Description Usage Arguments Value Examples
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.
1 2 3 4 5 6 7 8 9 10 11 12 | mrconso_upload(
path,
language = "ENG",
subsets,
max_grams = 7,
uri_fun,
user,
password,
host,
port,
database
)
|
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. |
port |
MongoDB port. |
database |
MongoDB database name. |
Progress report of dictionary processing and upload.
1 2 3 4 5 6 7 | ## 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)
|
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