mimic4fhir

Introduction

mimic4fhir converts data from MIMIC IV database (PostgreSQL) to HL7 FHIR R4 resources or the German core data set of Medical Informatics Initiative. Currently the following modules are supported:

• Patient
• Encounter
• Diagnosis
• Procedure
• Laboratory Results
• Medication
• Imaging techniques

To get access to MIMIC-IV , you have to complete a privacy course, see here for more information. In addition to the MIMIC data, four FHIR ConceptMaps are needed for the translation of the codes. You can find a program to generate the necessary FHIR ConceptMaps here.

How to use

Bundles are created per patient admission/encounter. If the number of resources in a bundle exceeds 15000, a new bundle will be created. This limits the bundle size to ~20MB and are transcaction bundles with conditional creates. Resource bundles can be

• printed to console
• saved as xml file
• pushed to a fhir server

by setting the "outputMode":

app.setOutputMode(OutputMode.PRINT_FILE);

The parameter "topPatients" allows to limit the number of loaded patients; 0 means all patients. Transforming always starts with Patient 1.

app.setTopPatients(10);

A RabbitMQ server is required to run on localhost. Please note: Performance is highly dependent on the following and might be quite low:

• database partitioning and indexing for table chartevents (by HADM_ID)
  • There is a script here which adds additional indeces to the PostgresSQL DB
• server performance (if pushed to a server)

We recommend starting with a low number of patients and with saving to xml files to check the database performance.

Example main method:

// Add server and config data..
	Config configObj = new Config();
	
	// Postgres
	configObj.setPassPostgres("Pa33word!");
	configObj.setPortPostgres("5432");
	configObj.setUserPostgres("user");
	configObj.setPostgresServer("192.168.0.1");
	configObj.setDbnamePostgres("postgres");

	// Fhir
	configObj.setFhirServer("http://server.com/fhir/");
	configObj.setFhirxmlFilePath("output/");

	// Validation
	// Set to true, if you want to validate with the InstanceValidator
	configObj.setValidateResources(false);

	// ConceptMaps URI needed for the conversion
	configObj.setICD9toICD10GM("https://server.com/fhir/ConceptMap/d9be1278-282b-4e80-8be5-226cb30a9eb5");
	configObj.setICD9ToSnomed("https://server.com/fhir/ConceptMap/9f0b2a1f-8253-47fc-a8cf-118226823e22");
	configObj.setICD9ProcToSnomed("https://server.com/fhir/ConceptMap/01c83771-6524-46ef-aaa8-4f63e1d837ea");
	configObj.setICD10PCStoSnomed("https://server.com/fhir/ConceptMap/03ea8e3a-7fc3-4fb3-8e30-21af497c2a63");
		
	// Use CXR 
	// If you have access to the CXR, the conversion will added DiagnosticReport and ImagingStudying
	// for the corresponding patients
	configObj.setUseCXR(false);
		
	//Specification 
	// Choose plain R4 or the German MII KDS output
	configObj.setSpecification(ModelVersion.KDS);

	Mimic4Fhir app = new Mimic4Fhir();
	app.setConfig(configObj);
	app.setOutputMode(OutputMode.PRINT_FILE);
	// 25 Patients chosen random (boolean flag) from the MIMIC IV
	app.setTopPatients(25, true);
	// You can run the conversion single-threaded
	//app.start();
	// Or with 10 Threads
	app.startWithThread();

In addition, there is a command line interface to accelerate the creation for automated testing.

java -jar target/mimic4fhir-1.0.0-jar-with-dependencies.jar --help
  -d, --database=<postgresDatabase>
                             The PostgreSQL Database
      --debug                Prints bundle into the console
      --fhir=<fhirEndpoint>  FHIR Endpoint to submit the Resources
      --file=<filePath>      Output Path the Resources
  -h, --help                 Show this help message and exit.
      --kds                  Enable to German MII KDS as the output
  -p, --port=<postgresPort>  The PostgreSQL Port
      --patients=<patients>  Number of Patients to transform
      -pwd, --password=<postgresPassword>
                             The PostgreSQL User Password
      --random               Randomly choose patients to convert
  -s, --server=<postgresServerIP>
                             The PostgreSQL Server IP
      --thread               Enable Threading
  -u, --user=<postgresUser>  The PostgreSQL User
  -V, --version              Print version information and exit.
      -validate              Validates the Resources
      --10PCSToSCT=<ICD10PCStoSCT>
                             FHIR ConceptMap to translate ICD10 PCS to SNOMED CT
      --9ProcToSCT=<ICD9ProcToSCT>
                             FHIR ConceptMap to translate ICD9 Procedure to
                               SNOMED CT
      --9To10GM=<ICD9toICD10GM>
                             FHIR ConceptMap to translate ICD9 to ICD10GM
      --9ToSCT=<ICD9toSCT>   FHIR ConceptMap to translate ICD9 to SNOMED CT
      --cxr                  Enable the MIMIC IV CXR

Example:

java -jar target/mimic4fhir-1.0.0-jar-with-dependencies.jar --server=192.186.0.1 --user=user --password=Pa33word! --patients=20 --thread --file=output/

License

This source code is licensed under Apache 2.