Implementation of Ontologies for Zebrafish Developmental Toxicity Screening
Toxicological evaluation of chemicals using early life stage zebrafish (Danio rerio) involves the observation and recording of altered phenotypes. Variability has been observed among researchers in phenotypes reported from similar studies. This variation and a lack of consistent data annotation indicate a need for harmonization of both terminology and data. When examined from a data science perspective, many apparent differences can be parsed into the same or similar endpoints whose measurements differ only in time, methodology, or nomenclature. Standardized nomenclature systems known as ontologies can be leveraged to integrate diverse data sets. Building on this premise, the NTP’s Systematic Evaluation of the Application of Zebrafish in Toxicology program coordinated a collaborative exercise to evaluate how the application of standardized phenotype terminology improved data consistency (Thessen et al. 2022). Zebrafish researchers were asked to assess images of zebrafish larvae for morphological malformations in two surveys. In the first survey, researchers were asked to annotate observed malformations using their own terminology. In the second survey, researchers were asked to annotate the images from a list of terms and definitions from the Zebrafish Phenotype Ontology. Analysis of the results suggested that the use of ontology terms increased consistency and decreased ambiguity, and that utilizing a common data standard should reduce the heterogeneity of reported terms and potentially increase agreement and repeatability between different laboratories.