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Welcome to InterSystems OMOP Platform!

The InterSystems OMOP Platform, available as a HealthShare service through the InterSystems Cloud Services Portal, transforms FHIR data into the Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM). The InterSystems OMOP Platform looks at FHIR data stored in an S3 bucket and automatically transforms and sends the data to the cloud-hosted repository in the OMOP CDMOpens in a new tab format. You can then use external Observational Health Data Sciences and Informatics (OHDSI) tools, such as ATLAS or HADES, in conjunction with a database driverOpens in a new tab, such as JDBC, to perform analytical tasks on your data.

Using InterSystems OMOP Platform

To get started with InterSystems OMOP Platform, load the InterSystems Cloud Services PortalOpens in a new tab to sign up for a trial or subscription. Select InterSystems OMOP Platform from the list of services. Provide the name of the S3 bucket that stores FHIR data and follow the instructions to create a deployment. The FHIR data must be in the Bulk FHIR format and contained in a single zip file. For more information about the NDJSON format used in Bulk FHIR, see the official HL7 documentationOpens in a new tab.

Next, open your deployment in the Portal. The InterSystems OMOP Platform service pulls FHIR data from the S3 bucket specified during deployment creation and starts the data transformation automatically. The transformation takes time to process, and you may not see results immediately, especially if you are transforming a large volume of data. To understand how the transformation maps FHIR fields to OMOP CDM fields, see InterSystems OMOP Platform Transformation Details.

You can view any transformation errors or warnings on the Errors page and metrics about the resources loaded on the Metrics page. See the Understanding Transformation Errors section for information on the errors and warnings that the transformation reports.

The deployment periodically looks in the S3 bucket to see if new files have been added and performs the data transformation on these files automatically. Therefore, simply add bulk FHIR files to your S3 bucket to start the transformation of your data to the OMOP CDM. All transformed data is stored in the OMOP repository in your deployment. If new FHIR data is for an existing patient then, to ensure data integrity, the service deletes all the existing data for the patient in the OMOP repository and replaces it with the new FHIR data. Therefore, the new FHIR data should contain all the historical patient data previously sent to the OMOP platform.


When updating a patient, ensure the new FHIR data contains the historical patient data as the OMOP platform deletes all existing data for the patient.

The deployment automatically maps nonstandard terminologies in FHIR data to the standard terminology in OMOP ontology. Below is an example of mapping ICD10 to SCT:

Map nonstandard FHIR to standard OMOP

Access the Data

You can subsequently access this data from a Python, Java, .NET, or C++ application through the use of a database driver, in just three steps:

Once you have accessed the data, use OHDSI toolsOpens in a new tab to assess and analyze the data that has been standardized in the OMOP CDM.

Understanding Transformation Errors

The Errors page reports any issues that arose as your deployment processed files added to the S3 bucket. These issues fall into two distinct categories:

  • Warnings: The deployment raises a warning when there is a failure to map data in a field from a FHIR resource to a non-required field in an OMOP CDM record; this OMOP CDM record is created, but contains one (or more) empty fields. Data is not found in the OMOP CDM ontology. Therefore, it could be resolved by adding terminology mapping content to include the data.

  • Errors: The deployment raises an error when there is an issue processing the data contained in a particular field. In both cases, the deployment fails to create an OMOP CDM record and reports what FHIR resource the error originated from. The issue can arise from two different cases:

    • Missing a required field: The deployment raises an error when the transformation would create an OMOP CDM record that lacks one of the required fields of the OMOP CDM. This typically occurs when the FHIR resource does not have data in the field that maps to the required field.

    • Unrecognized terminology: When the deployment cannot recognize the FHIR terminology, it cannot map to standard OMOP concepts.

    • FHIR validation errors: The deployment validates all FHIR resources before attempting to transform them and any resource that fails validation is not transformed into an OMOP CDM record. Any FHIR resource that does not conform with the standard fails validation. For example, if a property has wrong datatype or if the FHIR resource does not contain a required property.

To fix any of these issues, you must modify the input FHIR data. Error messages reported on the Errors page indicate which resources the OMOP Platform was unable to transform, so you can find the origin of the error, modify the source, and re-upload the data that failed the transformation.

Transformation Error Examples

No source data found

The transformation cannot find a value in the source FHIR resource. For example: a Patient resource contains neither the gender element nor the birthSex extension.

Unrecognized or missing system

The system element is missing or contains a value that cannot convert to OMOP’s vocabulary ID. To remediate, add an entry to the system lookup table.

Unrecognized or missing code

The code element is missing or contains a value that cannot convert to the concept ID of a standard OMOP concept. To remediate, add an entry to the primary lookup table.

Learning Resources

To learn more about the InterSystems OMOP Platform, explore the following resources:

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