The Environmental Conditions, Treatments, and Exposures Ontology (ECTO): connecting toxicology and exposure to human health and beyond

Journal of Biomedical Semantics

Database

Christopher J. Mungall¹  Charles Schmitt²  Cynthia J. Grondin³  Lauren E. Chan⁴  Melissa A. Haendel⁵  Anne E. Thessen⁵  Nicolas Matentzoglu⁶  Peter N. Robinson⁷  Nicole Vasilevsky⁸  Julie A. McMurry⁸  William D. Duncan⁹ 

[1] Lawrence Berkeley National Laboratory, 94720, Berkeley, CA, USA;National Institute of Environmental Health Sciences, 27709, Durham, NC, USA;North Carolina State University, 27965, Raleigh, NC, USA;Oregon State University, 97331, Corvallis, OR, USA;Oregon State University, 97331, Corvallis, OR, USA;University of Colorado Anschutz Medical Campus, 80054, Aurora, CO, USA;Semanticly, Athens, Greece;The Jackson Laboratory for Genomic Medicine, 06032, Farmington, CT, USA;University of Colorado Anschutz Medical Campus, 80054, Aurora, CO, USA;University of Florida, 32610, Gainesville, FL, USA;

关键词: Biomedical ontology;    Environmental exposures;    Environmental health;   

DOI  :  10.1186/s13326-023-00283-x

 received in 2022-04-15, accepted in 2023-02-03,  发布年份 2023

来源: Springer

【 摘 要 】

BackgroundEvaluating the impact of environmental exposures on organism health is a key goal of modern biomedicine and is critically important in an age of greater pollution and chemicals in our environment. Environmental health utilizes many different research methods and generates a variety of data types. However, to date, no comprehensive database represents the full spectrum of environmental health data. Due to a lack of interoperability between databases, tools for integrating these resources are needed. In this manuscript we present the Environmental Conditions, Treatments, and Exposures Ontology (ECTO), a species-agnostic ontology focused on exposure events that occur as a result of natural and experimental processes, such as diet, work, or research activities. ECTO is intended for use in harmonizing environmental health data resources to support cross-study integration and inference for mechanism discovery.Methods and findingsECTO is an ontology designed for describing organismal exposures such as toxicological research, environmental variables, dietary features, and patient-reported data from surveys. ECTO utilizes the base model established within the Exposure Ontology (ExO). ECTO is developed using a combination of manual curation and Dead Simple OWL Design Patterns (DOSDP), and contains over 2700 environmental exposure terms, and incorporates chemical and environmental ontologies. ECTO is an Open Biological and Biomedical Ontology (OBO) Foundry ontology that is designed for interoperability, reuse, and axiomatization with other ontologies. ECTO terms have been utilized in axioms within the Mondo Disease Ontology to represent diseases caused or influenced by environmental factors, as well as for survey encoding for the Personalized Environment and Genes Study (PEGS).ConclusionsWe constructed ECTO to meet Open Biological and Biomedical Ontology (OBO) Foundry principles to increase translation opportunities between environmental health and other areas of biology. ECTO has a growing community of contributors consisting of toxicologists, public health epidemiologists, and health care providers to provide the necessary expertise for areas that have been identified previously as gaps.

【 授权许可】

CC BY   
© The Author(s) 2023

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