Dealing with multi-source and multi-scale information in plant phenomics: the ontology-driven Phenotyping Hybrid Information System

The New Phytologist
Pascal NeveuLlorenç Cabrera-Bosquet

Abstract

Phenomic datasets need to be accessible to the scientific community. Their reanalysis requires tracing relevant information on thousands of plants, sensors and events. The open-source Phenotyping Hybrid Information System (PHIS) is proposed for plant phenotyping experiments in various categories of installations (field, glasshouse). It unambiguously identifies all objects and traits in an experiment and establishes their relations via ontologies and semantics that apply to both field and controlled conditions. For instance, the genotype is declared for a plant or plot and is associated with all objects related to it. Events such as successive plant positions, anomalies and annotations are associated with objects so they can be easily retrieved. Its ontology-driven architecture is a powerful tool for integrating and managing data from multiple experiments and platforms, for creating relationships between objects and enriching datasets with knowledge and metadata. It interoperates with external resources via web services, thereby allowing data integration into other systems; for example, modelling platforms or external databases. It has the potential for rapid diffusion because of its ability to integrate, manage and visualize mu...Continue Reading

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Citations

Jan 8, 2019·Journal of Experimental Botany·Andrew J MillarTomasz Zielinski
Apr 26, 2019·Journal of Experimental Botany·Santiago Alvarez PradoNadine Hilgert
Feb 26, 2020·Annual Review of Plant Biology·Michelle WattUlrich Schurr
May 12, 2020·Plant & Cell Physiology·Keiichi MochidaTakashi Hirayama
May 22, 2019·Nature Genetics·Emilie J MilletFrançois Tardieu
Feb 29, 2020·Scientific Data·Hanna Ćwiek-KupczyńskaPaweł Krajewski
Mar 15, 2020·The New Phytologist·Evangelia A PapoutsoglouCyril Pommier
Apr 30, 2019·Plant Phenomics : a Science Partner Journal·C PommierA F Adam-Blondon
Apr 15, 2021·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Jacob I MarshDavid Edwards
Jul 2, 2021·Plant Phenomics : a Science Partner Journal·Wei GuoBaskar Ganapathysubramanian
Jul 25, 2021·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Anna LangstroffAstrid Junker
Apr 21, 2019·Plant Science : an International Journal of Experimental Plant Biology·Thomas RoitschEric S Ober
Aug 25, 2021·The Plant Journal : for Cell and Molecular Biology·Elisa BellucciRoberto Papa

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Methods Mentioned

BETA
dissection
Phenotyping

Software Mentioned

Mac
OEPO
Linux
ongo DB
ongo
Python
R
Phenotyping Hybrid Information System ( PHIS )
JAX
Java

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