Create a SemsqlConn connection — semsql

Opens a connection to a SemanticSQL SQLite database, either by supplying a direct file path or by referencing a short ontology name that is retrieved and cached via BiocFileCache.

Usage

semsql_connect(
  db_path = NULL,
  ontology_prefix = NULL,
  ontology = NULL,
  cache = BiocFileCache::BiocFileCache(),
  validate = TRUE,
  ...
)

Arguments

db_path: character(1) or NULL. Path to an existing SQLite database file. Either db_path or ontology must be supplied.
ontology_prefix: character(1) or NULL. Primary CURIE prefix for the ontology (e.g. "CL"). If NULL and ontology is supplied, defaults to toupper(ontology); otherwise auto-detected from the database.
ontology: character(1) or NULL. Short name of an INCAtools ontology (e.g. "cl", "go"). If supplied, retrieve_semsql_conn() is called to locate or download the cached database.
cache: a BiocFileCache instance used when ontology is supplied. Defaults to BiocFileCache::BiocFileCache().
validate: logical(1) if TRUE (the default value) the ontology code is checked against available Semantic SQL resources at INCAtools. Set to FALSE if using off line.
...: passed to retrieve_semsql_conn() and ultimately to utils::download.file().

Value

A SemsqlConn() object.

Note

The connection has flag SQLITE_RO for read-only access. There will be an attempt to validate the ontology tag that is supplied, against all available Semantic SQL resources available at INCAtools bucket. Function fails if a match cannot be made, which in general requires network access.

Examples

# by ontology short name (downloads if not cached)
goref <- semsql_connect(ontology = "go")
#> Connected to SemanticSQL database: /home/runner/.cache/R/BiocFileCache/1988cc470f_go.db
#> Primary ontology prefix: GO
goref
#> <SemsqlConn>  prefix: GO  | labeled terms: 88,849 
disconnect(goref)
#> Disconnected from '1988cc470f_go.db'