Detect alignment candidates (owl:equivalentClass, skos:exactMatch, rdfs:subClassOf) between two ontologies using label similarity, property overlap, parent overlap, instance overlap, restriction patterns, and graph neighborhood. Auto-applies high-confidence matches above threshold.

Accept or reject an alignment candidate to improve future confidence scoring. Stores feedback in align_feedback table for self-calibrating weights.

Apply the last plan. Modes: 'safe' (clear+reload, checks monitor), 'force' (ignores monitor), 'migrate' (adds owl:equivalentClass/Property bridges for renames).

Clear all triples from the in-memory ontology store

Convert an RDF file between formats: turtle, ntriples, rdfxml, nquads, trig

Look up clinical crosswalk mappings for a code and system (ICD10, SNOMED, MeSH). Requires data/crosswalks.parquet.

Compare two ontology files and show added/removed triples

Check if one class is subsumed by another using DL tableaux reasoning. Returns whether sub_class is a subclass of super_class, with justification.

Explain why a class is unsatisfiable using DL tableaux reasoning. Returns an explanation trace showing the logical contradictions that make the class impossible to instantiate.

Detect drift between two ontology versions. Returns added/removed terms, likely renames with confidence scores, and drift velocity.

Generate text + structural Poincaré embeddings for all classes in the loaded ontology. Requires the embedding model (run open-ontologies init to download). Embeddings enable semantic search via onto_search and improve alignment accuracy.

Enforce design patterns on the loaded ontology. Built-in packs: 'generic' (orphan classes, missing domain/range/label), 'boro' (BORO 4D patterns), 'value_partition' (disjoint/covering checks). Also runs any custom rules stored for the pack.

Accept or dismiss an enforce violation to improve future enforce runs. Dismissed violations are suppressed after 3 dismissals. Stores feedback for self-calibrating compliance.

Enrich an ontology class with a SKOS mapping triple from the clinical crosswalks.

Convenience pipeline: ingest data → validate with SHACL → run OWL reasoning, all in one call. Combines onto_ingest + onto_shacl + onto_reason.

List all saved ontology version snapshots

Resolve and load all owl:imports from the currently loaded ontology

Import a PostgreSQL database schema as an OWL ontology. Introspects tables, columns, primary keys, and foreign keys, then generates OWL classes, datatype/object properties, and cardinality restrictions.

Parse a structured data file (CSV, JSON, NDJSON, XML, YAML, XLSX, Parquet) into RDF triples and load into the ontology store. Optionally uses a mapping config to control field-to-predicate mapping.

Get the compact lineage log for the current or specified session.

Check an ontology for quality issues: missing labels, comments, domains, ranges

Accept or dismiss a lint issue to improve future lint runs. Dismissed issues are suppressed after 3 dismissals. Stores feedback for self-calibrating severity.

Load an RDF file into the in-memory ontology store for querying

Lock IRIs to prevent removal during plan/apply. Locked IRIs will show as violations in plan output.

Generate a mapping config by inspecting a data file's schema against the currently loaded ontology. Returns a JSON mapping that can be reviewed and passed to onto_ingest.

Run active monitoring watchers. Optionally add new watchers via inline JSON. Returns ok/alert/blocked status with details.

Clear the monitor blocked flag, allowing apply operations to proceed.

Terraform-style plan: diff current store against proposed Turtle. Shows added/removed classes/properties, blast radius, risk score, and locked IRI violations.

Fetch an ontology from a remote URL or SPARQL endpoint and load it into the store

Push the current ontology store to a remote SPARQL endpoint

Run a SPARQL query against the loaded ontology store

Run inference over the loaded ontology. Profiles: 'rdfs' (subclass, domain/range), 'owl-rl' (+ transitive/symmetric/inverse, sameAs, equivalentClass), 'owl-rl-ext' (+ someValuesFrom, allValuesFrom, hasValue, intersectionOf, unionOf), 'owl-dl' (Full OWL2-DL SHOIQ tableaux: satisfiability, classification, qualified number restrictions with node merging, inverse/symmetric roles, functional properties, parallel agent-based classification, explanation traces, ABox reasoning). Materializes inferred triples.

Restore the ontology store to a previously saved version

Save the current ontology store to a file

Semantic search over the loaded ontology using natural language. Returns the most similar classes by text meaning, structural position, or both. Requires onto_embed to have been run first.

Validate the loaded ontology data against SHACL shapes. Checks cardinality (minCount/maxCount), datatypes, and class constraints. Returns a conformance report with violations.

Compute embedding similarity between two IRIs — returns cosine similarity (text), Poincaré distance (structural), and product score.

Get statistics about the loaded ontology (triple count, classes, properties, individuals)

Returns health status of the Open Ontologies server

Validate RDF/OWL syntax. Accepts a file path or inline Turtle content.

Validate all class labels in the loaded ontology against clinical crosswalk data. Shows which terms match known clinical codes.

Save a named snapshot of the current ontology store