Work

PBPKO: an ontology for standardizing and harmonizing physiologically based pharmacokinetic (PBPK) models

Year: 2026

Type: article

Abstract: Physiologically Based Pharmacokinetic (PBPK) Modelling have emerged as a critical method in pharmaceutical and environmental sciences. Despite its widespread adoption, inconsistent vocabulary used across models, software platforms, and literature remains a significant challenge. Such inconsistency limits the potential for data harmonization and model interoperability. This gap also hinders the adoption of machine-readable semantic technologies that could enhance PBPK model reporting, validation, and interoperability. To address this gap, we developed PBPKO (Physiologically Based Pharmacokinetic Ontology), a dedicated ontology for the kinetic modelling community. PBPKO captures mechanisms and terminology commonly used in PBPK modelling, including concepts related to physiological parameters, biochemical parameters, biological processes, enzymes, transporters, and related concepts. As of release of v2026-07-15, the ontology comprises 858 classes and 7 object properties native to PBPKO. OBO Foundry to support semantic interoperability within the broader biomedical ontology ecosystem, PBPKO is aligned with upper-level ontologies such as the Basic Formal Ontology (BFO) and the Relation Ontology (RO), and reuses terms from established resources including Gene Ontology (GO) and the Ontology for Biomedical Investigations (OBI). In this work, we further applied PBPKO to the annotation of PFAS multi-compartment PBPK models as a case study, while also highlighting the parallel development effort of “FAIR PBPK Inspector”, which leverages the ontology for model annotation. Together, these efforts support FAIR sharing of PBPK models and facilitate their regulatory acceptance through improved standardization. PBPK ontology is accessible with CC4 licences on https://github.com/InSilicoVida-Research-Lab/pbpko .

Source: Computational Toxicology

DOI: 10.1016/j.comtox.2026.100445