mrconso_upload: Upload UMLS Dictionary

In simon-hans/CEDARS: Simple and Efficient Pipeline for Electronic Health Record Annotation

Upload UMLS Dictionary

Description

Prepares and uploads UMLS MRCONSO.RRF file. This file is not included in the CEDARS package and can be obtained on the NIH web site at https://www.nlm.nih.gov/research/umls/index.html.

Usage

mrconso_upload(
  path,
  language = "ENG",
  subsets,
  max_grams = 7,
  uri_fun,
  user,
  password,
  host,
  replica_set,
  port,
  database
)

Arguments

path	Path to file MRCONSO.RRF.
language	Language of biomedical lexicon, default is English (ENG).
subsets	Character vector of lexicon subsets to retain. UMLS is quite large so most applications can use only a few lexicon subsets.
max_grams	Maximum length of token in grams. Tokens above the thresold length will not be retained. Empirically, a value of 7 suffices for most applications.
uri_fun	Uniform resource identifier (URI) string generating function for MongoDB credentials.
user	MongoDB user name.
password	MongoDB user password.
host	MongoDB host server.
replica_set	MongoDB replica set, if indicated.
port	MongoDB port.
database	MongoDB database name.

Value

Progress report of dictionary processing and upload.

Examples

## Not run: 
mrconso_upload(path = 'dictionaries/MRCONSO.RRF', language = 'ENG', subsets = c('SNOMEDCT_US',
'MTHICD9', 'ICD9CM', 'ICD10', 'ICD10CM', 'DSM-5', 'MSH', 'RXNORM', 'NCI'), max_grams = 7,
user = 'John', password = 'db_password_1234', host = 'server1234', port = NA,
database = 'TEST_PROJECT')

## End(Not run)

simon-hans/CEDARS documentation built on Feb. 14, 2024, 3:16 a.m.