Identifying, naming and interoperating data in a Phenotyping platform network : the good, the bad and the ugly.

The EPPN2020 is a research project funded by Horizon 2020 Programme of the EU that will provide European public and private scientific sectors with access to a wide range of state-of-the-art plant phenotyping installations, techniques and methods. Specifically, EPPN2020 includes access to 31 plant phenotyping installations, and joint research activities to develop: novel technologies and methods for environmental and plant measurements. Here we present the results of the discussions of the 2019 annual project meeting to adopt community-approved architectural choices. It focuses on persistent identification of data and real objects, the naming of variables and the priorities for increasing interoperability among phenotyping installations. We describe the main elements to prioritize (the good) in order to enhance Findable, Accessible, Interoperable and Reusable (FAIR) quality for each data management system with a pragmatic concern for all partners. The plant phenotyping community gathers different actors with various means and practices. Among all the recommendations (including the bad: avoiding bad practices), the community requests identification methods (including the use of ontologies) compatible with the ‘local’ pre-existing ones. The identification scheme being adopted is based on Uniform Resource Identifiers (URIs) with independant left and right parts for each identifier. It focuses on the associated objects and variables common to all EPPN2020 members, namely the experimental units (which can be a plant in a pot or a plot), sensors and variables. A common architecture for identifiers and variable names is presented in order to enable a first level of interoperation between information systems. In conclusion, we present some of the next challenges (the ugly) that need to be addressed by the EPPN2020 community related with i) the partial reuse of pre-existing ontologies, ii) the persistence of long-term access to data iii) interoperation between all potential users of the phenotyping data. Audience researchers, research Infrastructures and research communities, repository managers, publishers and content providers, libraries, research administrators, data managers. References Neveu, P. , Tireau, A. , Hilgert, N. , Nègre, V. , Mineau‐Cesari, J. , Brichet, N. , Chapuis, R. , Sanchez, I. , Pommier, C. , Charnomordic, B. , Tardieu, F. and Cabrera‐Bosquet, L. (2019), Dealing with multi‐source and multi‐scale information in plant phenomics: the ontology‐driven Phenotyping Hybrid Information System. New Phytol, 221: 588-601. doi:10.1111/nph.15385 Roitsch T, Cabrera-Bosquet L, Fournier A, Ghamkhar K, Jimenez-Berni J, Pinto F, Ober ES. 2019. Review: New sensors and data-driven approaches-A path to next generation phenomics. Plant Science 282: 2-10.

Tags
Data and Resources
To access the resources you must log in

This item has no data

Identity

Description: The Identity category includes attributes that support the identification of the resource.

Field Value
PID https://www.doi.org/10.5281/zenodo.3402948
PID https://www.doi.org/10.1111/nph.15385
PID pmc:PMC6585972
PID pmid:30152011
PID https://www.doi.org/10.5281/zenodo.3402947
PID https://www.doi.org/10.5281/zenodo.3539259
URL http://dx.doi.org/10.5281/zenodo.3539259
URL http://onlinelibrary.wiley.com/wol1/doi/10.1111/nph.15385/fullpdf
URL https://hal.inrae.fr/hal-02627721/document
URL http://dx.doi.org/10.5281/zenodo.3402947
URL https://hal.archives-ouvertes.fr/hal-02164160
URL http://dx.doi.org/10.5281/zenodo.3402948
URL http://dx.doi.org/10.1111/nph.15385
URL http://europepmc.org/articles/PMC6585972
URL https://figshare.com/articles/Identifying_naming_and_interoperating_data_in_a_Phenotyping_platform_network_the_good_the_bad_and_the_ugly_/11528292
URL https://pesquisa.bvsalud.org/portal/resource/pt/mdl-30152011
URL https://nph.onlinelibrary.wiley.com/doi/full/10.1111/nph.15385
URL https://dx.doi.org/10.1111/nph.15385
URL https://academic.microsoft.com/#/detail/2889025470
URL https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111%2Fnph.15385
URL http://prodinra.inra.fr/record/475112
URL https://hal.archives-ouvertes.fr/hal-02164160/document
URL https://hal.archives-ouvertes.fr/hal-02164160/file/A0_Romain_David_PHIS_RDA_Helsinki_poster02102019%20%281%29.pdf
URL https://figshare.com/articles/Identifying_naming_and_interoperating_data_in_a_Phenotyping_platform_network_the_good_the_bad_and_the_ugly_/11466006
URL http://prodinra.inra.fr/record/442308
URL https://hal.inrae.fr/hal-02627721
URL https://zenodo.org/record/3539259
URL https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/nph.15385
URL https://zenodo.org/record/3402948
URL https://hal.inrae.fr/hal-02627721/file/publis18-mistea-029_neveu_daling_1.pdf
URL https://nph.onlinelibrary.wiley.com/doi/pdfdirect/10.1111/nph.15385
Access Modality

Description: The Access Modality category includes attributes that report the modality of exploitation of the resource.

Field Value
Access Right Open Access
Attribution

Description: Authorships and contributors

Field Value
Author Romain, David, 0000-0003-4073-7456
Author Jean-Eudes, Hollebecq, 0000-0002-5089-9179
Author Llorenç, Cabrera-Bosquet, 0000-0002-2147-2846
Author Hanna, Ćwiek-Kupczyńska, 0000-0001-9113-567X
Author Tardieu, François, 0000-0002-7287-0094
Author Neveu, Pascal
Contributor Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie (MISTEA) ; Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)
Contributor Écophysiologie des Plantes sous Stress environnementaux (LEPSE) ; Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)
Contributor Institute of Plant Genetics (IPG) ; Polish Academy of Sciences (PAN)
Contributor Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie (MISTEA) ; Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)
Contributor Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie (MISTEA) ; Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro) ; Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de la Recherche Agronomique (INRA)
Contributor Écophysiologie des Plantes sous Stress environnementaux (LEPSE) ; Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro) ; Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)
Contributor Domaine expérimental de Melgueil (MONTP MELGUEIL UE) ; Institut National de la Recherche Agronomique (INRA)
Contributor Unité de Recherche Génomique Info (URGI) ; Institut National de la Recherche Agronomique (INRA)
Contributor 'Infrastructure Biologie Sante' PHENOME-EMPHASIS project ; 'Programme d'Investissements d'Avenir' (PIA)
Contributor ANR-11-INBS-0012/11-INBS-0012,PHENOME,Centre français de phénomique végétale(2011)
Contributor David Romain
Contributor Hollebecq Jean-Eudes
Contributor Cabrera-Bosquet Llorenç
Contributor Ćwiek-Kupczyńska Hanna
Contributor François Tardieu
Contributor Pascal Neveu
Contributor Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie (MISTEA) ; Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro) ; Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)
Contributor Écophysiologie des Plantes sous Stress environnementaux (LEPSE) ; Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro) ; Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)
Publishing

Description: Attributes about the publishing venue (e.g. journal) and deposit location (e.g. repository)

Field Value
Collected From HAL-Inserm; ORCID; Datacite; Hal-Diderot; HAL - UPEC / UPEM; Mémoires en Sciences de l'Information et de la Communication; Microsoft Academic Graph; Europe PubMed Central; PubMed Central; ZENODO; figshare; UnpayWall; HAL-Pasteur; ProdInra; Hyper Article en Ligne; Crossref; FigShare; Sygma
Hosted By Zenodo; HAL-Inserm; Hal-Diderot; HAL - UPEC / UPEM; Mémoires en Sciences de l'Information et de la Communication; Europe PubMed Central; ZENODO; New Phytologist; figshare; HAL-Pasteur; ProdInra; Hyper Article en Ligne; FigShare
Publication Date 2019-09-16
Additional Info
Field Value
Country France
Format application/pdf
Language English
Resource Type Other literature type; Conference object; Article; Research; UNKNOWN
keyword système d'information
keyword sélection phénomique
keyword data integration;data science;Information System;interoperability;knowledge;ontology;open source;phenomics
keyword Phenotyping platform network, persistent identifier, variables names, interoperability
keyword plateforme de phénotypage
keyword Phenotyping platform network;persistent identifier;variables names;interoperability
system:type publication
Management Info
Field Value
Source https://science-innovation-policy.openaire.eu/search/publication?articleId=dedup_wf_001::2429813ce0e5258bbec82c66076b57e0
Author jsonws_user
Last Updated 24 December 2020, 17:12 (CET)
Created 24 December 2020, 17:12 (CET)