:fire: fhiry - FHIR for AI and ML

About

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 into a pandas data frame for analysis and importing into ML packages such as Tensorflow and PyTorch. Test it with the synthea sample. Use the 'Discussions' tab above for feature requests.

Installation

pip install fhiry

Usage

from fhiry import Fhiry
f = Fhiry()
f.folder = '/path/to/fhir/resources'
f.process_df()
print(f.df.head(5))

Multiprocessing

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

Columns

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

Contributors

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