Package index • ducksemantics

Ontology Graphs

ducksemantics_connect(): Connect to a DuckDB semantic store
ducksemantics_init(): Initialize semantic graph tables
ducksemantics_schema_sql(): DuckDB semantic graph schema
ducksemantics_tables(): Semantic table names
ducksemantics_read_obo(): Read an OBO ontology into graph relations
ducksemantics_write_obo(): Write an OBO ontology into the graph
ducksemantics_write_graph(): Write ontology graph rows
ducksemantics_projection_sql(): Project edge-shaped data to graph SQL
ducksemantics_closure_sql(): Materialize transitive closure SQL
ducksemantics_normalize(): Normalize semantic text
ducksemantics_tokens(): Tokenize source text
ducksemantics_index_aliases(): Build the lexical alias index
ducksemantics_annotate(): Generate lexical HPO/ontology candidates

HPO Observations

ducksemantics_hpo_observation_contract(): HPO observation contract
ducksemantics_hpo_observations(): Validate accepted HPO observations against source documents

Monarch and Literature Relations

ducksemantics_monarch_release_catalog(): Validate a typed Monarch release catalog
ducksemantics_monarch_project_pack(): Project one attached, dated Monarch annotation pack
ducksemantics_monarch_import(): Import caller-supplied Monarch relations
ducksemantics_monarch_query(): Select one cataloged Monarch release
ducksemantics_monarch_gene_disease_holdout_audit(): Audit a historical Monarch gene-disease holdout
ducksemantics_literature_snapshot_catalog(): Validate an append-only literature snapshot catalog
ducksemantics_literature_retrieve(): Retrieve exact literature spans from append-only caller-owned relations

Semantic Retrieval

ducksemantics_embedding_batch(): Construct embedding rows
ducksemantics_write_embeddings(): Store embedding rows in DuckDB
ducksemantics_embedding_search(): Search dense embeddings
ducksemantics_materialize_embedding_index(): Materialize a fixed-dimension embedding table
ducksemantics_token_embedding_batch(): Construct token embedding rows
ducksemantics_token_embedding_batch_from_provider(): Construct token embedding rows from a provider
ducksemantics_write_token_embeddings(): Store token embedding rows in DuckDB
ducksemantics_late_interaction_search(): Exact token-level late-interaction search

Provider Protocols and Judgments

DucksemanticsAnnotator: Grounding-provider protocol
DucksemanticsPromptRunner: Prompt-runner provider protocol
DucksemanticsJudgmentParser: Judgment-parser provider protocol
DucksemanticsEmbeddingProvider: Embedding-provider protocol
DucksemanticsTokenEmbeddingProvider: Token-embedding-provider protocol
ducksemantics_run() ducksemantics_embed() ducksemantics_token_embed() ducksemantics_parse() ducksemantics_ground(): Provider protocol generics
ducksemantics_lexical_annotator(): Create the default lexical grounding provider
ducksemantics_prompt_runner(): Wrap a prompt function as a prompt provider
ducksemantics_embedding_provider(): Wrap an embedding function as an embedding provider
ducksemantics_token_embedding_provider(): Wrap a token embedding function as a token provider
ducksemantics_json_judgment_parser(): Create a JSON judgment parser
ducksemantics_bebel_runner(): Create a BebeLM prompt provider
ducksemantics_embeddinggemma_provider(): Create an EmbeddingGemma provider
ducksemantics_colbert_provider(): Create a native ColBERT provider
ducksemantics_bebel_tool_judgment_parser(): Create a BebeLM tool-call judgment parser
ducksemantics_default_judgment_instructions(): Default source-grounded judgment instructions
ducksemantics_judgment_prompt(): Build a source-grounded judgment prompt
ducksemantics_judge(): Judge lexical candidates with a provider
ducksemantics_record_judgments(): Record source-grounded judgments