Phenomics

Phenomics is the study of phenotypic dynamics defining phenotype from the quantum to the ecosystem scales and its emergence as a discipline is attributed to the Plant Sciences. Phenomics uses phenotyping methods to systematically measure phenotypic traits that characterize an organism. Traits can vary their state over space and time, due to development, aging, metamorphosis or interactions with the environment. As such, phenomics investigates the dynamics generated by phenes constituting the phenome to form measurable phenotypes and their variation across all spatio-temporal scales in living systems, including plants, microbes, animals, and humans.

The definition of the phenome has evolved over the last few decades. Its first definition dates to 1949 as "... the sum total of extragenic, non-autoreproductive portions of the cell, whether cytoplasmic or nuclear. The phenome would be the material basis of the phenotype, just as the genome is the material basis of the genotype.". Subsequently, the phenome was associated with an infinite set of traits that cannot be fully determined and was attributed to the evolutionary biologist Michel Soule. Later definitions, however, contradicted this initial notion of the phenome in which phenes are the fundamental building blocks of the phenotype, which implied a finite space. A recent definition unified both concepts by defining the phenome as a set phenes that denote an infinite set of transformations of unit traits that describe the dynamics forming a phenotype with respect to environmental interactions and any chosen set of trait measurements.

All phenome definitions enable researchers to better understand concepts like pleiotropy and phenotypic plasticity. Yet, the major technical challenges involve improving, both qualitatively and quantitatively, the capacity to measure phenomes and relate these measurements to biological and environmental processes.

Phenomics is also a transdisciplinary scientific discipline that unites elements from the life, formal, and physical sciences. The phenotyping process involves the formulation of formal systems with their mathematical foundation to analyze and model phenotyping data that reflects the underlying biological multi-scale dynamics forming a phenotype. An essential aspect of this process is the quantitative and qualitative parametrization of phenes to capture phenotypic variation. However, as of September 2026, there is no undergraduate or graduate program to study phenomics specifically, yet its profession, the phenomicist, has been defined in basic and applied contexts.