Contributing to PBPKO

Thank you for contributing to the Physiologically Based Pharmacokinetic Ontology.

The full contributor guide lives in the repository: CONTRIBUTING.md.

Quick start

PBPKO uses edit-file-only authoring in Protégé. All native terms and logical axioms are edited in a single file:

src/ontology/pbpko-edit.owl

Change	Where
New class, label, definition, parent	`pbpko-edit.owl` (Protégé)
Object property	`pbpko-edit.owl` (Protégé)
Logical axioms (`has_X some Y`)	`pbpko-edit.owl` (Protégé)
Structural foreign parent	`src/ontology/imports/<source>_terms.txt` + `make refresh-imports`
Cross-ontology xref (annotation only)	`src/mappings/pbpko-sssom.sssom.tsv`

Do not edit release files at repo root (pbpko.owl, imports/*.owl), archived TSV seeds (src/templates/archive/), or the legacy reference monolith (orginal pbpk owl/).

Quality control

From src/ontology/:

sh run.sh make test IMP=false PAT=false MIR=false

Commit messages

This repository uses Conventional Commits with commitlint. Allowed types include feat, fix, term, refactor, docs, ci, and chore.

Examples:

term: add menstrual plasma compartment
fix(import): add GO excretion term to go_terms.txt
docs: update import policy for edit-file workflow
chore(release): 2026-07-15

Requesting terms

Open an issue: https://github.com/InSilicoVida-Research-Lab/pbpko/issues/new/choose

Before requesting, search existing terms in OLS.

Releases

Release managers trigger dated OBO releases with:

git commit --allow-empty -m "chore(release): YYYY-MM-DD"
git push origin main

See Release workflow and CONTRIBUTING.md — Cutting a release.