loadSNOMED {Rdiagnosislist}

Load SNOMED CT files from a folder(s) into R data.table objects

Description

Identifies relevant SNOMED CT files from the folder structure of a SNOMED CT distribution. This includes the core 'Snapshot' tables mapping tables from the 'Refset' folder and the history substitution table and query table. The relevant tables are loaded into an R environment, which can be saved and then easily retrieved for future use. Files from two folders (e.g. International and UK versions) can be loaded together, and are automatically appended by the function.

Usage

loadSNOMED(folders, active_only = TRUE, version = NULL)

Arguments

folders

Vector of folder paths containing SNOMED CT files

active_only

Whether to limit to current (active) SNOMED CT concepts

version

Version description. If NULL, it is derived from the folder paths and expressed in the form: INTdate & UKdate

Details

The SNOMED CT files are available from the NHS Digital Technology Reference Update Distribution: https://isd.digital.nhs.uk/trud/user/guest/group/0/home

(Note: May 2022 - This function needs to be updated to use the latest SNOMED CT TRUD versions including the SNOMED CT definitions).

Value

An environment containing data.table objects: CONCEPT, DESCRIPTION, RELATIONSHIP, STATEDRELATIONSHIP, REFSET, SIMPLEMAP, EXTENDEDMAP, HISTORY (optional), QUERY (optional)

See Also

loadREADMAPS, CONCEPT, DESCRIPTION, RELATIONSHIP, STATEDRELATIONSHIP, REFSET, SIMPLEMAP, EXTENDEDMAP, QUERY, HISTORY sampleSNOMED, getSNOMED, exportSNOMEDenvir

Examples

# Create a TEST environment and load the sample dictionaries
TEST <- sampleSNOMED()

# Export to temporary directory
exportSNOMEDenvir(TEST, tempdir())

# Try to import using the loadSNOMED function
TEST2 <- loadSNOMED(tempdir(), active_only = FALSE)

# Check that reimported SNOMED dictionary is the same as the original
all.equal(TEST$CONCEPT, TEST2$CONCEPT)
all.equal(TEST$DESCRIPTION, TEST2$DESCRIPTION)
all.equal(TEST$RELATIONSHIP, TEST2$RELATIONSHIP)
all.equal(TEST$STATEDRELATIONSHIP, TEST2$STATEDRELATIONSHIP)
all.equal(TEST$REFSET, TEST2$REFSET)
all.equal(TEST$SIMPLEMAP, TEST2$SIMPLEMAP)
all.equal(TEST$EXTENDEDMAP, TEST2$EXTENDEDMAP)