PROCEDURE: Mapping of FHIR Procedure Resources to OMOP Entities

This document details the design and decisions for implementing mapping of FHIR Procedure resources to OMOP. The following referenced were used to inform this implementation.

References for Procedure

General Mapping Resources	This is the fhir-to-omop documentation for general FHIR and OMOP information.
FHIR Procedure (STU3)	FHIR Documentation for the Procedure resource. The following version have been considered. Procedure (Current Build) Procedure (R4) Procedure (STU3)
PROCEDURE_OCCURRENCE	This is the OMOP documentation for the PROCEDURE_OCCURRENCE table.

Reference Data

The resoures show below are used for specific use cases and examples

0a2a950e-59b0-4669-8007-a505a3f14cbc	This patient has examples of FHIR Procedure resources, and specifically has examples of Procedure resources that use codes other than procedure codes (e.g. Measurement, Observation, and Condition). The set of files in this folder represent the full set of FHIR resources for the synthmass patient 0a2a950e-59b0-4669-8007-a505a3f14cbc.

Mapping Details

OMOP procedure records are mapped from FHIR Procedure resources. Attribute level details of how FHIR Procedure resources are parsed are in the ProcedureParser class.

Attribute level details of how the parser is mapped to OMOP records are in the OmopProcedureBuilder class.

We have found FHIR Procedure resources using codes that are not procedure codes. These codes include codes for Measurements, Observations, and Conditions. The OMOP Data Quality Dashboard (DQD) tests indicated all records in the procedure table should have a procedure_concept_id that mapps to a concept that is in the Procedure domain (i.e. domain_id = "Procedure"). Therefore, when Procedure FHIR resources are found that have a coding that is for a Measurement, Observation, or Condition these FHIR procedures are not written to the OMOP procedure table but are respetively written to the measurement, observation_occurrence, or condition tables. The code for this is also in the OmopProcedureBuilder class. DQD results before and after making these distinctions are shown below.

Update Testing Results 2022-04-08

On April 08, 2022 we updated our DQD instance to the latest version. This included a number of new tests that were failing. These failures have been remediated and the testing results are shown below.

Procedure Tests Passing 2022-04-08

All but two of the procedure tests are passing. For the failing tests: procedure_detail is not being implemented at this time. The number of patients that do not have a record in the procedure table is an accurate reflection of our test data set.

Procedure Tests Previously Failing 2022-04-08

Origingal Data Quality Dashboard results when mapping FHIR procedure resources exclusively to the OMOP procedure table

Prior to mapping FHIR Procedure resources to Measurement, Observation, Condition, and Procedure the following results were obtainded after running the DQD.

Data Quality Dashboard results when mapping FHIR procedure resources exclusively to the procedure, measurement, observation, and condition_occurrence tables

After mapping FHIR Procedure resources to Measurement, Observation, Condition, and Procedure all tests for Procedure are passing.

Examples of FHIR Procedure Resources That Have Non-procedure Codings

The following is a list of FHIR resources found to have non-procedure codings (i.e. domain_id should be "Procedure" and is not). The person_source_code shown is the ID for the patient found on synthmass. Click here to download the larger list.