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

Abstract

Summary 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 multi‐source and multi‐scale data, but also because it is based on 10 yr of trial and error in our groups.

Plant phenotyping relevance

植物フェノタイピング実験の多ソース・多スケールデータを統合、管理、可視化するオントロジー駆動システム自体が中心的な方法論的貢献である。

Code and data availability

The paper's PHIS software (the ontology-driven phenotyping information system that manages the paper's phenotyping data and analysis) is publicly released by the authors on GitHub under an open license. The application-example datasets are stated to be available at http://www.phis.inra.fr/under, but that exact URL is不在