Project one attached, dated Monarch annotation pack — ducksemantics_monarch_project

Projects an already attached read-only official Monarch DuckDB pack into connection-local temporary views. It never attaches, downloads, collects, copies, rewrites, or merges pack rows. source_catalog must name an attached DuckDB catalog whose main schema contains the official denormalized_edges, nodes, information_content, and node_has_phenotype tables. The edge table is checked before any view is made, including its scalar role categories, provider-serialized text negation, and array provenance fields. The official required nodes, node_has_phenotype, and information_content projection columns/types are also validated.

Usage

ducksemantics_monarch_project_pack(
  conn,
  source_catalog,
  releases,
  provider_id,
  release_id,
  prefix = "semantic_monarch"
)

Arguments

conn: Valid DBI connection with the pack already attached.
source_catalog: Attached DuckDB catalog name, not the current catalog.
releases: Typed Monarch release catalog or caller-owned catalog table. This binds provider/release semantics; the caller must verify the immutable file receipt before attaching the pack.
provider_id: Exact provider identity in releases.
release_id: Exact, dated release identity in releases; "latest" is rejected.
prefix: Safe unqualified prefix for temporary view names.

Value

A data frame naming the seven connection-local temporary views, with relation, view_name, provider_id, and release_id columns. It does not return pack contents.

Details

associations retains every source edge and all source columns exactly, then adds the selected provider and release. Each role view is likewise a total projection: it retains raw source columns and adds normalized role columns, source_subject, source_object, source_direction, and association_status. Only supported_subject_to_object and supported_object_to_subject rows have non-missing normalized roles. missing_endpoint, missing_predicate, malformed_negation, missing_role_category, malformed_role_category, negated, and unsupported_orientation are not support. negation_status separately distinguishes not_provided, not_negated, negated, and malformed: Monarch omits the optional qualifier on many positive assertion rows, so omission is retained but does not erase the assertion. In particular, a missing predicate never becomes a causal predicate.