CompTox Ontology: Leveraging Knowledge Graphs for PFAS Monitoring and Decision-Making

Per- and polyfluoroalkyl substances (PFAS) are persistent environmental contaminants that require integrated, semantically structured representations of chemical identity, classification, and properties to support integrated contaminant monitoring and analysis. This work presents the CompTox ontology, an expert-guided ontology describing commonly analyzed PFAS and designed to support PFAS data integration and querying. The ontology organizes PFAS hierarchically according to key physicochemical characteristics and incorporates authoritative identifiers and properties from EPA's CompTox Chemicals Dashboard. Individual PFAS are annotated with core chemical identifiers, including DTXSID, CASRN, InChIKey, and SMILES; with physicochemical attributes such as molecular mass, carbon chain length, and functional group information; and with observed or predicted environmental fate and transport and toxicological information. The ontology was constructed using the Knowledge Acquisition and Representation Methodology (KNARM), employing a template-driven workflow implemented with the ROBOT tool to generate an OWL-formatted ontology. An expert-guided hierarchy captures major PFAS classes, including fluorotelomers, perfluoroalkyl acids (both Perfluoroalkyl Carboxylic and Sulfonic Acids), and perfluoroalkyl ether acids. Human-readable IRIs and SKOS alternative labels enhance usability. The ontology helps facilitate integrated querying and analysis of PFAS contamination within the SAWGraph knowledge graphs but also serves as a flexible and extensible framework for unified chemical identification and classification.