automatic_NLP_processor: Process NLP Annotations on the Current Patient Cohort

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

Description

Accepts a list of patient ID's or alternatively can perform NLP annotations on all available patients in the database.

Usage

automatic_NLP_processor(
  patient_vect = NA,
  text_format = "latin1",
  nlp_engine = "udpipe",
  uri_fun = mongo_uri_standard,
  user,
  password,
  host,
  port,
  database,
  max_n_grams_length = 7,
  negex_depth = 6,
  select_cores = NA,
  URL = NA
)

Arguments

patient_vect	Vector of patient ID's. Default is NA, in which case all available patient records will undergo NLP annotation.
text_format	Text format for NLP engine.
nlp_engine	Which NLP engine should be used? UDPipe is the only one supported for now.
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.
max_n_grams_length	Maximum length of tokens for matching with UMLS concept unique identifiers (CUI's). Shorter values will result in faster processing. If 0 is chosen, UMLS CUI tags will not be provided.
negex_depth	Maximum distance between negation item and token to negate. Shorter distances will result in decreased sensitivity but increased specificity for negation.
select_cores	How many CPU cores should be used for parallel processing? Max allowed is total number of cores minus one. If 1 is entered, parallel processing will not be used.
URL	UDPipe model URL.

Value

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

Examples

## Not run: 
automatic_NLP_processor(patient_vect = NA, text_format = 'latin1', nlp_engine = 'udpipe',
URL = 'models/english-ewt-ud-2.4-190531.udpipe', uri_fun = mongo_uri_standard, user = 'John',
password = 'db_password_1234', host = 'server1234', port = NA, database = 'TEST_PROJECT',
max_n_grams_length = 7, negex_depth = 6, select_cores = 1)

## End(Not run)

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