AllergyIntolerance Resource Considerations

Mapping FHIR Allergy and Intolerance resources to OMOP present unique challenges that require consideration of data granularity, standardization, and preservation of clinical relationships. Note: The AllergyIntolerance resource serves as a use case example in the CodeableConcept and Value as Concept mapping patterns. The principles and patterns are described there in more detail.

Allergy Mapping Examples

No Known Allergies: CodeableConcept Pattern

The simplest mapping scenario involves patients with no known allergies. In this case:

• FHIR Representation: The AllergyIntolerance resource contains a standardized SNOMED CT code indicating "No Known Allergies"
• OMOP Mapping: This code maps directly to a corresponding standard concept in the OMOP vocabulary following the basic CodeableConcept pattern
• Implementation: Use standard vocabulary mapping tables to identify the appropriate OMOP concept_id for the "No Known Allergies" status

Allergy to Specific Substances: Value as Concept Pattern

When patients have documented allergies to specific substances, the mapping complexity increases significantly. Consider the example of "Allergy to Penicillin G":

• Challenge: The allergy encompasses both the general concept of drug allergy and the specific substance involved
• Solution: Utilize the OMOP "value as concept" pattern to capture both dimensions of the information

The "value as concept" mapping pattern to OMOP addresses scenarios where an observation has both a general category and a specific value that must be captured separately. This pattern is employed for allergy mappings, involving two key fields:

1. Observation Concept ID: Represents the type of observation (e.g., "Allergy to Drug")
2. Value as Concept ID: Represents the specific substance or agent (e.g., "Penicillin G")

Mapping Allergic Reactions

When allergy data FHIR resouces includes specific reactions (e.g., rash, anaphylaxis), two records should be created:

1: Primary Allergy Record

• observation_concept_id: "Allergy to Drug"
• value_as_concept_id: Specific allergen (e.g., "Penicillin G")

2: Reaction Record

• observation_concept_id: "Allergic Reaction to Drug"
• value_as_concept_id: Specific reaction (e.g., "Rash")

Linking Related Observations

To maintain the clinical relationship between allergies and their reactions:

1. Use observation_event_id: Set the observation_event_id in the reaction record to reference the observation_id of the primary allergy record
2. Alternative Linking: For tables without event linking fields, utilize the OMOP fact_relationship table to establish connections between related clinical facts

/// url = 'http://hl7.org/fhir/uv/omop/StructureMap/AllergyMap'
/// name = 'AllergyMap'
/// title = 'Mapping Allergy resource to Observation OMOP Domain'
/// status = 'draft'

uses "http://hl7.org/fhir/StructureDefinition/AllergyIntolerance" alias Allergy as source
uses "http://hl7.org/fhir/uv/omop/StructureDefinition/Observation" alias ObservationTable as target

group Observation(source src : Allergy, target tgt : ObservationTable) {
  src.code as s -> tgt then {
    s.coding as sc -> tgt then {
      sc.code ->  tgt.observation_concept_id,  tgt.observation_source_value,  tgt.observation_source_concept_id;
    };
  }; // src.id as id -> tgt.observation_id = cast(id, "integer");
  src.onset : dateTime as osd ->  tgt.observation_date = cast(osd, 'date'),  tgt.observation_datetime = osd; // src.patient as s -> tgt then {
  src.reaction as s -> tgt then {
    s.manifestation as sman -> tgt then {
      sman.concept as smanc -> tgt then {
        smanc.coding as sc -> tgt then {
          sc.code ->  tgt.value_as_concept_id,  tgt.value_source_value;
        };
      };
    };
  };
}