create_project: Create a New CEDARS Project

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

Description

Creates a new MongoDB database and collections needed for a CEDARS annotation project. The MongoDB account used must have sufficient privileges.

Usage

create_project(
  uri_fun,
  user,
  password,
  host,
  port,
  database,
  project_name,
  investigator_name
)

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.
project_name	Research or QA project name.
investigator_name	Investigator name.

Value

Confirmation that requested operation was completed, or error message if attempt failed.

Examples

# The code below creates an instance of CEDARS project on a public test MongoDB cluster, populated
# with fictitious EHR corpora.

# MongoDB credentials
db_user_name <- "testUser"
db_user_pw <- "testPW"
db_host <- "cedars.yvjp6.mongodb.net"
db_port <- NA

# Using standard MongoDB URL format
uri_fun <- mongo_uri_standard

# Name for MongoDB database which will contain the CEDARS project
# In this case we generate a random name
mongo_database <- find_project_name()

# We create the database and all required collections on a test cluster
create_project(uri_fun, db_user_name, db_user_pw, db_host, db_port, mongo_database,
"CEDARS Example Project", "Dr Smith")

# Adding one CEDARS end user
add_end_user(uri_fun, db_user_name, db_user_pw, db_host, db_port, mongo_database, "John",
"strongpassword")

## Not run: 

# Negex is included with CEDARS and required for assessment of negation
negex_upload(uri_fun, db_user_name, db_user_pw, db_host, db_port, mongo_database)

## End(Not run)

# Uploading the small simulated collection of EHR corpora
upload_notes(uri_fun, db_user_name, db_user_pw, db_host, db_port, mongo_database,
simulated_patients)

# This is a simple query which will report all sentences with a word starting in
# "bleed" or "hem", or an exact match for "bled"
search_query <- "bleed* OR hem* OR bled"
use_negation <- TRUE
hide_duplicates <- TRUE
skip_after_event <- TRUE
save_query(uri_fun, db_user_name, db_user_pw, db_host, db_port, mongo_database, search_query,
use_negation, hide_duplicates, skip_after_event)

## Not run: 

# Running the NLP annotations on EHR corpora
# We are only using one core, for large datasets parallel processing is faster
automatic_NLP_processor(NA, "latin1", "udpipe", uri_fun, db_user_name, db_user_pw,
db_host, db_port, mongo_database, max_n_grams_length = 0, negex_depth = 6, select_cores = 1)

# Pre-searching based on query
# This is optional but will speed-up the interface
pre_search(patient_vect = NA, uri_fun, db_user_name, db_user_pw, db_host, db_port, mongo_database)

# Start the CEDARS GUI locally
# Your user name is "John", password is "strongpassword"
# Once you have entered those credentials, click on button "ENTER NEW DATE" and CEDARS will
# seek the first record to annotate
# Try out the interface, adjudicating sentences, entering event dates, comments, moving
# between sentences and searching for records
# Once you have entered some data, close the GUI
start_local(db_user_name, db_user_pw, db_host, db_port, mongo_database)

# Obtaining events and info associated with data entry
# The annotations entered in the GUI are now available in this dataframe
event_output <- download_events(uri_fun, db_user_name, db_user_pw, db_host, db_port, mongo_database)

## End(Not run)

# Remove project from MongoDB
terminate_project(uri_fun, db_user_name, db_user_pw, db_host, db_port, mongo_database, fast=TRUE)

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