Commands

Reference

Commands, extension points, and environment variables.

Command-line interfaces

agonto --help
agonto inspect ONTOLOGY.owl
agonto search ONTOLOGY.owl "natural-language text"
agonto query ONTOLOGY.owl "question"
agonto chat ONTOLOGY.owl [--log]
agonto memory clear ONTOLOGY.owl
agonto run --help
agonto-hypergraph --help
agonto-lint ONTOLOGY.ttl
./scripts/run_experiments.sh SUITE --dry-run

Supported ontology inputs

The path-based CLI detects OWL/RDF XML (.owl, .rdf, .xml), Turtle, N3, N-Triples, TriG, TriX, and JSON-LD. Use --format when a file extension is ambiguous.

Public extension points

API	Purpose
`create_web_search(name, **options)`	Select static, dataset, MediaWiki, Google CSE, or a registered provider
`register_web_search(plugin, factory)`	Add a visible project-specific search provider
`create_vector_index(name, **options)`	Create exact, ANN, DiskANN, or vector-database indexes
`register_vector_index(name, factory)`	Register a vector-index adapter
`OnlineOntologyRefiner.refine(graph, updates)`	Apply streamed ontology updates and return deferred validation cases
`Parser(path).to_ontology()`	Parse supported RDF or relation-dataset formats through one facade
`create_model_router()`	Choose `local`, `standard`, or `careful` once per run when `AGONTO_MODEL_ROUTING=jev`
`create_tool_gate()`	Block configured external tool calls when `AGONTO_TOOL_GATE=jev`

Repository layout

`src/agentic_ontologist/`	Installable library
`tests/`	Automated tests
`examples/`	Runnable examples
`experiments/`	Runner and maintained configurations
`scripts/`	Maintained experiment entry points
`data/`	Ontology and benchmark data
`docs/`	This static instruction website
`results/`	Ignored generated artifacts

Jev environment

Variable	Purpose
`JEV_API_KEY`	TypeSafe key. Copied to `TYPESAFE_API_KEY` when that variable is empty.
`AGONTO_CONTEXT_HARNESS`	Set to `jev` to score retrieved context. `AGONTO_CONTEXT_MODE` is `shadow` or `live`.
`AGONTO_MODEL_ROUTING`	Set to `jev` to route each run. Pair with `AGONTO_ROUTE_LOCAL`, `AGONTO_ROUTE_STANDARD`, and `AGONTO_ROUTE_CAREFUL`.
`AGONTO_TOOL_GATE`	Set to `jev` to gate tools. `AGONTO_GATED_TOOLS` lists names, and `AGONTO_TOOL_RISK_THRESHOLD` defaults to `0.5`.

Routing fails open to LLM_MODEL. An enabled tool gate fails closed for gated tools only. Query text and redacted tool arguments are sent to TypeSafe. Decisions appear on the existing trace as model.routed and tool.blocked.

Security

pre-commit run --all-files
gitleaks git --config .gitleaks.toml

Store credentials only in .env. Never place secrets in source, experiment configs, logs, manifests, or data files.

Authors

Lam Nguyen
Ethan Frakes