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FHIR to pandas.dataframe for AI and ML

Project description

:fire: fhiry - FHIR for AI and ML

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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/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

Synthea

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

SMART Bulk Data Server Export

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

Columns

  • see df.columns
patientId
fullUrl
resource.resourceType
resource.id
resource.name
resource.telecom
resource.gender
...
...
...

Modules

Contributors

Project details


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Files for fhiry, version 1.0.0
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