Simple and Efficient Pipeline for Electronic Health Record Annotation


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Documentation for package ‘CEDARS’ version 1.90

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add_end_user Add a CEDARS End User
automatic_NLP_processor Process NLP Annotations on the Current Patient Cohort
create_project Create a New CEDARS Project
delete_end_user Delete a CEDARS End USer
download_events Download Event Data
end_users Download End User List
find_project_name Generate unique test project name (i.e. DB name) on MongoDB CEDARS testing cluster
get_model Get a NLP Model
get_wrapper Wrap the get_data() Function
initialize_annotations Initialize Annotations Deletes all NLP annotations and patient-specific information, including clinical event dates.New, empty 'ANNOTATIONS' and 'PATIENTS' collections are created. Dictionaries and original patient notes are preserved.
initialize_notes Initialize EHR Notes
initialize_patients Initialize Patient List
initialize_users Initialize End User List
mongo_uri_standard Prepare MongoDB URI string, most commonly used format
mrconso_upload Upload UMLS Dictionary
mrrel_upload Upload UMLS Relationships
negex Negex data Apache License 2.0
negex_upload Upload NegEx
post_wrapper Wrap the post_data() Function
pre_search Execute Search on a Set of Records
save_credentials Save MongoDB Credentials
save_query Save Search Query
save_tags Save Document Tags
simulated_patients Simulated patient data GPL-3 license
start_local Start CEDARS Locally
terminate_project Terminate CEDARS Project
unlock_user Unlock User-Specific Records Removes any pending lock(s) for a specific user. Normally there should not be more than one record locked per user at any given time, but if there were more than one, i.e. DB corruption, all locks would be lifted at once.
upload_events Upload Event Data
upload_notes Upload Notes to Database