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Read the SNOMED CT UK Monolith Edition into R

Source: R/read_snomed_ct_uk_monolith.R
read_snomed_ct_uk_monolith.Rd

Reads the Terminology and Refset snapshot tables from a local copy of the SNOMED CT UK Monolith Edition release files.

Usage

read_snomed_ct_uk_monolith(
  path,
  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

A character string giving the path to the SNOMED CT UK Monolith Edition. This can be either:

  • A zip file (e.g., from get_snomed_ct_uk_monolith()) - will be extracted to a temporary directory on-demand

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

tables

Character vector of table names to read. Available tables are:

  • Lookup table: "sct_lookup"

  • Relationship table: "sct_relationship"

  • Mapping tables: "sct_icd10", "sct_opcs4"

By default, all tables are read.

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" (UK Clinical Extension Extended Map to ICD-10). This is an advanced parameter that typically does not need to be changed.

.opcs4_refset_id

Character string. The SNOMED CT Concept ID identifying the specific Reference Set (Refset) used for OPCS-4 mappings. Defaults to "999002321000000109" (UK Clinical Extension Extended Map to OPCS-4). This is an advanced parameter that typically does not need to be changed.

Value

A named list with elements corresponding to requested tables, each containing tables and metadata:

  • sct_lookup: Lookup table with SNOMED CT concepts and descriptions. Contains table (data.table) and metadata (list).

  • sct_relationship: Relationship table with concept relationships. Contains table (data.table) and metadata (list).

  • sct_icd10: Mapping table with SNOMED CT to ICD-10 mappings. Contains table (data.table) and metadata (list).

  • sct_opcs4: Mapping table with SNOMED CT to OPCS-4 mappings. Contains table (data.table) and metadata (list).

Details

This function imports the key data files as data.table objects, performs basic normalisation, and constructs joined tables for concept descriptions and ICD-10/OPCS-4 mappings.

For more information on the SNOMED CT UK Monolith Edition, see the NHS TRUD website.

Examples

if (FALSE) { # \dontrun{
# Read from a zip file (extracts on-demand)
snomed_zip <- get_snomed_ct_uk_monolith()
snomed <- read_snomed_ct_uk_monolith(snomed_zip)

# Read from an already-extracted directory
snomed <- read_snomed_ct_uk_monolith("~/SNOMEDCT_Release_UK")

# Read only specific tables
snomed <- read_snomed_ct_uk_monolith(
  path = snomed_zip,
  tables = c("sct_lookup", "sct_icd10")
)

# Access lookup table and metadata
sct_lookup <- snomed$sct_lookup$lookup$table
sct_metadata <- snomed$sct_lookup$lookup$metadata

# Specify custom version
snomed <- read_snomed_ct_uk_monolith(
  path = "~/SNOMEDCT_Release_UK",
  version = "UK_20240101"
)
} # }