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Measures for interoperability of phenotypic data

  • 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 combin‑ ing 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 docu‑ ment called “Minimum Information About a Plant Phenotyping Experiment”, which specifies what information about each experimentBackground: 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 combin‑ ing 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 docu‑ ment 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.show moreshow less

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Author:Hanna Ćwiek-Kupczyńska, Thomas Altmann, Daniel Arend, Elizabeth Arnaud, Dijun ChenORCiD, Guillaume Cornut, Fabio Fiorani, Wojciech Frohmberg, Astrid Junker, Christian Klukas, Matthias Lange, Cezary Mazurek, Anahita Nafissi, Pascal Neveu, Jan van Oeveren, Cyril Pommier, Hendrik Poorter, Philippe Rocca-Serra, Susanna-Assunta Sansone, Uwe Scholz, Marco van Schriek, Ümit Seren, Björn Usadel, Stephan Weise, Paul Kersey, Paweł Krajewski
URN:urn:nbn:de:kobv:517-opus4-407299
Parent Title (English):Plant methods
Subtitle (English):minimum information requirements and formatting
Series (Serial Number):Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe (450)
Document Type:Postprint
Language:English
Date of first Publication:2018/06/27
Year of Completion:2016
Publishing Institution:Universität Potsdam
Release Date:2018/06/27
Tag:data standardisation and formatting; experiment description; experimental metadata; minimum information recommendations; plant phenotyping
Pagenumber:18
Source:BMC Plant Methods (2016); Bd. 12 Nr.1, Art. 44 ; DOI: 10.1186/s13007-016-0144-4
Organizational units:Mathematisch-Naturwissenschaftliche Fakultät
Mathematisch-Naturwissenschaftliche Fakultät / Institut für Biochemie und Biologie
Dewey Decimal Classification:5 Naturwissenschaften und Mathematik / 57 Biowissenschaften; Biologie / 570 Biowissenschaften; Biologie
5 Naturwissenschaften und Mathematik / 58 Pflanzen (Botanik) / 580 Pflanzen (Botanik)
Peer Review:Referiert
Publication Way:Open Access
Grantor:BioMed Central
Licence (German):License LogoCreative Commons - Namensnennung, 4.0 International