populate_dictionaries: Prepare Database for Dictionary Data Upload

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

Prepare Database for Dictionary Data Upload

Description

Set ups collections for the UMLS MRCONSO/MRREL and NegEx files. MRCONSO consists of a list of UMLS concept unique identifiers (CUI's) with corresponding text strings and NegEx is a simple negation lexicon. The UMLS files are not provided as paer of the CEDARS package and must be dowloaded the NIH web site at https://www.nlm.nih.gov/research/umls/index.html. NegEx is included in CEDARS and its use is governed by the Apache License 2.0.

Usage

populate_dictionaries(
  uri_fun,
  user,
  password,
  host,
  replica_set,
  port,
  database
)

Arguments

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.

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