This web application demonstrates the use of the fhir2hpo Java library for converting FHIR-encoded laboratory results with LOINC information to terms in the Human Phenotype Ontology. Users can search for patients in an unauthenticated FHIR sandbox and display the phenotypes derived from converting Observation LOINCs.

This application can connect to STU2 and STU3 servers, and uses the HAPI Converter library to format responses as STU3 for use in the fhir2hpo library.

Compiling this library requires installation of Maven and Java 8.

In addition, you need to locally install two libraries that are not yet available on Maven Central. The monarch-initiative phenol library defines the domain around the HPO. From the command line:

git clone https://github.com/monarch-initiative/phenol.git
cd phenol
git checkout v.1.2.6
mvn install

This checks out and builds Release 1.2.6 of phenol.

Next install the fhir2hpo library.

git clone https://github.com/OCTRI/fhir2hpo
cd fhir2hpo
git checkout v1.0.0
mvn install

This checks out and builds Release 1.0.0 of fhir2hpo. Both libraries are now installed in your local Maven repository.

Finally, clone this library and run mvn install to build the jar.

You can run this application in a few different ways. Run as a jar:

java -jar target/hpoOnFhir.jar

Or as a spring-boot app:

mvn spring-boot:run

You can also set up the Eclipse Spring Tool Suite with all the projects and run using the Boot dashboard. This is best for development as it will track changes in the underlying library so you don't have to rerun maven each time.

The application is configured by default to work with the R3 SmartHealth IT sandbox. It is designed with SMART principles in mind and should work with any other open FHIR servers. To modify the sandbox, open the file application.properties and look for the following variables:

fhir-server-configuration.name=SmartHealth IT
fhir-server-configuration.url=https://r3.smarthealthit.org
fhir-server-configuration.version=STU3

Change these properties and restart the application to connect to a different sandbox. The properties file has connection details to the Open Epic STU2 server commented out as another example.

Other servers we have tested with are:

• http://hapi.fhir.org/baseDstu3 (The HAPI FHIR STU3 server)
• https://api-stu3.hspconsortium.org/STU301withSynthea/open (The HSPC STU3 server)
• https://r2.smarthealthit.org (The SmartHealth IT STU2 server)