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mimic4fhir converts data from MIMIC IV database (PostgreSQL) to HL7 FHIR R4 resources or the German Medical Informatics Initiative core data sets.
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skfit-uni-luebeck/mimic4fhir
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mimic4fhir converts data fromMIMIC IV database (PostgreSQL) to HL7 FHIR R4 resources or the German core data set ofMedical 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, seehere 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 ConceptMapshere.
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 withconditional 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);ARabbitMQ 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 scripthere 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.
// Add server and config data..ConfigconfigObj =newConfig();// PostgresconfigObj.setPassPostgres("Pa33word!");configObj.setPortPostgres("5432");configObj.setUserPostgres("user");configObj.setPostgresServer("192.168.0.1");configObj.setDbnamePostgres("postgres");// FhirconfigObj.setFhirServer("http://server.com/fhir/");configObj.setFhirxmlFilePath("output/");// Validation// Set to true, if you want to validate with the InstanceValidatorconfigObj.setValidateResources(false);// ConceptMaps URI needed for the conversionconfigObj.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 patientsconfigObj.setUseCXR(false);//Specification// Choose plain R4 or the German MII KDS outputconfigObj.setSpecification(ModelVersion.KDS);Mimic4Fhirapp =newMimic4Fhir();app.setConfig(configObj);app.setOutputMode(OutputMode.PRINT_FILE);// 25 Patients chosen random (boolean flag) from the MIMIC IVapp.setTopPatients(25,true);// You can run the conversion single-threaded//app.start();// Or with 10 Threadsapp.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 thishelp 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/This source code is licensed under Apache 2.
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mimic4fhir converts data from MIMIC IV database (PostgreSQL) to HL7 FHIR R4 resources or the German Medical Informatics Initiative core data sets.