Convert - FHIR (R4) to OMOP

POST /convert/v1/fhirr4toomop

This operation converts a FHIR R4 bundle (including one from CDA-to-FHIR, HL7-to-FHIR, or Combine Bundles) into the Observational Medical Outcomes Partnership (OMOP) Common Data Model format.

See the Analyzing with OMOP use case for more in-depth discussion of how to use this operation.

Inputs and Outputs

The input is a FHIR R4 bundle for a single patient.

The output for the OMOP conversion is a ZIP archive, so specify accept: application/zip in your request header. The ZIP archive contains multiple Comma-Separated Value (CSV) files, one for each supported OMOP data table. See data tables for a complete list of contents.

Query Parameters

Logging and Error Handling

If the input data is invalid (such as improperly-formatted FHIR data), the ZIP archive will not be created. Instead, the response will be a FHIR Operation Outcome in JSON format detailing the errors.

However, in many cases the Convert service can continue processing even when there are issues with the input data, such as missing fields or unexpected data types. In such cases, issues are reported in a custom file in the ZIP archive named PROCESSING_LOG.csv. This processing log categorizes issues as:

• Informational - Basic information about the data processing, e.g., added a medication.
• Warning - The service had to modify the record due to a problem, e.g., a string was truncated because it exceeded the maximum length.
• Error - The service rejected some data because of an unrecoverable problem, e.g., a required field was missing.

OMOP Conformance

The Convert service uses v5.4 of the OMOP Common Data Model (CDM) specification, with a few exceptions described in Processing Notes. You can alternately request CDM v5.3 using the omopversion query parameter, as described in Inputs and Outputs.

Processing Notes

There are several nuances involved in converting data from FHIR to OMOP, discussed below.

Identifiers

In OMOP, the main ID field in each data table uses the integer data type, but the Convert service uses string values representing paths within the FHIR bundle. For example: a person_id of Patient/35b77437-425d-419c-90b5-af4bc433ebe9 or an observation_id of Procedure/7.2ed0fe30094a46e7bf6b3ebe69ead24a describe the FHIR resource type and ID within the FHIR bundle where the data originated.

Additionally, the following mapping exists between OMOP identifiers and FHIR identifiers:

Data Types

With the exception of ID fields (mentioned above), the Convert service will enforce the data types defined in the OMOP standard. When importing OMOP data into a database, ensure your schema aligns with those data types.

Primary Keys

The Convert service will enforce primary and foreign key references (including concept_ids, which should reference standard OMOP concepts as of export time).

Lossiness

By the nature of the specification, OMOP is lossy. It focuses on standard, validated data most suitable for analysis, and assumes that any necessary data cleanup has been performed prior to OMOP export. Rows containing errors are dropped from the output, as described in error handling.

PII

OMOP does not include names and patient identifiers (such as SSN or MRNs) from the FHIR input, though it does include personally-identifiable information like date of birth.

Pass the query parameter includePIITables with a value of true to export additional custom tables with more identifying information. These tables let you associate details like names, addresses, and emails with OMOP person identifiers.

These extra PII tables include:

• pii_address.csv
• pii_email.csv
• pii_mrn.csv
• pii_name.csv
• pii_phone_number.csv

Concepts and Vocabularies

As part of the OMOP conversion, the Convert service will attempt to match coded values within the bundle to corresponding concepts from OMOP’s Standard Vocabularies, and populate several potential fields for each data row:

• The main concept ID (e.g., condition_concept_id or observation_concept_id) will contain the corresponding OMOP concept ID if the concept is designated standard. If no standard concept was found, this will be set to a concept ID of 0 (“no matching concept”).
• The source concept ID (e.g.,condition_source_concept_id or procedure_source_concept_id) will contain the corresponding OMOP concept ID if the concept is designated non-standard.
• The source value (e.g., condition_source_value or procedure_source_value) will contain a string value that combines the original source code and display name.

For example, a condition was originally coded with the ICD-10 code J45.5 (severe persistent asthma). the Convert service finds a corresponding OMOP concept 45591559, which is non-standard. OMOP contains a cross-walk mapping from 45591559 to the standard OMOP concept 4145356. Thus, the data will be:

Domains and Data Tables

OMOP requires that certain domains go into specific data tables, which may differ from their original FHIR resource. For example, a FHIR Procedure may be placed into the OMOP MEASUREMENT table rather than the PROCEDURE_OCCURRENCE table.

Example

FHIR Bundles and OMOP contents are verbose, so the example below just shows a small sample to illustrate how the data is structured. For a more complete example, try out the API in the Developer Portal Sandbox.

{
  "resourceType": "Bundle",
  "type": "batch-response",
  "entry": [
    {
      "resource": {
        "resourceType": "Patient",
        "id": "35b77437-425d-419c-90b5-af4bc433ebe9",
        ... (patient fields)
      }
    },
    {
      "resource": {
        "resourceType": "Procedure",
        "id": "7.2ed0fe30094a46e7bf6b3ebe69ead24a",
        ... (encounter fields)
      }
    },
    {
      "resource": {
        "resourceType": "Procedure",
        "id": "7.14e26bb09d7649b2a6ce10f794ca8960",
        ... (encounter fields)
      }
    },
    ...
  ]
}

PERSON.csv:

person_id,gender_concept_id,year_of_birth,month_of_birth,day_of_birth,birth_datetime,race_concept_id,ethnicity_concept_id,location_id,provider_id,care_site_id,person_source_value,gender_source_value,gender_source_concept_id,race_source_value,race_source_concept_id,ethnicity_source_value,ethnicity_source_concept_id
Patient/35b77437-425d-419c-90b5-af4bc433ebe9,8532,1956,8,13,1956-08-13T00:00:00.0000000,0,0,,,,35b77437-425d-419c-90b5-af4bc433ebe9,female,,,,,

OBSERVATION.csv:

observation_id,person_id,observation_concept_id,observation_date,observation_datetime,observation_type_concept_id,value_as_number,value_as_string,value_as_concept_id,qualifier_concept_id,unit_concept_id,provider_id,visit_occurrence_id,visit_detail_id,observation_source_value,observation_source_concept_id,unit_source_value,qualifier_source_value,value_source_value,observation_event_id,obs_event_field_concept_id
Procedure/7.2ed0fe30094a46e7bf6b3ebe69ead24a,Patient/35b77437-425d-419c-90b5-af4bc433ebe9,0,2009-07-01,2009-07-01T12:00:00.0000000,32817,,,,,,,,,465 Treatment for Upper Respiratory Infection,,,,,,
Procedure/7.14e26bb09d7649b2a6ce10f794ca8960,Patient/35b77437-425d-419c-90b5-af4bc433ebe9,0,2009-06-07,2009-06-07T20:30:00.0000000,32817,,,,,,,,,OtherThymusOperations Oth thorac op thymus NOS,,,,,,

etc.