi.ac.uk
                pkra@igr.poznan.pl
                Journal
                Plant Methods
                Plant Methods
                Plant Methods
                BioMed Central (London )
                1746-4811
                9 November 2016
                9 November 2016
                2016
                : 12
                : 44
                Affiliations
                [1 ]Institute of Plant Genetics, Polish Academy of Sciences, ul. Strzeszyńska 34, 60-479 Poznań, Poland
                [2 ]Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstraße 3, 06466 Stadt Seeland, Germany
                [3 ]Bioversity International, parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France
                [4 ]Institute for Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
                [5 ]INRA, UR1164 URGI - Research Unit in Genomics-Info, INRA de Versailles-Grignon, Route de Saint-Cyr, 78026 Versailles, France
                [6 ]Forschungszentrum Jülich GmbH, IBG-2 Plant Sciences, 52425 Jülich, Germany
                [7 ]Institute of Computing Science, Poznań University of Technology, ul. Piotrowo 3a, 60-479 Poznań, Poland
                [8 ]LemnaTec GmbH, Pascalstraße 59, 52076 Aachen, Germany
                [9 ]Poznań Supercomputing and Networking Center Affiliated to the Institute of Bioorganic Chemistry, Polish Academy of Sciences, ul. Jana Pawła II 10, 61-139 Poznań, Poland
                [10 ]UMR MISTEA, INRA SupAgro, Place Pierre Viala 2, 34060 Montpellier, France
                [11 ]Keygene N.V., Agro Business Park 90, 6708 PW Wageningen, The Netherlands
                [12 ]Oxford e-Research Centre, University of Oxford, 7 Keble Road, Oxford, OX1 3QG UK
                [13 ]Gregor Mendel Institute, Austrian Academy of Sciences, 1030 Vienna, Austria
                [14 ]Institute of Biology I, BioSC, RWTH Aachen, Worringer Weg 3, Aachen, Germany
                [15 ]The European Molecular Biology Laboratory–The European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD UK
                Article
                144
                10.1186/s13007-016-0144-4
                5103589
                27843484
                afd68e92-338f-48ee-9f2f-10b8aa04a295
                © The Author(s) 2016

                Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

                History
                : 15 April 2016
                : 18 October 2016
                Funding
                Funded by: FundRef http://dx.doi.org/10.13039/501100004963, Seventh Framework Programme;
                Award ID: 283496
                Award ID: 28443
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/501100002347, Bundesministerium für Bildung und Forschung;
                Award ID: 031A053A/B/C
                Funded by: FundRef http://dx.doi.org/10.13039/501100001665, Agence Nationale de la Recherche;
                Award ID: ANR-11-INBS-0012
                Categories
                Methodology
                Custom metadata
                © The Author(s) 2016

                Plant science & Botany
                data standardisation and formatting,experimental metadata,minimum information recommendations,plant phenotyping,experiment description

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