Import a PubMed baseline or update XML source — rclinvarbitration_import

Streams concrete PubMed baseline or update XML through the package-owned libxml2 DuckDB extension. PMID is the article authority; DOI and PMCID are retained as ordinary article identifiers when supplied. Each import appends immutable source-versioned rows. DeleteCitation appends an explicit deleted article event; it does not erase earlier article or child facts.

Usage

rclinvarbitration_import_pubmed(
  con,
  path,
  source_id,
  source_kind = c("baseline", "update")
)

Arguments

con: A DuckDB DBI connection with rclinvarbitration_enable() loaded.
path: Path to a PubMed baseline or update XML or XML.GZ file.
source_id: Immutable source snapshot or update label.
source_kind: Whether path is a "baseline" or "update" source.

Value

Invisibly returns source identity, typed source ordinal, and scalar row counts.

Details

The caller's current DuckDB or DuckLake catalog owns the resulting pubmed_* relations. pubmed_current_* selects the latest non-deleted event per PMID, while pubmed_*_as_of(source_id) table macros select a historical cutoff. This importer does not fetch Europe PMC or perform semantic screening.