FHIR for Research Workshop¶

Exercise 1¶

Intro: see https://github.com/NIH-NCPI/fhir-101/blob/master/FHIR%20101%20-%20Practical%20Guide.ipynb as a great example

What is this notebook?¶

(common overview of the FHIR Training)

(overview of this specific notebook)

Icons in this Guide¶

📘 A link to a useful external reference related to the section the icon appears in

⚡️ A key takeaway for the section that this icon appears in

🖐 A hands-on section where you will code something or interact with the server

(any required MITRE legalese should either go here or at the very bottom of the notebook)

Motivation / Purpose¶

Scenario¶

(this section describes the specifics of the use case: what is the problem statement, what is the basic approach we are going to take, etc)

Initial Setup¶

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# import any required libraries here.
#  - requests
#  - fhirclient: https://github.com/smart-on-fhir/client-py
#  - Pandas - DataFrames
#  - NumPy - basic data analysis
#  - matplotlib
#  - maybe seaborn for viz on top of matplotlib ?

Step 1 Connect to Client¶

sync to source server for data extraction

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Step 2 Query Data¶

Submit query to source and retreive data. Save it locally

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Step 3 Mount Data onto Pandas Dataframe¶

Take FHIR formatted data and convert it to a pandas dataframe for subsequent analysis.

This resource seems like a good one! https://github.com/dermatologist/fhiry

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Step 4 Exploratory Data Analysis¶

Conduct some limited, EDA for demonstration purposes.

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Summary¶

(A review of what was done in this notebook, possibly reinforcing how this kind of use case could be useful in the real world)