Analyze FHIR Data in R via ODBC

Access FHIR data with pure R script and standard SQL. You can use the CData ODBC Driver for FHIR and the RODBC package to work with remote FHIR data in R. By using the CData Driver, you are leveraging a driver written for industry-proven standards to access your data in the popular, open-source R language. This article shows how to use the driver to execute SQL queries to FHIR data and visualize FHIR data in R.

Install R

You can complement the driver's performance gains from multi-threading and managed code by running the multithreaded Microsoft R Open or by running R linked with the BLAS/LAPACK libraries. This article uses Microsoft R Open (MRO).

Connect to FHIR as an ODBC Data Source

Information for connecting to FHIR follows, along with different instructions for configuring a DSN in Windows and Linux environments.

Set URL to the Service Base URL of the FHIR server. This is the address where the resources are defined in the FHIR server you would like to connect to. Set ConnectionType to a supported connection type. Set ContentType to the format of your documents. Set AuthScheme based on the authentication requirements for your FHIR server.

Generic, Azure-based, AWS-based, and Google-based FHIR server implementations are supported.

Sample Service Base URLs

• Generic: http://my_fhir_server/r4b/
• Azure: https://MY_AZURE_FHIR.azurehealthcareapis.com/
• AWS: https://healthlake.REGION.amazonaws.com/datastore/DATASTORE_ID/r4/
• Google: https://healthcare.googleapis.com/v1/projects/PROJECT_ID/locations/LOCATION/datasets/DATASET_ID/fhirStores/FHIR_STORE_ID/fhir/

Generic FHIR Instances

The product supports connections to custom instances of FHIR. Authentication to custom FHIR servers is handled via OAuth (read more about OAuth in the Help documentation. Before you can connect to custom FHIR instances, you must set ConnectionType to Generic.

When you configure the DSN, you may also want to set the Max Rows connection property. This will limit the number of rows returned, which is especially helpful for improving performance when designing reports and visualizations.

Windows

If you have not already, first specify connection properties in an ODBC DSN (data source name). This is the last step of the driver installation. You can use the Microsoft ODBC Data Source Administrator to create and configure ODBC DSNs.

Linux

If you are installing the CData ODBC Driver for FHIR in a Linux environment, the driver installation predefines a system DSN. You can modify the DSN by editing the system data sources file (/etc/odbc.ini) and defining the required connection properties.

/etc/odbc.ini

[CData FHIR Source]
Driver = CData ODBC Driver for FHIR
Description = My Description
URL = http://test.fhir.org/r4b/
ConnectionType = Generic
ContentType = JSON
AuthScheme = None

For specific information on using these configuration files, please refer to the help documentation (installed and found online).

Load the RODBC Package

To use the driver, download the RODBC package. In RStudio, click Tools -> Install Packages and enter RODBC in the Packages box.

After installing the RODBC package, the following line loads the package:

library(RODBC)

Note: This article uses RODBC version 1.3-12. Using Microsoft R Open, you can test with the same version, using the checkpoint capabilities of Microsoft's MRAN repository. The checkpoint command enables you to install packages from a snapshot of the CRAN repository, hosted on the MRAN repository. The snapshot taken Jan. 1, 2016 contains version 1.3-12.

library(checkpoint)
checkpoint("2016-01-01")

Connect to FHIR Data as an ODBC Data Source

You can connect to a DSN in R with the following line:

conn <- odbcConnect("CData FHIR Source")

Schema Discovery

The driver models FHIR APIs as relational tables, views, and stored procedures. Use the following line to retrieve the list of tables:

sqlTables(conn)

Execute SQL Queries

Use the sqlQuery function to execute any SQL query supported by the FHIR API.

patient <- sqlQuery(conn, "SELECT Id, [name-use] FROM Patient WHERE [address-city] = 'New York'", believeNRows=FALSE, rows_at_time=1)

You can view the results in a data viewer window with the following command:

View(patient)

Plot FHIR Data

You can now analyze FHIR data with any of the data visualization packages available in the CRAN repository. You can create simple bar plots with the built-in bar plot function:

par(las=2,ps=10,mar=c(5,15,4,2))
barplot(patient$[name-use], main="FHIR Patient", names.arg = patient$Id, horiz=TRUE)

👁 A basic bar plot. (Salesforce is shown.)