Semantic standards of external exposome data

Abstract

An individual's health and conditions are associated with a complex interplay between the individual's genetics and his or her exposures to both internal and external environments. Much attention has been placed on characterizing of the genome in the past; nevertheless, genetics only account for about 10% of an individual's health conditions, while the remaining appears to be determined by environmental factors and gene-environment interactions. To comprehensively understand the causes of diseases and prevent them, environmental exposures, especially the external exposome, need to be systematically explored. However, the heterogeneity of the external exposome data sources (e.g., same exposure variables using different nomenclature in different data sources, or vice versa, two variables have the same or similar name but measure different exposures in reality) increases the difficulty of analyzing and understanding the associations between environmental exposures and health outcomes. To solve the issue, the development of semantic standards using an ontology-driven approach is inevitable because ontologies can (1) provide a unambiguous and consistent understanding of the variables in heterogeneous data sources, and (2) explicitly express and model the context of the variables and relationships between those variables. We conducted a review of existing ontology for the external exposome and found only four relevant ontologies. Further, the four existing ontologies are limited: they (1) often ignored the spatiotemporal characteristics of external exposome data, and (2) were developed in isolation from other conceptual frameworks (e.g., the socioecological model and the social determinants of health). Moving forward, the combination of multi-domain and multi-scale data (i.e., genome, phenome and exposome at different granularity) and different conceptual frameworks is the basis of health outcomes research in the future.

Keywords: Environmental exposure; External exposome; Ontology; Semantic standard.

Fig. 1.

A conceptual framework of the exposome. *The exposure to Education can either be a specific external exposome (i.e., the individual’s own education history) or general external exposome (i.e., the education environment where the individual lives)

Fig. 2.

The ontological representation for education attainment at the individual-level and census tract-level. Note that the blue rectangular represents the class, the circle represents the individual of the class, and the green rectangular represents the data values (literals). (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

Fig. 3.

The screening process of ontology designed for the external exposome.