FHIR for Research - From Data Analysis to Clinical Decision Support
Workshop Overview
This hands-on workshop introduces researchers to FHIR data analysis and clinical decision support implementation, with a focus on genomics applications.
Prerequisites
- Basic familiarity with Python and JavaScript will allow for a deeper understanding, but you can follow the workshop notebooks without prior experience.
- Web browser (Chrome recommended)
- Google account to run notebooks in Google Colab (optional)
- Recommended background: Basic understanding of FHIR concepts
- See our FHIR from 1,000 Feet module for introductory material
- For Part 2, familiarity with Genomics Data Standardization with FHIR
- Helpful concepts: CDS Hooks and SMART on FHIR
Workshop Materials
At the top of each notebook (see links to Part 1 and Part 2 below), you will see a series of badges like those below:
This page can be viewed or run as a Jupyter notebook:
See Running Workshop Notebooks for more information about these options.
Use one of these options to view or run the workshop notebooks.
Part 1: FHIR Data Analysis
Key concepts covered:
- Connecting to FHIR servers
- Converting FHIR resources to Pandas DataFrames
- Common analysis patterns
- Working with nested data
Part 2: Clinical Decision Support with Genomics
Key concepts covered:
- Working with FHIR genomics resources
- Processing genetic variants
- Implementing Clinical Decision Support (CDS) logic
- Generating clinical recommendations
Synthetic Data
This tutorial uses the Synthea Coherent Data Set, a comprehensive synthetic health dataset that includes:
- FHIR resources
- Digital Imaging and Communications in Medicine (DICOM, an international standard for storing, retrieving, and sending medical images like those from an MRI, CT scan, or x-ray) images
- Genomic data
- Physiological data (ECGs)
- Clinical notes
The dataset is managed by The MITRE Corporation and is available under the Creative Commons Attribution 4.0 International License. It’s specifically designed to provide realistic, linked healthcare data for development and testing. For more information, see Synthea Overview.
Citation:
Walonoski J, Hall D, Bates KM, et al. The “Coherent Data Set”: Combining Patient Data and Imaging in a Comprehensive Synthetic Health Record. Electronics. 2022; 11(8):1199. https://doi.org/10.3390/electronics11081199
Access:
The dataset can be downloaded from the Synthea downloads page. You only need to download the data if you are running your own server. For more information on running your own server, see Standing Up a FHIR Testing Server.
Additional Resources
Contributing
This workshop is open source. We welcome contributions via pull requests and issues on GitHub.