Particle Health Sandbox

This GitHub Repository is published as a part of the Synthetic Health Data Challenge. This includes a Synthea synthetic patient population generator that outputs point-in-time CCDA files with in-document provider notes, as well as stores the original Synthea CCDA, FHIR, and Note files for reference. A CSV for Validation results as well as population demographics will also be output to the resulting folder.

Please visit https://www.particlehealth.com/ and sign up for a free account to interact with pre-loaded patient populations generated from this solution via our API and User Interface!

Requirements:

brew install jenv
os.system('brew install jenv')
os.system('jenv local 1.8')

Open Source Tools and Libraries Used:

Tools and Languages:

Python 3.8.3
jenv 1.8
Synthea (latest release)
HealthIT.gov’s open source CCDA 2.0 scorecard API (For Validation)

Python Libraries:

import os
import argparse
import sys
from difflib import get_close_matches
import re
import shutil
from shutil import copyfile
from datetime import date
import pandas as pd
import json
import requests
import urllib3
import jinja2
from jinja2 import Environment
from jinja2 import FileSystemLoader
from lxml import etree
from io import StringIO, BytesIO
import csv
import string

Usage:

Ensure you are working in the 'synthea-master' directory

Run:

python Synthea_Runner.py --condition {condition_of_interest} --num-patients {population}

Entry options for condition_of_interest include: ['covid19', 'diabetes', 'lung cancer', 'opioid addiction']

Recommended entry options for population are any numerical value 1 - 5000

Example:

  python Synthea_Runner.py --condition 'diabetes' --num-patients 50

Output:

A folder names with the condition specified, as well as the date of generation will be output

Example output folder: 'diabetes_output_2021-07-07'

The following sub-directories and files will be contained:

generator_output: (main)

contains output point-in-time CCDA files with in-document provider notes

synthea_ccda:

contains original synthea CCDA documents for reference

synthea_fhir:

contains original synthea FHIR documents for reference

synthea_notes:

contains original synthea txt note files for reference

output_directory.csv:

CSV file containing demographics of the population created

validation_results.csv:

CSV file containing the validation results for each point-in-time document generated (from HealthIT.gov’s open source CCDA 2.0 scorecard API)

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