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Improving interoperability between phenomics and modelling communities by designing a Plant Modelling Ontology (PMO)

Saint Cast C., Lobet G., Cabrera-Bosquet L., Couvreur V., Pradal C., Muller B., Tardieu F., Draye X.. 2020. In : Kahlen Katrin (ed.), Chen Tsu-Wei (ed.), Fricke Andreas (ed.), Stützel Hartmut (ed.). Book of abstracts of the 9th International Conference on Functional-Structural Plant Models: FSPM2020, 5 - 9 October 2020. Hanovre : Institute of Horticultural Production Systems, p. 57-58. International Conference on Functional-Structural Plant Models (FSPM 2020), 2020-10-05/2020-10-09, (Allemagne).

In recent years, plant phenomics has produced massive datasets involving millions of images in experiments performed in the field and in controlled conditions, concerning hundreds of genotypes at different phenological stages and scales (Tardieu et al., 2017). In the future, information extracted from these datasets will be used increasingly as variables or parameters of mathematical and computational models, thereby broadening the scope of information extracted from phenomics data (Muller and Martre, 2019). Feeding such data to structural plant models (SPMs), functional plant models (FPMs), functional-structural plant models (FSPMs) and process-based crop simulation models (CSMs) in ad hoc pipelines has the potential to derive high-throughput predictions of integrated (e.g. yield) or functional traits (e.g. root system architecture) across a wide range of target environments or management practices (Chen et al., 2019). Unfortunately, the connectivity between these two communities is greatly limited by the absence of a common semantic framework and harmonized vocabulary. Currently, the terminology (e.g. objects, variables) used by these communities can be quite heterogeneous depending on the research discipline, scale and objective and even can differ between research groups. This limits the ability to accurately relate information within and across communities. A solution to facilitate the connection and the exchange of information is the use of a controlled and standardized vocabulary of common and internationally recognized descriptive terminology that can be connected and shared uniformly among the communities. The phenomics community has tackled these issues by reusing existing ontologies (e.g. Plant Ontology – PO or Plant Trait Ontology – TO), developing new standards (e.g. MIAPPE) as well as ontology-driven information systems (e.g. PHIS). Similarly, some initiatives have been developed within the crop modelling community such as the ICASA Master Variables Li

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