Journal Article

FZJ-2016-05958

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Measures for interoperability of phenotypic data: minimum information requirements and formatting

Ćwiek-Kupczyńska, H. ; Altmann, T. ; Arend, D. ; Arnaud, E. ; Chen, D. ; Cornut, G. ; Fiorani, F.FZJ* ; Frohmberg, W. ; Junker, A. ; Klukas, C. ; Lange, M. ; Mazurek, C. ; Nafissi, A.FZJ* ; Neveu, P. ; van Oeveren, J. ; Pommier, C. ; Poorter, H.FZJ* ; Rocca-Serra, P. ; Sansone, S.-A. ; Scholz, U. ; van Schriek, M. ; Seren, Ü. ; Usadel, B.FZJ* ; Weise, S. ; Kersey, P. ; Krajewski, P. (Corresponding author)

2016
BioMed Central London

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Please use a persistent id in citations: http://hdl.handle.net/2128/12951  doi:10.1186/s13007-016-0144-4

Abstract: BackgroundPlant 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.ResultsIn 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.ConclusionsAcceptance of the rules described in this paper by the plant phenotyping community will help to achieve findable, accessible, interoperable and reusable data.

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Contributing Institute(s):

1. Pflanzenwissenschaften (IBG-2)

Research Program(s):

1. 582 - Plant Science (POF3-582) (POF3-582)
2. DPPN - Deutsches Pflanzen Phänotypisierungsnetzwerk (BMBF-031A053A) (BMBF-031A053A)
3. EPPN - European Plant Phenotyping Network (284443) (284443)

Appears in the scientific report 2016

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Database coverage:
; ; ; ; BIOSIS Previews ; Current Contents - Agriculture, Biology and Environmental Sciences ; Current Contents - Life Sciences ; DOAJ Seal ; Ebsco Academic Search ; IF < 5 ; JCR ; NCBI Molecular Biology Database ; SCOPUS ; Science Citation Index Expanded ; Thomson Reuters Master Journal List ; Web of Science Core Collection

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