| Title: | PBPKO : an ontology for standardizing and harmonizing physiologically based pharmacokinetic (PBPK) models |
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| Authors: | ID Kumar, Saurav (Author)
ID Panov, Panče, Institut "Jožef Stefan" (Author)
ID Kumar, Vikas (Author), et al. |
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| Files: |  URL - Source URL, visit https://www.sciencedirect.com/science/article/pii/S2468111326000460?via%3Dihub
 PDF - Presentation file, download (4,94 MB)
MD5: 67D28B39FD6771705291EA9013FC3391
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| Language: | English |
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| Typology: | 1.01 - Original Scientific Article |
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| Organization: |  IJS - Jožef Stefan Institute
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| 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. 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). |
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| Keywords: | mathematical modelling, visualization types, physiologically based pharmacokinetic model, semantics, ontology |
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| Publication status: | Published |
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| Publication version: | Version of Record |
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| Submitted for review: | 11.05.2026 |
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| Article acceptance date: | 11.08.2026 |
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| Publication date: | 12.08.2026 |
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| Publisher: | Elsevier |
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| Year of publishing: | 2026 |
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| Number of pages: | str. 1-9 |
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| Numbering: | Vol. 39, 100445 |
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| Source: | Nizozemska |
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| PID: | 20.500.12556/DiRROS-32248  |
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| UDC: | 519.6 |
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| ISSN on article: | 2468-1113 |
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| DOI: | 10.1016/j.comtox.2026.100445 |
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| COBISS.SI-ID: | 288214787 |
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| Copyright: | © 2026 The Authors. |
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| Note: | Nasl. z nasl. zaslona;
Opis vira z dne 19. 8. 2026;
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| Publication date in DiRROS: | 02.09.2026 |
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| Views: | 33 |
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| Downloads: | 20 |
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| Metadata: |    |
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