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PBPK Ontology (PBPKO)

The Physiologically Based Pharmacokinetic Ontology (PBPKO) provides a dedicated vocabulary for describing PBPK models, compartments, parameters, processes, and related pharmacokinetic concepts. It supports consistent reporting and automation in pharmaceutical and environmental life-science applications.

Resource URL
Documentation (this site) https://insilicovida-research-lab.github.io/pbpko/
GitHub repository https://github.com/InSilicoVida-Research-Lab/pbpko
Latest Zenodo release (v2026-07-15) https://doi.org/10.5281/zenodo.21372240
How to cite cite.md
OBO Foundry PURL http://purl.obolibrary.org/obo/pbpko.owl
OLS browser https://www.ebi.ac.uk/ols4/ontologies/pbpko
OntoBee http://www.ontobee.org/ontology/PBPKO
Issue tracker https://github.com/InSilicoVida-Research-Lab/pbpko/issues

Release artefacts

Current releases are built with the Ontology Development Kit (ODK) and published at the repository root:

File Purpose
pbpko.owl Primary release (full ontology with slim imports)
pbpko.obo OBO-format release
pbpko-base.owl Native PBPKO terms only — best for review
pbpko-full.owl Full artefact variant
mappings/pbpko-sssom.sssom.tsv Cross-ontology SSSOM mappings

Dated versions are tagged vYYYY-MM-DD (OBO convention) and resolve via PURL under /releases/.

Architecture (ODK migration)

PBPKO follows modern OBO modular practice:

  • Edit file — all native PBPKO classes, properties, labels, definitions, parents, and logical axioms are authored in src/ontology/pbpko-edit.owl using Protégé.
  • Slim imports — only required foreign terms are extracted into per-source modules (obi, go, bfo, ro, iao), not full upstream ontologies.
  • SSSOM mappings — annotation-only cross-references to UBERON, FMA, BTO, SBO, and others live in the mappings file, not as imports.
  • Automated QC and release — GitHub Actions runs ROBOT validation, commits release artefacts, and publishes dated GitHub/Zenodo releases.

See Import policy and Import inventory for details.

Editing workflow

  1. Edit pbpko-edit.owl in Protégé.
  2. Run QC from src/ontology/: 
    cd src/ontology
sh run.sh make test IMP=false PAT=false MIR=false
  3. Open a pull request against main.

Optional spreadsheet views (read-only exports):

cd src/ontology
sh run.sh make export-term-views

Full contributor guide: Contributing and the ODK editors workflow.

Licence

PBPKO is released under CC BY 4.0.