Project deliverable Open Access

EMPHASIS-PREP Deliverable 4.1: Map of data practices

Tardieu, Francois; Alary, Pierre-Etienne; Usadel, Björn; van Zedde, Rick; Pridmore, Tony; Neveu, Pascal

Executive Summary


The objective of this deliverable is to map the current information systems and data management practices used in plant phenotyping installations and national infrastructures. The map of existing information systems is the base for identifying both the adequate level of abstraction that will allow connection between related variables at different scales and the minimum requirements needed for inclusion in an EMPHASIS information system.


Main results

The data management landscape in European plant phenotyping facilities is highly heterogeneous but in progress. At the beginning of EMPHASIS prep, there were as many methods to handle phenotypic data and metadata as there are plant phenotyping infrastructures. However, a common effort with the companion project EPPN2020 results in information systems as integrative as possible to specifically handle plant phenotypic data following FAIR rules. Briefly, large effort needs to be dedicated to the identification of plants, sensors and objects that are involved in experiments, in a persistent way that makes them "Findable" (FAIR). Data storage, as it stood at the beginning of EMPHASIS-PREP was closer to satisfying the "Reusable" rule, although datasets are most often not "Accessible". Metadata are stored in most infrastructures, although in a way that is only accessible by humans and not machine readable, thereby making difficult data "Reuse". The same applies to the way how traits were named, whereas international initiatives allow rapid progress in this topic. In most places, information systems were in their infancy at the beginning of the project, and still less "Interoperable". Rapid progress also occurs in this topic with the deployment of local information systems developed in the EMPHASIS community, which follow FAIR principle and are compatible with those of the genomic and of the modelling communities, and with the involvement of EMPHASIS in the European Open Science Cloud (EOSC).

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