Structured Application of Biological Ontologies to Annotate High-Throughput Screening Assays and their Targets of Activity
Jimmy Phuong · Carolina Digital Repository (University of North Carolina at Chapel Hill) · 2019
High-throughput screening (HTS) assays have changed the pace of chemical data collection, enabling assessments at various levels of biological relevance. EPA's ToxCast Program has 328 assays (experiments) generating 541 assay components (readouts), which produces 795 assay component endpoints (analyses), with intentions to increase the number of assays and the number of substances tested. As new assays are developed, it becomes a challenge to communicate what kind of data and features are associated with each assay. This report uses the BioAssay Ontology and other publicly available ontologies to produce the ToxCast Assay Annotation, a structured resource for descriptive information that uses controlled vocabulary to aid in the communication and use of ToxCast HTS assay data. Organized by 34 annotations including 'assay design type' and 'detection technology type', this structure allows for a concise reference to the pertinent attributes of an assay. Additionally, the perspective differences between the technological and intended target are separately captured. This structured annotation also allows for the identification of comparable ToxCast assay endpoints, and offers the potential to link with other HTS data repositories.