dermatologist/omopfhirmap

OMOP <-> FHIR mapper

omopfhirmap for mapping FHIR <--> OHDSI OMOP CDM

About

Omopfhirmap is a command-line tool for mapping a OHDSI cohort, defined in ATLAS, to a FHIR bundle that can be optionally submitted to a FHIR server for processing. Conversely, it can process a FHIR bundle and add resources to an existing CDM database ignoring duplicates. Unlike GT-FHIR2, the OMOP on FHIR Project at Georgia Tech omopfhirmap does not expose OMOP database as FHIR endpoints.

javadoc

Use cases

• To export a cohort to a FHIR based analytics tool.
• To load new resources to OMOP CDM databases for incremental ETL.

Build

mvn clean install spring-boot:repackage

Usage

java -jar <omopfhirmap.jar> <function> <source> <destination> --spring.config.location=<properties file>

Examples

• java -jar target/omopfhirmap-0.0.1.jar help

• java -jar target/omopfhirmap-0.0.1.jar tofhirbundle 2 test-fhir.json --spring.config.location=application.properties This will convert the cohort defined in Atlas with an ID of 2 (looks in the cohort table in results schema) and writes the FHIR (collection) bundle.

• java -jar target/omopfhirmap-0.0.1.jar toomop test-fhir.json 3 --spring.config.location=application.properties Imports the FHIR bundle in the above file, creates persons, observations, measurements, procedure and visit occurences. Finally it creates a new cohort with ID 3 (Can be seen in Atlas)

• Sample application.properties

spring.main.banner-mode=off
logging.level.org.springframework=ERROR
logging.level.root=ERROR
logging.level.org.foo.bar.baz=INFO

spring.jpa.hibernate.ddl-auto=none

spring.datasource.initialization-mode=always
spring.datasource.platform=postgres
spring.datasource.url=jdbc:postgresql://localhost:5432/username_db?currentSchema=synpuf_results,synpuf5,ohdsi
spring.datasource.username=username
spring.datasource.password=secret

spring.jpa.properties.hibernate.jdbc.lob.non_contextual_creation=true

# used for saving the OMOP identifier in FHIR resource
omopfhir.system.name=mySystem

Work in progress

• I have only mapped FHIR.Patient <-> OMOP.Person so far.
• PRs welcome if you want to map others.
• Please star the repo, if you find this useful and want to see other mappings completed.

Design

• JAVA >= 13
• FHIR R4
• Multi-Threaded
• Uses spring-boot and JPA for wiring of services and abstraction of database.
• Can easily add support for other databases using spring-boot

Other projects

• Check out csv-fhir-mapper
• Python package for OMOP CDM
• .Net library for OMOP CDM
• Go library for OMOP CDM

Contributors

• Bell Eapen | contact |
• PR welcome. Please see CONTRIBUTING.md for details.

Demo

omopfhirmap's Issues

Mapping rest of FHIR resources to OHDSI

Help needed to complete mappers of other resources in this command-line tool for OHDSI <-> FHIR. This should be relatively simple as the Patient resource mapping can be a template. Ideal for those interested in healthIT, FHIR and OHDSI data models.

Tests fail on bumping spring-boot-starter-parent from 2.4.5 to 2.5.2

bumping spring-boot-starter-parent from 2.4.5 to 2.5.2 leads to
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'dataSourceScriptDatabaseInitializer'
while initializing h2 database for tests.

Steps to reproduce:

1. Update spring boot in parent pom

	<parent>
		<groupId>org.springframework.boot</groupId>
		<artifactId>spring-boot-starter-parent</artifactId>
		<version>2.5.2</version>
		<relativePath/> <!-- lookup parent from repository -->
	</parent>

2. mvn clean test