NLP_to_FHIR

The process read in clinical notes generated by Synthea, feed and text to cTAKES NLP. The result is converted in to FHIR R4 resources. Current version support medical terms in 4 categories, with one-to-one FHIR resource mapping DiseaseDisorderMention => Condition SignSymptomMention => Observation MedicationMention => MedicationStatement ProcedureMention => Procedure

Python

python extract_cuis_edits.py ./fake_data/notes ./fake_data/output Or use full path for the input folder and output folder

Dependency

Code is tested on python 3.8.3

The code requires the ctakes NLP container running in Localhost Refer to: https://github.com/Machine-Learning-for-Medical-Language/ctakes-covid-container