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Wrapper that runs the four per-ontology generation skills in sequence on a single ontology directory — README, citings, internal mermaid, external mermaid. Use this for the
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Based on SOC occupation classification
Given two existing functors going in opposite directions between two ontologies, scaffold an Adjunction impl with unit/counit and the gap-analysis test suite. Used after functor-author for both directions, when the goal is to detect missing distinctions between scales.
Given two pr4xis ontologies, scaffold a Functor impl that maps the source ontology's entities to the target's, with map_morphism and the check_functor_laws test. Produces a draft for human review — the user fills in the cases the skill can't infer with confidence.
The full ontology authoring workflow as a single skill. Take a topic or source paper, research it, extract concepts/relations/axioms, scaffold the ontology with define_ontology!, scaffold candidate functors and adjunctions to existing related ontologies, run the laws check, run gap analysis, and report. Produces a draft for human review — does not auto-commit.
Generate a citings.md file for one pr4xis ontology directory by extracting source-paper citation comments from the surrounding code. Produces a structured bibliography with full citations, DOIs/URLs, and one-line annotations of which axioms each source grounds. Where the code references a paper without a full bibliography entry, scaffold a placeholder for human filling.
Generate a mermaid diagram showing one pr4xis ontology's external connections — the functors and adjunctions that link it to other ontologies in the workspace. Inserts the diagram into the per-ontology README between auto-generated markers.
Generate a mermaid diagram showing the internal structure of one pr4xis ontology — its concepts (entities) as nodes and its relationships (morphisms) as edges, with arrow styles distinguishing taxonomy / mereology / causation / opposition. Inserts the diagram into the per-ontology README between auto-generated markers.
| name | per-ontology-rollout |
| description | Wrapper that runs the four per-ontology generation skills in sequence on a single ontology directory — README, citings, internal mermaid, external mermaid. Use this for the |
Wrapper skill that runs the full per-ontology generation pack on one ontology directory. Composes four sibling skills.
When you want to bring a single ontology directory to the #57/#59 standard (README + citings + two mermaid diagrams) in one shot. For batch processing all 106 ontologies, invoke this wrapper repeatedly with different paths.
crates/domains/src/--overwrite flag to overwrite existing files (default: refuse and ask per skill)In order, with each step's failure halting the rest:
Validate the input: confirm the directory exists, contains ontology.rs, and the file has a define_ontology! block. If not, stop with an error.
Invoke per-ontology-readme to generate the README skeleton. This produces the file with the structural sections; the mermaid diagrams will be added by steps 4 and 5.
Invoke per-ontology-citings to extract citation comments from the code and produce citings.md next to the README.
Invoke per-ontology-mermaid-internal to generate the internal-structure diagram and insert it into the README between auto-generated markers.
Invoke per-ontology-mermaid-external to generate the cross-ontology connections diagram and insert it into the same README.
Relocate cited PDFs into <ontology-dir>/papers/. For each primary source in the newly generated citings.md that resolves to a PDF in docs/papers/, git mv the PDF into <ontology-dir>/papers/ (create the directory if needed) and update the citings.md link to papers/<filename>.pdf. If the same PDF is cited by multiple ontologies, leave it in docs/papers/ and link across — do not duplicate.
Run cargo test -p pr4xis-domains <ontology-name> to confirm the new files (which are markdown, not Rust) haven't somehow disturbed any build script or test runner.
A consolidated summary from all four sub-skills:
--overwrite is set)crates/domains/src/natural/biomedical/ contains many child ontologies): only operate on the directory passed in. Recursing is the caller's job, not this skill's.This wrapper exists for ergonomics — running four skills with one command. It does not add logic beyond sequencing. If you need finer control (e.g., regenerate only the diagrams), invoke the individual sibling skills directly.