Enabling reusability of plant phenomic datasets with MIAPPE 1.1

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

doi:10.1111/nph.16544

Enabling reusability of plant phenomic datasets with MIAPPE 1.1

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

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

79 Citations (Scopus)

1219 Downloads (Pure)

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.

Original language	English
Pages (from-to)	260-273
Number of pages	14
Journal	New Phytologist
Volume	227
Issue number	1
DOIs	https://doi.org/10.1111/nph.16544
Publication status	Published - Jul 2020

Bibliographical note

Copyright the Author(s) 2020. Version archived for private and non-commercial use with the permission of the author/s and according to publisher conditions. For further rights please contact the publisher.

Keywords

findability
interoperability
metadata
phenomics
plant phenotyping
reusability
standards

Access to Document

10.1111/nph.16544

Publisher version (open access)Final published version, 1.89 MBLicence: CC BY

Cite this

Papoutsoglou, E. A., Faria, D., Arend, D., Arnaud, E., Athanasiadis, I. N., Chaves, I., Coppens, F., Cornut, G., Costa, B. V., Ćwiek-Kupczyńska, H., Droesbeke, B., Finkers, R., Gruden, K., Junker, A., King, G. J., Krajewski, P., Lange, M., Laporte, M. A., Michotey, C., ... Pommier, C. (2020). Enabling reusability of plant phenomic datasets with MIAPPE 1.1. New Phytologist, 227(1), 260-273. https://doi.org/10.1111/nph.16544

@article{572e8643de134ad9845e0224df4f5bbd,

title = "Enabling reusability of plant phenomic datasets with MIAPPE 1.1",

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.",

keywords = "findability, interoperability, metadata, phenomics, plant phenotyping, reusability, standards",

author = "Papoutsoglou, {Evangelia A.} and Daniel Faria and Daniel Arend and Elizabeth Arnaud and Athanasiadis, {Ioannis N.} and In{\^e}s Chaves and Frederik Coppens and Guillaume Cornut and Costa, {Bruno V.} and Hanna {\'C}wiek-Kupczy{\'n}ska and Bert Droesbeke and Richard Finkers and Kristina Gruden and Astrid Junker and King, {Graham J.} and Pawe{\l} Krajewski and Matthias Lange and Laporte, {Marie Ang{\'e}lique} and C{\'e}lia Michotey and Markus Oppermann and Richard Ostler and Hendrik Poorter and Ricardo Ram{\'ı}rez-Gonzalez and {\v Z}iva Ram{\v s}ak and Reif, {Jochen C.} and Philippe Rocca-Serra and Sansone, {Susanna Assunta} and Uwe Scholz and Fran{\c c}ois Tardieu and Cristobal Uauy and Bj{\"o}rn Usadel and Visser, {Richard G.F.} and Stephan Weise and Kersey, {Paul J.} and Miguel, {C{\'e}lia M.} and Adam-Blondon, {Anne Fran{\c c}oise} and Cyril Pommier",

note = "Copyright the Author(s) 2020. Version archived for private and non-commercial use with the permission of the author/s and according to publisher conditions. For further rights please contact the publisher. ",

year = "2020",

month = jul,

doi = "10.1111/nph.16544",

language = "English",

volume = "227",

pages = "260--273",

journal = "New Phytologist",

issn = "0028-646X",

publisher = "Wiley-Liss, Wiley",

number = "1",

}

Papoutsoglou, EA, Faria, D, Arend, D, Arnaud, E, Athanasiadis, IN, Chaves, I, Coppens, F, Cornut, G, Costa, BV, Ćwiek-Kupczyńska, H, Droesbeke, B, Finkers, R, Gruden, K, Junker, A, King, GJ, Krajewski, P, Lange, M, Laporte, MA, Michotey, C, Oppermann, M, Ostler, R, Poorter, H, Ramı́rez-Gonzalez, R, Ramšak, Ž, Reif, JC, Rocca-Serra, P, Sansone, SA, Scholz, U, Tardieu, F, Uauy, C, Usadel, B, Visser, RGF, Weise, S, Kersey, PJ, Miguel, CM, Adam-Blondon, AF & Pommier, C 2020, 'Enabling reusability of plant phenomic datasets with MIAPPE 1.1', New Phytologist, vol. 227, no. 1, pp. 260-273. https://doi.org/10.1111/nph.16544

TY - JOUR

T1 - Enabling reusability of plant phenomic datasets with MIAPPE 1.1

AU - Papoutsoglou, Evangelia A.

AU - Faria, Daniel

AU - Arend, Daniel

AU - Arnaud, Elizabeth

AU - Athanasiadis, Ioannis N.

AU - Chaves, Inês

AU - Coppens, Frederik

AU - Cornut, Guillaume

AU - Costa, Bruno V.

AU - Ćwiek-Kupczyńska, Hanna

AU - Droesbeke, Bert

AU - Finkers, Richard

AU - Gruden, Kristina

AU - Junker, Astrid

AU - King, Graham J.

AU - Krajewski, Paweł

AU - Lange, Matthias

AU - Laporte, Marie Angélique

AU - Michotey, Célia

AU - Oppermann, Markus

AU - Ostler, Richard

AU - Poorter, Hendrik

AU - Ramı́rez-Gonzalez, Ricardo

AU - Ramšak, Živa

AU - Reif, Jochen C.

AU - Rocca-Serra, Philippe

AU - Sansone, Susanna Assunta

AU - Scholz, Uwe

AU - Tardieu, François

AU - Uauy, Cristobal

AU - Usadel, Björn

AU - Visser, Richard G.F.

AU - Weise, Stephan

AU - Kersey, Paul J.

AU - Miguel, Célia M.

AU - Adam-Blondon, Anne Françoise

AU - Pommier, Cyril

N1 - Copyright the Author(s) 2020. Version archived for private and non-commercial use with the permission of the author/s and according to publisher conditions. For further rights please contact the publisher.

PY - 2020/7

Y1 - 2020/7

N2 - 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.

AB - 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.

KW - findability

KW - interoperability

KW - metadata

KW - phenomics

KW - plant phenotyping

KW - reusability

KW - standards

UR - http://www.scopus.com/inward/record.url?scp=85083230937&partnerID=8YFLogxK

U2 - 10.1111/nph.16544

DO - 10.1111/nph.16544

M3 - Article

C2 - 32171029

AN - SCOPUS:85083230937

SN - 0028-646X

VL - 227

SP - 260

EP - 273

JO - New Phytologist

JF - New Phytologist

IS - 1

ER -

Enabling reusability of plant phenomic datasets with MIAPPE 1.1

Abstract

Bibliographical note

Keywords

Access to Document

Other files and links

Fingerprint

Cite this