R: Load mappings from Read to SNOMED CT into an R data.table

loadREADMAPS {Rdiagnosislist}

R Documentation

Load mappings from Read to SNOMED CT into an R data.table

Description

Creates a mapping table derived from NHS Digital Data Migration distribution. These tables are available from the Technology Reference Update Distribution: https://isd.digital.nhs.uk/trud/user/guest/group/0/pack/9/subpack/9/releases

Usage

loadREADMAPS(
  not_assured_rcsctmap_uk,
  not_assured_rctermsctmap_uk,
  assured_ctv3sctmap2_uk
)

Arguments

`not_assured_rcsctmap_uk`	File containing Read 2 codes mapped to SNOMED CT, in file: 'Not Clinically Assured/rcsctmap_uk_20200401000001.txt'
`not_assured_rctermsctmap_uk`	File containing Read 2 terms mapped to SNOMED CT, in file: 'Not Clinically Assured/rctermsctmap_uk_20200401000001.txt'
`assured_ctv3sctmap2_uk`	File containing CTV3 concepts and terms mapped to SNOMED CT, in file: 'Clinically Assured/ctv3sctmap2_uk_20200401000001.txt'

Details

The final release was in April 2020. The mapping tables are intended for converting entires in clinical records from Read Version 2 (Read 2) to SNOMED CT, and Clinical Terms Version 3 (CTV3) to SNOMED CT.

These maps can be used for converting SNOMED CT codelists into Read 2 or CTV3 format for running queries, such as to characterise patient phenotypes or identify patient populations for research. They cannot be used in the reverse direction (to map a Read 2/CTV3 codelist to SNOMED CT) because some of the SNOMED CT terms will be missed out, and the list will be incomplete.

This function uses the following three mapping files:

not_assured_rcsctmap_uk File containing Read 2 codes mapped to SNOMED CT, in file: 'Not Clinically Assured/rcsctmap_uk_20200401000001.txt'
not_assured_rctermsctmap_uk File containing Read 2 terms mapped to SNOMED CT, in file: 'Not Clinically Assured/rctermsctmap_uk_20200401000001.txt'
assured_ctv3sctmap2_uk File containing CTV3 concepts and terms mapped to SNOMED CT, in file: 'Clinically Assured/ctv3sctmap2_uk_20200401000001.txt'

The output data.table has the following columns:

conceptId integer64: SNOMED CT conceptId (primary key)
read2_code list: character list of 7-character Read 2 codes
read2_term list: character list of Read 2 terms
ctv3_concept list: character list of CTV3 concept codes
ctv3_termid list: character list of CTV3 term description codes

Value