phenopackets / omop-exporter

Export Phenopackets from OMOP

OMOP Phenopacket Exporter

This is a Spring Boot app which runs a webserver on top of an OMOP database and will export data in Phenopacket format for an individual.

This tool was developed as part of the Biohackathon Europe 2021 by members of by Project 36.

People

The following people are acknowledged for their input:

• Núria Queralt Rosinach
• Anastasios Siapos
• Danielle Welter
• Jules Jacobsen

Build

./mvnw clean package

Configuration

Set the correct connection settings for your Synthia/OMOP database in the application.properties file.

Launching

Ensure your new aplication.properties file is in the target/ directory. Then do:

java -jar target/omop-exporter-0.0.1-SNAPSHOT.jar

Querying

The server will be running on localhost:8080 data can be retrieved by OMOP person_id e.g. http://localhost:8080/phenopacket/{patient_id} (substituting {patient_id} with the patient_id integer value)