FHIR-to-OMOP Concept Resolver

R6 class providing access to the FHIR-to-OMOP Concept Resolver endpoints. Translates FHIR coded values (system URI + code) into OMOP standard concepts, CDM target tables, and optional Phoebe recommendations.

Value

A list with input and resolution containing source/standard concepts, target CDM table, and optional enrichments.

When as_tibble = FALSE (default), a list with results (per-item) and summary (total/resolved/failed). When as_tibble = TRUE, a tibble::tibble suitable for dplyr/tidyr pipelines.

A list with best_match, alternatives, and unresolved.

Details

Access via the fhir active binding on an OMOPHubClient:

client <- OMOPHubClient$new(api_key = "oh_xxx")
result <- client$fhir$resolve(
  system = "http://snomed.info/sct",
  code = "44054006",
  resource_type = "Condition"
)
result$data$resolution$target_table
# "condition_occurrence"

Methods

Public methods

• FhirResource$new()

• FhirResource$resolve()

• FhirResource$resolve_batch()

• FhirResource$resolve_codeable_concept()

• FhirResource$clone()

---

Method new()

Create a new FhirResource.

Usage

FhirResource$new(base_req)

Arguments

base_req

Base httr2 request object.

---

Method resolve()

Resolve a single FHIR Coding to an OMOP standard concept.

Provide at least one of (system + code), (vocabulary_id + code), or display.

Usage

FhirResource$resolve(
  system = NULL,
  code = NULL,
  display = NULL,
  vocabulary_id = NULL,
  resource_type = NULL,
  include_recommendations = FALSE,
  recommendations_limit = 5L,
  include_quality = FALSE
)

Arguments

system

FHIR code system URI (e.g. "http://snomed.info/sct").

code

Code value from the FHIR Coding.

display

Human-readable text (semantic search fallback).

vocabulary_id

Direct OMOP vocabulary_id, bypasses URI resolution.

resource_type

FHIR resource type (e.g. "Condition", "Observation").

include_recommendations

Logical. Include Phoebe recommendations. Default FALSE.

recommendations_limit

Integer. Max recommendations (1-20). Default 5L.

include_quality

Logical. Include mapping quality signal. Default FALSE.

---

Method resolve_batch()

Batch-resolve up to 100 FHIR Codings.

Failed items are reported inline without failing the batch.

Usage

FhirResource$resolve_batch(
  codings,
  resource_type = NULL,
  include_recommendations = FALSE,
  recommendations_limit = 5L,
  include_quality = FALSE,
  as_tibble = FALSE
)

Arguments

codings

A list of coding lists, each with optional elements system, code, display, vocabulary_id.

resource_type

FHIR resource type applied to all codings.

include_recommendations

Logical. Default FALSE.

recommendations_limit

Integer. Default 5L.

include_quality

Logical. Default FALSE.

as_tibble

Logical. When TRUE, returns a tibble::tibble with one row per input coding and flat columns for the source concept, standard concept, target CDM table, mapping type, and resolution status. The batch summary (total/resolved/failed) is attached as attr(result, "summary"). Default FALSE keeps the legacy list-shaped return.

---

Method resolve_codeable_concept()

Resolve a FHIR CodeableConcept with vocabulary preference.

Picks the best match per OHDSI preference order (SNOMED > RxNorm > LOINC > CVX > ICD-10). Falls back to text via semantic search if no coding resolves.

Usage

FhirResource$resolve_codeable_concept(
  coding,
  text = NULL,
  resource_type = NULL,
  include_recommendations = FALSE,
  recommendations_limit = 5L,
  include_quality = FALSE
)

Arguments

coding

A list of coding lists, each with system, code, and optional display.

text

Optional CodeableConcept.text for semantic fallback.

resource_type

FHIR resource type.

include_recommendations

Logical. Default FALSE.

recommendations_limit

Integer. Default 5L.

include_quality

Logical. Default FALSE.

---

Method clone()

The objects of this class are cloneable with this method.

Usage

FhirResource$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.