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

Plant Methods

Elizabeth Arnaud¹  Björn Usadel²  Anahita Nafissi²  Fabio Fiorani²  Hendrik Poorter²  Ümit Seren³  Guillaume Cornut⁴  Cyril Pommier⁴  Dijun Chen⁵  Wojciech Frohmberg⁶  Paweł Krajewski⁶  Hanna Ćwiek-Kupczyńska⁶  Jan van Oeveren⁷  Marco van Schriek⁷  Stephan Weise⁸  Uwe Scholz⁸  Matthias Lange⁸  Astrid Junker⁸  Thomas Altmann⁸  Daniel Arend⁸  Christian Klukas⁹  Philippe Rocca-Serra^1,10  Susanna-Assunta Sansone^1,10  Cezary Mazurek^1,11  Paul Kersey^1,12  Pascal Neveu^1,13 

[1] Bioversity International;Forschungszentrum Jülich GmbH, IBG-2 Plant Sciences;Gregor Mendel Institute, Austrian Academy of Sciences;INRA, UR1164 URGI - Research Unit in Genomics-Info, INRA de Versailles-Grignon;Institute for Biochemistry and Biology, University of Potsdam;Institute of Plant Genetics, Polish Academy of Sciences;Keygene N.V.;Leibniz Institute of Plant Genetics and Crop Plant Research (IPK);LemnaTec GmbH;Oxford e-Research Centre, University of Oxford;Poznań Supercomputing and Networking Center Affiliated to the Institute of Bioorganic Chemistry, Polish Academy of Sciences;The European Molecular Biology Laboratory–The European Bioinformatics Institute;UMR MISTEA, INRA SupAgro;

关键词: Data standardisation and formatting;    Experimental metadata;    Minimum information recommendations;    Plant phenotyping;    Experiment description;   

DOI  :  10.1186/s13007-016-0144-4

来源: DOAJ

【 摘 要 】

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.

【 授权许可】

Unknown