sofa-on-fhir

Python script that generates some of the data needed to compute the SOFA-score in FHIR format

Info

• This is a minimal standalone script to generate data needed to compute the SOFA score based on FHIR. The script will generate FHIR Bundles containing a Patient resource and additional measurements. The measurements include Observation resources for:
  • PaO2
  • FiO2
  • Bilirubin
  • Platelets
  • Creatinine
  • 24h Urine
  • Glasgow Coma Scale (GCS)

Plus there is a MedicationStatement resource for adminisration of dopamine, adrenaline and noradrenaline. There is some randomization implemented in creating the measurement values.

The SOFA-Score is based on the publication Vincent JL, Moreno R, Takala J, et al. The SOFA (Sepsis-related Organ Failure Assessment) score to describe organ dysfunction/failure. On behalf of the Working Group on Sepsis-Related Problems of the European Society of Intensive Care Medicine. Intensive Care Med. 1996;22(7):707-710. doi:10.1007/BF01709751

Prerequisites

• Python >3.6
• SMART on FHIR Python client

Usage

• Adjust the settings.yaml for your needs
  • if you are using a FHIR-server, specify the url and set to enabled
  • number of patients is the amount of data to be generated
  • all resources can be dumbed to the local data folder if enabled
• Run sofa-on-fhir.py

License

• MIT

Links

• FHIR profiles from the Medical Informatics Initiative (MII)
• SMART on FHIR Python Client