PBPKO Import Policy

Principles

Edit file — pbpko-edit.owl is the sole authoring source for all native PBPKO classes, object properties, labels, definitions, parents, metadata, and logical axioms (edited in Protégé).
TSV views are export-only — run make export-term-views to generate pbpko-vocab-view.tsv / pbpko-properties-view.tsv for spreadsheet review; legacy seeds live in src/templates/archive/.
Foreign terms live in slim import modules — one module per source ontology, generated from seed lists via ODK SLME/BOT.
Cross-references use SSSOM mappings — not imports — for annotation-only links (UBERON, FMA, BTO, SBO, GO xrefs).
Reviewers should browse the base artifact — pbpko-base.owl (native PBPKO terms only).

Import vs map decision tree

Is the foreign term used as rdfs:subClassOf / rdfs:subPropertyOf in PBPKO?
├── YES → add to src/ontology/imports/<source>_terms.txt, run make refresh-imports
└── NO  → add to src/mappings/pbpko-sssom.sssom.tsv (skos:exactMatch or skos:closeMatch)

Current import modules (5)

Module	Seed file	Source
`obi_import.owl`	`obi_terms.txt`	OBI (1 term: data representation model)
`go_import.owl`	`go_terms.txt`	GO (4 ADME process terms)
`bfo_import.owl`	`bfo_terms.txt`	BFO (3 terms)
`ro_import.owl`	`ro_terms.txt`	RO (3 annotation properties)
`iao_import.owl`	`iao_terms.txt`	IAO (12 annotation properties + 2 classes)

OBCS is not imported — no PBPKO structural axioms reference OBCS terms; statistical evaluation terms are native PBPKO classes.

UBERON, FMA, BTO, SBO are mapped only via src/mappings/pbpko-sssom.sssom.tsv.

Build commands (ODK)

From src/ontology/:

cd src/ontology
sh run.sh make refresh-imports     # regenerate import modules (requires network)
sh run.sh make export-term-views   # export read-only TSV views from edit file
sh run.sh make prepare_release     # full release pipeline
sh run.sh make test                # QC on edit and base artifacts

Adding a new external term

Decide import vs map (see decision tree above).
If import: add IRI to src/ontology/imports/<source>_terms.txt, run sh run.sh make refresh-imports.
If map: add row to src/mappings/pbpko-sssom.sssom.tsv.
Run sh run.sh make prepare_release.
Update import-inventory.md.

Release artifacts

File	Purpose
`pbpko.owl`	Full release with imports merged
`pbpko-base.owl`	Native PBPKO terms only — use for review
`imports/*_import.owl`	Slim per-source modules
`mappings/pbpko-sssom.sssom.tsv`	Cross-ontology mappings