populate_annotations: Prepare Database for NLP Annotation

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

Description

Creates 'ANNOTATIONS' and 'PATIENTS' collections, assuming main DB collection and notes were already set up.This is necessary before launching the NLP annotation process.

Usage

populate_annotations(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.