mrrel_upload: Upload UMLS Relationships

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

Upload UMLS Relationships

Description

Prepares and uploads UMLS MRREL.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. It is very large and not currently used by CEDARS.

Usage

mrrel_upload(path, uri_fun, user, password, host, replica_set, port, database)

Arguments

path	Path to file MRREL.RRF.
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 UMLS processing and upload.

Examples

## Not run: 
mrrel_upload(path = 'dictionaries/MRREL.RRF', uri_fun = mongo_uri_standard, 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.