Add SNOMED CT UK Monolith tables to CodeMiner database

Reads SNOMED CT UK Monolith Edition RF2 files and adds these tables to the active codeminer database. This is a convenience wrapper around read_snomed_ct_uk_monolith() that automatically calls add_lookup_table(), add_mapping_table(), and add_relationship_table() for each table.

The function processes lookup tables, mapping tables, and relationship tables from the SNOMED CT release and adds them to the database with their associated metadata.

Usage

add_snomed_ct_uk_monolith(
  path = get_snomed_ct_uk_monolith(),
  tables = c("sct_lookup", "sct_relationship", "sct_icd10", "sct_opcs4"),
  version = NULL,
  source = "https://isd.digital.nhs.uk/trud/",
  .icd10_refset_id = "999002271000000101",
  .opcs4_refset_id = "999002321000000109"
)

Arguments

path

Path to the SNOMED CT UK Monolith Edition. This can be either:

• A zip file (e.g., from get_snomed_ct_uk_monolith())

• An unzipped directory containing the subdirectories Snapshot/Terminology and Snapshot/Refset

Default uses get_snomed_ct_uk_monolith() to download the latest release.

tables

Character vector of table names to read and add. Available tables:

• Lookup table: "sct_lookup"

• Relationship table: "sct_relationship"

• Mapping tables: "sct_icd10", "sct_opcs4"

By default, adds all tables.

version

Character string specifying the version label for the SNOMED CT release. If not provided, it will be derived from the zip filename or folder name.

source

Character string specifying the source URL or description. Defaults to the NHS TRUD website.

.icd10_refset_id

Character string. The SNOMED CT Concept ID identifying the specific Reference Set (Refset) used for ICD-10 mappings. Defaults to "999002271000000101". This is an advanced parameter.

.opcs4_refset_id

Character string. The SNOMED CT Concept ID identifying the specific Reference Set (Refset) used for OPCS-4 mappings. Defaults to "999002321000000109". This is an advanced parameter.

Value

Invisibly returns the result from read_snomed_ct_uk_monolith() (a named list of tables with metadata).

Details

The function performs the following steps:

1. Calls read_snomed_ct_uk_monolith() to read the specified tables

2. Iterates through each table and table type (lookup/mapping/relationship)

3. Adds each table to the database using the appropriate add_* function

4. Returns the parsed data invisibly

This function requires an active database connection set up via build_database() or similar.

See also

• read_snomed_ct_uk_monolith() for reading without adding to database

• add_lookup_table(), add_mapping_table(), add_relationship_table()

• get_snomed_ct_uk_monolith() for downloading from NHS TRUD

Examples

if (FALSE) { # \dontrun{
# Set up database connection
build_database(db_path = "my_codes.db")

# Download latest release and add all tables
add_snomed_ct_uk_monolith()

# Add specific tables only
add_snomed_ct_uk_monolith(
  tables = c("sct_lookup", "sct_icd10")
)

# Use local zip file
snomed_zip <- "~/data/uk_sct2mo_41.3.0_20251217000001Z.zip"
add_snomed_ct_uk_monolith(path = snomed_zip)

# Use already-extracted directory
add_snomed_ct_uk_monolith(
  path = "~/data/SnomedCT_MonolithRF2_PRODUCTION_20251217T120000Z"
)
} # }

# Example with dummy data (for testing/demonstration)
if (FALSE) { # \dontrun{
build_database(db_path = tempfile(fileext = ".db"))
add_snomed_ct_uk_monolith(
  path = dummy_snomed_ct_uk_monolith_path()
)
} # }