tool-reference.md

Tool reference

Every tool this server registers, with one line each. Generated from the #[tool(...)] attributes in src/server.rs and gated by tests/tool_reference_test.rs, so a tool added without a line here fails the build rather than going unlisted.

The front page does not list these. It shows one loop — plan, apply, drift, certify, rollback — because that is what this is for, and a reader who meets a catalogue first cannot tell what it is for. Everything below keeps its code and its own documentation; it loses its place above the fold.

Tool profiles

A profile is a named subset of this catalogue sized for one job. A client that is aligning two vocabularies has no use for most of what is listed below, and every tool it has no use for is one more chance to call the wrong one. Select one with --tool-profile <name> on serve or serve-http, with OPEN_ONTOLOGIES_TOOL_PROFILE, or with profile under [tools] in config.toml, in that order of precedence. The default is full, which is every tool this build can serve, so a deployment that selects nothing keeps exactly the surface it has today.

• full: every tool this build can serve. The default.
• authoring: write and edit an ontology. Validate, lint, enforce patterns, version, extract modules, and pull in vocabularies to build on.
• validation: judge data against an ontology. SHACL shapes, closed-world vocabulary checks, shape induction, what the rule table can see, and the provenance of what the graph claims.
• reasoning: derive consequences and produce the artefacts that can be checked. Certificates, justifications, first-order export and proof checking, DL tableaux, model finding.
• alignment: relate two vocabularies. Alignment candidates and their feedback loop, clinical crosswalks, and the embeddings the scorer uses.
• governance: change an ontology in production and answer for it afterwards. Plan, apply, lock, drift, monitor, policy, packs, conservativity and the lineage trail.
• data: land external data in the graph and keep it there. File and SQL ingest, schema induction, mapping, CDC watermarks, and the two temporal clocks.
• planning: act on the graph under laws. Registered actions, BC+ invariants and defaults, PDDL compilation and plan validation.
• retrieval: ground a model on the graph. Neighbourhood slices, modules, community skeletons, schema-guided extraction, and whether a slice kept what the answer rests on.
• evaluation: score the thing rather than run it. Competency questions, mmRAG and OAEI metrics, and the borderline-verdict loop.

Every profile carries the same floor: onto_status, onto_validate, onto_load, onto_query, onto_stats and onto_clear. Nothing else in any profile can do anything until a graph is loaded, and a client that cannot check what it loaded or clear a bad load is stuck inside its own profile.

An unknown profile name refuses to start rather than falling back to full. Publishing the whole catalogue to a deployment that asked for one job's worth of it, silently, because someone mistyped a flag, is the one failure worth declining to boot over.

The older --tools-allow and --tools-deny axis still works and is applied after the profile. Both axes only ever narrow, so naming a tool in --tools-allow that the selected profile does not carry does not bring it back. The two ask different questions: a profile asks what a client is here to do, and the allow/deny groups ask what a caller may be trusted to do.

The profiles are defined in src/toolfilter.rs. No size is written on this page, and that is deliberate: tests/toolfilter_profiles_test.rs measures them from the router and fails if any registered tool belongs to no profile, so the next tool added to src/server.rs carries a failing test until its author files it. A size typed here would be a second copy of a number nothing derives. Selecting a profile and calling onto_status reports the one in force and what it withheld.

Every tool

122 tools.

Tool	What it does
borderline_partition	Generalised borderline-pair partitioning (#37, NORA NeurIPS 2025).
borderline_record_verdict	Persist an orchestrator's verdict on a borderline candidate (#37).
eval_rag	mmRAG benchmark scoring (#41, ISWC 2025).
eval_rag_mmrag	Parse a full mmRAG dataset JSON and score it in one call.
graph_projection_entailment_check	Does a retrieved slice still support the claims an answer rests on? Supply the claims as Turtle (goals_ttl); for each one this reports whether the projection entails it exactly when the source does, under one pinned rule profile, with a machine-checked Lean certificate (OOCert.certificate_sound) for each claim the…
graph_projection_lossy_check	Audit a projected Turtle slice against the loaded ontology's full neighbourhood of the seed IRIs.
onto_action_applicable	Evaluate a registered action's SPARQL preconditions against the loaded graph under the given parameter bindings.
onto_action_apply	Apply a registered action's effects with the given parameter bindings.
onto_action_apply_concurrent	Fire a tick of concurrent BC+ actions atomically.
onto_action_list	List the names of all action schemas registered in this server's Dynamics store.
onto_action_register	Persist a named action schema (Dynamics layer #43).
onto_align	Detect alignment candidates (owl:equivalentClass, skos:exactMatch, rdfs:subClassOf) between two ontologies or SKOS vocabularies (owl:Class and skos:Concept) using label similarity, property overlap, parent overlap, instance overlap, restriction patterns, and graph neighborhood.
onto_align_feedback	Accept or reject an alignment candidate to improve future confidence scoring.
onto_align_flora	End-to-end FLORA alignment (#38).
onto_align_fuzzy	FLORA-style fuzzy-logic alignment adjudication (#38, ISWC 2025 Best Paper).
onto_apply	Apply a plan produced by onto_plan, defaulting to the most recent one.
onto_cache_list	List all cached ontologies with metadata (name, source_path, triple_count, source_mtime, source_size, cache_path, compiled_at, last_access_at) and runtime flags (is_active, in_memory).
onto_cache_remove	Remove a cached ontology by name.
onto_cache_status	Inspect the compile cache: active ontology, all cached entries, and the cache configuration (TTL, auto_refresh, dir).
onto_certify_action	CIVeX-style causal certificate for a proposed state-changing ontology action.
onto_classify_el	Classify the loaded ontology by OWL 2 EL completion (#30, #324); complete: true only when the input is inside EL.
onto_clear	Clear all triples from the in-memory ontology store and unload the active registry slot (cache file is preserved)
onto_closure_diff	Which CONCLUSIONS a projection preserves, with no goals supplied.
onto_coevolve_dependency_graph	Build the shape→OWL-dependency map for a SHACL document.
onto_communities	Detect communities in the loaded entity graph and return a SKELETON per community: size, top members by degree, internal relations, and the bridges connecting it to other communities.
onto_conservative_check	Does adding these axioms change anything the ontology ALREADY said? Reasons base and base+extension to a fixpoint under one rule table and reports closure(base ∪ extension) minus closure(base), restricted to triples every name of which the base already used.
onto_convert	Convert an ontology file to turtle, ntriples, rdfxml, nquads, trig or ofn (OWL 2 functional syntax, with every unexported construct named and counted).
onto_cq_run	Run a batch of competency questions (CQs) against the loaded ontology (#29).
onto_cq_verdicts_list	List all stored verdicts for a CQ id, most-recent first.
onto_crosswalk	Look up clinical crosswalk mappings for a code and system (ICD10, SNOMED, MeSH).
onto_default_apply	Apply every registered BC+ default-value law whose condition currently holds.
onto_default_register	Register a BC+ default-value law.
onto_defects	Check the ONTOLOGY itself, before any data is judged against it.
onto_diff	Compare two ontology files and show added/removed triples
onto_dl_check	Check if one class is subsumed by another using DL tableaux reasoning.
onto_dl_explain	Explain why a class is unsatisfiable using DL tableaux reasoning.
onto_dlp_boundary	Ask which of YOUR axioms the rule engine can actually SEE, before trusting a reasoning result.
onto_drift	Detect drift between two ontology versions.
onto_embed	Generate text + structural Poincaré embeddings for all classes in the loaded ontology.
onto_enforce	Enforce design patterns on the loaded ontology.
onto_enforce_feedback	Accept or dismiss an enforce violation to improve future enforce runs.
onto_enrich	Enrich an ontology class with a SKOS mapping triple from the clinical crosswalks.
onto_eval_alignment	OAEI-style P/R/F1 scoring (#31).
onto_extend	Convenience pipeline: ingest data → validate with SHACL → run OWL reasoning, all in one call.
onto_extract_scaffold	Build a schema-guided structured-extraction scaffold for a class (#28, OntoGPT SPIRES MCP-native).
onto_extract_validate	Validate an LLM-supplied extraction (JSON array of objects) against a scaffold previously emitted by onto_extract_scaffold.
onto_fol_export	Export the loaded ontology as first-order logic, so it can be handed to the automated-theorem-proving ecosystem.
onto_fol_model	Find a finite model of the loaded ontology and CHECK IT, so the answer names what it rests on.
onto_fol_prove	Run a first-order prover, READ the derivation it prints back, and RE-CHECK what can honestly be re-checked.
onto_history	List all saved ontology version snapshots
onto_hnsw_build	Build (or rebuild) the HNSW cosine index over the loaded text embeddings with explicit ef_construction and ef_search parameters.
onto_import	Resolve and load all owl:imports from the currently loaded ontology
onto_import_schema	Import a relational database schema as an OWL ontology.
onto_induce	ONE SHEET IN, ONE ONTOLOGY OUT: induce an OWL class, typed properties, a SHACL shape and a loading mapping from one data sheet, with the evidence for every line.
onto_ingest	Parse a structured data file (CSV, JSON, NDJSON, XML, YAML, XLSX, Parquet) into RDF triples and load into the ontology store.
onto_invariant_check	Evaluate every registered BC+ invariant against the current graph and return the names + descriptions of any that fail.
onto_invariant_list	List all registered BC+ static causal laws (invariants).
onto_invariant_register	Persist a BC+ static causal law (SPARQL ASK invariant).
onto_invariant_remove	Remove a registered BC+ invariant by name.
onto_justify	AXIOM PINPOINTING: which ASSERTED triples are responsible for a conclusion, or for a contradiction.
onto_lineage	Get the compact lineage log for the current or specified session.
onto_lint	Check an ontology for quality issues: missing labels, comments, domains, ranges
onto_lint_feedback	Accept or dismiss a lint issue to improve future lint runs.
onto_load	Load an ontology file or inline Turtle content into the in-memory ontology store.
onto_lock	Lock IRIs to prevent removal during plan/apply.
onto_map	Generate a mapping config by inspecting a data file's schema against the currently loaded ontology.
onto_marketplace	Browse and install ontologies from the curated catalogue of 33 W3C/ISO/industry standards plus the open community-pack registry (community/registry.json, fetched at runtime; override with OPEN_ONTOLOGIES_COMMUNITY_REGISTRY).
onto_module_extract	A MODULE over a signature, not a slice: the smallest subset of the axioms syntactic locality can justify, such that every entailment of the WHOLE ontology over those IRIs is still an entailment of the subset.
onto_monitor	Run active monitoring watchers.
onto_monitor_clear	Clear the monitor blocked flag, allowing apply operations to proceed.
onto_ossie_import	Compile an Apache Ossie (incubating, formerly Open Semantic Interchange) ontology document into OWL 2 DL + SHACL, and optionally load it into the active store so every other tool here works on it.
onto_owl_shacl_coevolve_check	Combined OWL+SHACL validation (#33, K-CAP 2025).
onto_owl_shacl_coevolve_incremental	Incremental coevolve check (#33 follow-on, K-CAP 2025).
onto_pack	Write the loaded graph, its verification evidence and, optionally, its derivation certificate to a portable, versioned pack: sorted N-Triples plus a manifest (name, version, counts, timestamp, sha256, the lint/enforce results recorded at pack time, and a content_sha256 covering the graph AND the certificate together). Pass certificate_dir to carry the proof.
onto_plan	Terraform-style plan: diff current store against proposed Turtle.
onto_plan_classical	Invoke Fast Downward as a subprocess on a precompiled PDDL domain + problem (#50).
onto_plan_compile_pddl	Compile a PDDL domain from registered Dynamics action schemas (#43) plus a problem instance from the loaded graph and a goal Turtle slice (#45 Planner stub).
onto_plan_validate	Validate a candidate plan (sequence of registered-action steps) against the loaded graph WITHOUT mutating the real store.
onto_plugin_call	Invoke a tool on an installed WASM plugin.
onto_plugin_list	Discover installed WASM plugins and the tools they provide.
onto_policy_check	Evaluate a proposed action's target IRIs against every registered policy rule.
onto_policy_list	List all registered ARGOS policy rules.
onto_policy_register	Register an ARGOS-style policy rule (#40, ISWC 2025 WOP).
onto_provenance	PROVENANCE SEMIRINGS: the algebraic expression over the ASSERTED triples that a derived triple carries.
onto_pull	Fetch an ontology from a remote URL or SPARQL endpoint and load it into the store
onto_push	Push the current ontology store to a remote SPARQL endpoint
onto_query	Run a SPARQL query against the loaded ontology store.
onto_reason	Run inference over the loaded ontology.
onto_reason_incremental	Derive the consequences of newly added triples WITHOUT recomputing the whole closure.
onto_recompile	Force-recompile an ontology from its source file, ignoring the on-disk cache.
onto_repo_list	List RDF/OWL files in the configured ontology repository directories ([general] ontology_dirs).
onto_repo_load	Load an ontology from one of the configured repository directories ([general] ontology_dirs) into the active store.
onto_rollback	Restore the ontology store to a previously saved version
onto_rules_import	Read rules written in a STANDARD rule syntax into the Horn rule table onto_reason evaluates with rules_file and the proved-sound Lean checker verifies with lake exe oo-horn check.
onto_save	Save the current ontology store to a file
onto_search	Semantic search over the loaded ontology using natural language.
onto_segment_retrieve	Retrieve a TBox-slice neighbourhood of seed IRIs for grounding LLM reasoning (#34, SEMANTiCS 2025 GrOWL-RAG).
onto_shacl	Validate the loaded ontology data against SHACL shapes.
onto_shacl_check	Dry-run structural check on proposed SHACL shapes against the loaded ontology.
onto_shape_combinatorics	Enumerate the property-combination lattice for a class (#36, K-CAP 2025 Kastor).
onto_shape_induce	Kastor-style data-driven SHACL shape induction (#36, K-CAP 2025).
onto_similarity	Compute embedding similarity between two IRIs — returns cosine similarity (text), Poincaré distance (structural), and product score.
onto_sql_ingest	Run a SQL query against a relational backbone (PostgreSQL or DuckDB) and ingest the resulting rows into the triple store as RDF.
onto_sql_sync_reset	Clear the recorded CDC watermark for a sync_key.
onto_sql_sync_state	Read the recorded CDC watermark for a sync_key.
onto_sql_sync_states_list	List every recorded CDC sync state across all sync_keys.
onto_stats	Get statistics about the loaded ontology (triple count, classes, properties, individuals)
onto_status	Returns health status of the Open Ontologies server
onto_support_check	Check whether the graph's claims are backed by the sources they cite.
onto_support_report	Summarise provenance quality: the unsourced-claim rate over the whole graph, and the support rate across the claims judged so far.
onto_support_verdict	Record whether a cited source supports a claim: supported, refuted, or unrelated.
onto_temporal_conflicts	Disjointness violations that claim OVERLAPPING validity, separated from those that do not.
onto_temporal_query	Run a SPARQL graph pattern against only the graphs in temporal scope: what the graph said at a given valid time, as known at a given recorded time.
onto_temporal_snapshot	Which named graphs are in scope at a point in time, and which are excluded and why.
onto_trace_label	Label each step of a reasoning trace against the rule table, with a machine-checked verdict per step: entailed, not_entailed, or outside_the_fragment, plus the local answer over the premises the step itself cited.
onto_unload	Unload an ontology from memory.
onto_unpack	Load a pack written by onto_pack, refusing it if either digest does not match, and re-run this machine's Lean checker over the certificate the pack carries. A refused certificate blocks the load; an absent checker reports that nothing was checked, which is not a pass.
onto_validate	Validate RDF/OWL syntax.
onto_validate_clinical	Validate all class labels in the loaded ontology against clinical crosswalk data.
onto_verify_cq	Persist an LLM-supplied (or human-supplied) verdict on a CQ result (#39, ISWC 2025 Lippolis).
onto_version	Save a named snapshot of the current ontology store
onto_vocab_check	Closed-world vocabulary check on a Turtle DATA graph: verify that every predicate and every rdf:type class used in the data is actually DECLARED in the loaded ontology.