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FHIR R4 Mapping Protocols
From Fragmented Data to Global Interoperability
Abstract
A comprehensive technical guide to mapping fragmented clinical data sources to HL7 FHIR R4 resources. Covers Patient, Encounter, Observation, MedicationRequest, and DiagnosticReport resource mappings with real-world examples from OpenMRS, Bahmni, and proprietary EMR systems.
Key Topics Covered
1. FHIR Resource Fundamentals
Every FHIR resource follows a predictable structure: resourceType, id, meta (versionId, lastUpdated), and domain-specific elements. The Patient resource, for instance, contains identifiers (NID, MRN), name (HumanName), telecom (ContactPoint), gender, birthDate, and address. Understanding cardinality (0..1, 1..1, 0..*) is critical for valid resource construction.
2. OpenMRS → FHIR Observation Mapping
OpenMRS stores clinical data as key-value "observations" (concept_id → value). Mapping this to FHIR Observation requires: (1) Extracting concept_id and mapping to LOINC/SNOMED codes via ConceptMap resources. (2) Converting obs_datetime to effectiveDateTime. (3) Mapping numeric/coded/text values to valueQuantity, valueCodeableConcept, or valueString. (4) Linking to Patient (subject) and Encounter (encounter) references.
3. Handling Missing Data & Extensions
Not all local EMR data fits cleanly into FHIR's rigid structure. Use Extensions for custom fields (e.g., tribal affiliation, caste). The data-absent-reason extension indicates why a required field is missing. Custom extensions must be registered with a canonical URL and documented in a StructureDefinition.
4. Real-World Example: Lab Results
A lab analyzer sends HL7 v2.x ORU^R01 messages. The mediator parses OBX segments, creates FHIR Observation resources (status: final, category: laboratory), maps LOINC codes, and POSTs to the FHIR server. The DiagnosticReport resource bundles multiple Observations and links to the ordering ServiceRequest.
This is a condensed version. Download the full white paper (45+ pages) for code samples, architecture diagrams, and deployment checklists.
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