PBPKO Import Inventory
Foreign IRI usage audit for the modular import architecture (2026 ODK migration).
Structural imports (seed-based modules)
| IRI | Source | Usage | Module |
|---|---|---|---|
| OBI:0000658 | OBI | subClassOf parent (compartment, PBPK model) | obi_import.owl |
| GO:0008150 | GO | subClassOf parent (biological processes) | go_import.owl |
| GO:0008152 | GO | subClassOf parent (metabolic processes) | go_import.owl |
| GO:0007588 | GO | subClassOf parent (excretion) | go_import.owl |
| GO:0009987 | GO | subClassOf parent (cellular process) | go_import.owl |
| BFO:0000040 | BFO | subClassOf parent (material entity) | bfo_import.owl |
| BFO:0000029 | BFO | referenced class (site) | bfo_import.owl |
| BFO:0000051 | BFO | subPropertyOf parent (has_part) | bfo_import.owl |
| IAO:0000027 | IAO | referenced class (data item) | iao_import.owl |
| IAO:0000100 | IAO | referenced class (data set) | iao_import.owl |
| IAO:0000111–0000425 | IAO | annotation properties (12) | iao_import.owl |
| RO:0002161, 0002171, 0002175 | RO | annotation properties (3) | ro_import.owl |
OBCS terms are not imported — evaluation/statistical concepts are native PBPKO classes.
Mapping only (SSSOM, not imported)
| Source | Count | Usage |
|---|---|---|
| UBERON | 47 IRIs | skos:closeMatch on PBPKO compartment terms |
| SBO | 0000025, 0000027, 0000290, 0000005 | skos:exactMatch/closeMatch on parameters |
| VT | VT:0004020 | skos:closeMatch |
| FMA / BTO | recovered from historical release | skos:closeMatch on compartments |
| GO (annotation) | e.g. GO:0008015 | skos:exactMatch in vocab |
Removed (legacy merge artifacts)
- UBPROP:* annotation properties (from merged UBERON extract)
- Inlined foreign class declarations: SBO:0000027, GO:0007588, GO:0008152, BFO:0000029
- Full OBI and RO
owl:imports(replaced by slim modules)
Legacy PBPKO term ID fixes
| Old IRI | New ID | Label |
|---|---|---|
| ...#OWLClass_6a86eddf... | PBPKO:00652 | absorption rate constant (ka) |
| ...#OWLClass_91922c71... | PBPKO:00653 | glomerulus compartment |
Edit-file-only authoring (current)
Native terms are authored in
pbpko-edit.owl
(Protégé). ROBOT template components are disabled (use_templates: false).
| Artefact | Role |
|---|---|
pbpko-edit.owl |
Sole native source (classes, properties, axioms) |
src/templates/archive/*.tsv |
Archived legacy seeds (read-only) |
make export-term-views |
Generates read-only TSV views for spreadsheet review |
Recent term additions (2026-07)
27 new classes from the reference monolith pbpko_11_07.owl were integrated, including
kidney/liver sub-compartments, volume/fraction parameters, and amount-in-compartment terms
(PBPKO_02007–06068).