Man pages for CEDARS
Simple and Efficient Pipeline for Electronic Health Record Annotation
| add_end_user | Add a CEDARS End User |
| aggregate_note | Aggregate Contents of a Note |
| automatic_NLP_processor | Process NLP Annotations on the Current Patient Cohort |
| batch_processor_db | Batch NLP Annotations for a Cohort |
| colorize | Highlight Keywords and Concepts |
| commit_patient | Select and Lock Patient Record |
| complete_case | Mark a Case as Completed |
| create_project | Create a New CEDARS Project |
| db_download | Obtain Patient Notes |
| db_upload | Upload Annotations |
| delete_end_user | Delete a CEDARS End USer |
| document_processor | Functions to process documents with NLP engine Process a... |
| dot-onLoad | Load Options on Startup |
| download_events | Download Event Data |
| end_users | Download End User List |
| fast_merge_umls | Merge UMLS Tags |
| find_model | Find NLP Model |
| find_project_name | Generate unique test project name (i.e. DB name) on MongoDB... |
| format_keywords | Format Keyword Elements |
| get_data | Get one Sentence for Review |
| get_model | Get a NLP Model |
| get_patient | Retrieve Patient Data |
| get_wrapper | Wrap the get_data() Function |
| id_expander | Expand ID's |
| initialize_annotations | Initialize Annotations Deletes all NLP annotations and... |
| initialize_notes | Initialize EHR Notes |
| initialize_patients | Initialize Patient List |
| initialize_users | Initialize End User List |
| lemma_match | Match Lemmas to Regex Keywords |
| lock_records | Lock Record for one Patient |
| lock_records_admin | Lock Record for Admin Work When tasks need to be performed by... |
| mark | Mark Tokens |
| mongo_connect | Connect to MongoDB |
| mongo_uri_standard | Prepare MongoDB URI string, most commonly used format |
| mrconso_upload | Upload UMLS Dictionary |
| mrrel_upload | Upload UMLS Relationships |
| negation_tagger | Tag for Negation |
| negex | Negex data Apache License 2.0 |
| negex_processor | Annotate for Negation |
| negex_token_tagger | Compute Token Series |
| negex_upload | Upload NegEx |
| parse_query | Parse a Search Query |
| password_verification | Verify CEDARS End User Credentials |
| paste_sections | Paste Individual Note Sections |
| patient_processor_par | Process All Documents for One Patient |
| patient_roster_update | Update Patient List |
| populate_annotations | Prepare Database for NLP Annotation |
| populate_dictionaries | Prepare Database for Dictionary Data Upload |
| populate_notes | Prepare Database for Patient Notes |
| populate_query | Prepare Database to Receive the Search Query |
| populate_users | Prepare Database for User Credentials |
| post_data | Save Reviewer Annotations |
| post_wrapper | Wrap the post_data() Function |
| pre_search | Execute Search on a Set of Records |
| sanitize | Sanitize Text |
| sanitize_query | Sanitize Query |
| save_credentials | Save MongoDB Credentials |
| save_query | Save Search Query |
| save_tags | Save Document Tags |
| select_patient | Select Next Patient to Review |
| sentence_eval | Evaluate One Sentence |
| sentence_search | Functions which mediate keyword/CUI search on NLP-annotated... |
| simulated_patients | Simulated patient data GPL-3 license |
| standardize_nlp | Standardize Output From NLP Engine |
| start_local | Start CEDARS Locally |
| terminate_project | Terminate CEDARS Project |
| terminate_project_new | Terminate CEDARS Project - short version |
| token_splitter | Split a Token |
| umls_processor | Tag Tokens With UMLS Concepts |
| unlock_records | Unlock Old Locked Records Occasionally a CEDARS end user will... |
| unlock_records_admin | Remove Admin Lock |
| unlock_user | Unlock User-Specific Records Removes any pending lock(s) for... |
| upload_events | Upload Event Data |
| upload_notes | Upload Notes to Database |
