Abstract
GnpIS is a data repository for plant phenomics that stores whole field and greenhouse experimental data including environment measures. It allows long-term access to datasets following the FAIR principles: Findable, Accessible, Interoperable, and Reusable, by using a flexible and original approach. It is based on a generic and ontology driven data model and an innovative software architecture that uncouples data integration, storage, and querying. It takes advantage of international standards including the Crop Ontology, MIAPPE, and the Breeding API. GnpIS allows handling data for a wide range of species and experiment types, including multiannual perennial plants experimental network or annual plant trials with either raw data, i.e., direct measures, or computed traits. It also ensures the integration and the interoperability among phenotyping datasets and with genotyping data. This is achieved through a careful curation and annotation of the key resources conducted in close collaboration with the communities providing data. Our repository follows the Open Science data publication principles by ensuring citability of each dataset. Finally, GnpIS compliance with international standards enables its interoperability with other data repositories hence allowing data links between phenotype and other data types. GnpIS can therefore contribute to emerging international federations of information systems.
Highlights
Plant phenotyping regroups all the observations and measures that can be made on a precisely identified plant material in a characterized environment
In some cases, such as dense time series with up to hundreds of measures, multispectral images, or Near Infrared Spectrometry (NIRS) spectra, the data can be stored as files or can be cross-referenced to specialized platform information systems
It is designed to allow data access either by full experiment or by aggregating data across several experiments. It allows the linking of phenotypic data with genetic and genomic data for Quantitative Trait Loci (QTLs), Genome Wide Association Studies (GWAS), and gene annotations published in GnpIS
Summary
Plant phenotyping regroups all the observations and measures that can be made on a precisely identified plant material in a characterized environment This very general definition of phenomics [1] includes diverse types of properties and variables measured at different physical [2] and temporal scales, ranging from field observation of plant populations to molecular cell characterizations, including for some research community metabolomics or gene expression. The acquisition of these data is conducted in various experimental facilities like greenhouses, fields, phenotyping networks, or natural sites. The resulting rich wealth of data is usually formatted in a very heterogeneous manner and is difficult to integrate automatically
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