:fire: fhiry - FHIR to pandas dataframe for data analysis, AI and ML

Open Source Python library for import of FHIR resources to pandas dataframe

Bulk data export using FHIR may be important if you want to export a cohort for analysis or machine learning. :fire: Fhiry is a python package to facilitate this by converting a folder of FHIR bundles/ndjson into a pandas data frame for analysis and importing into ML packages such as Tensorflow and PyTorch. Test it with the synthea sample or the downloaded ndjson from the SMART Bulk data server. Use the 'Discussions' tab above for feature requests.

Installation

pip install fhiry

Usage

Import FHIR bundles (JSON) from folder to pandas dataframe

import fhiry.parallel as fp
df = fp.process('/path/to/fhir/resources')
print(df.info())

Example source data set: Synthea

Jupyter notebook example: notebooks/synthea.ipynb

Import NDJSON from folder to pandas dataframe

import fhiry.parallel as fp
df = fp.ndjson('/path/to/fhir/ndjson/files')
print(df.info())

Example source data set: SMART Bulk Data Server Export

Jupyter notebook example: notebooks/ndjson.ipynb

Import FHIR Search results to pandas dataframe

Fetch and import resources from FHIR Search API results to pandas dataframe.

Documentation: fhir-search.md

Example: Import all conditions with a certain code from FHIR Server

Fetch and import all condition resources with Snomed (Codesystem http://snomed.info/sct) Code 39065001 in the FHIR element Condition.code (resource type specific FHIR search parameter code) to a pandas dataframe:

from fhiry.fhirsearch import Fhirsearch

fs = Fhirsearch(fhir_base_url = "http://fhir-server:8080/fhir")

my_fhir_search_parameters = {
    "code": "http://snomed.info/sct|39065001",
}

df = fs.search(resource_type = "Condition", search_parameters = my_fhir_search_parameters)

print(df.info())

Columns

• see df.columns

patientId
fullUrl
resource.resourceType
resource.id
resource.name
resource.telecom
resource.gender
...
...
...

Documentation

Contributors

• Bell Eapen |
• Markus Mandalka
• WIP, PR welcome, please see CONTRIBUTING.md
• using CC