downloadOrphanet: Download Orphanet to assist with adding synonyms for rare...

In anoopshah/Rdiagnosislist: Manipulate SNOMED CT Diagnosis Lists

Download Orphanet to assist with adding synonyms for rare diseases

Description

Downloads the Orphanet nomenclature pack and converts it into a format to be appended to MANUAL_SYNONYMS and used in concept database creation.

Usage

downloadOrphanet(
  orphanet_url =
    "https://www.orphadata.com/data/nomenclature/packs/Orphanet_Nomenclature_Pack_EN.zip",
  masterfile_name = NULL,
  SNOMED = getSNOMED()
)

Arguments

orphanet_url	URL or filepath to Orphanet zip file
masterfile_name	name of xls file containing Orphanet synonyms. If omitted, it is assumed to be the only file with 'MasterFile' in its name, and the program will search for it in the Orphanet zip file.
SNOMED	environment containing SNOMED CT dictionary

Value

data.table containing Orphanet synonyms in the format

References

https://www.orphadata.com/pack-nomenclature/

See Also

downloadWordnet, MANUAL_SYNONYMS

Other CDB functions: addComposeLookupToCDB(), addWordnet(), batchDecompose(), createCDB(), downloadWordnet()

Examples

# Not run
# ORPHANET <- downloadOrphanet()

anoopshah/Rdiagnosislist documentation built on March 29, 2025, 10:46 a.m.