populate_dictionaries: Prepare Database for Dictionary Data Upload

In CEDARS: Simple and Efficient Pipeline for Electronic Health Record Annotation

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, 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.
port	MongoDB port.
database	MongoDB database name.

CEDARS documentation built on Feb. 7, 2021, 5:06 p.m.