majiayu000 FHIR R4 Resource Generator Skill
Overview
This skill enables Claude to generate valid FHIR R4 (Fast Healthcare Interoperability Resources) resources from extracted medical data. FHIR is the industry standard for healthcare data exchange.
When to Use This Skill
Use this skill when you need to:
- Convert OCR-extracted medical data to FHIR resources
- Create Patient, Observation, MedicationRequest resources
- Validate FHIR resource structure
- Prepare data for EHR (Electronic Health Record) integration
- Generate HL7 FHIR bundles for data exchange
Core FHIR Resources
1. Patient Resource
def create_fhir_patient(patient_data):
"""Generate FHIR R4 Patient resource"""
return {
"resourceType": "Patient",
"id": patient_data.get('id', 'example-patient'),
"identifier": [{
"use": "official",
"system": "http://hospital.example.org",
"value": patient_data.get('mrn', 'MRN12345')
}],
"active": True,
"name": [{
"use": "official",
"family": patient_data.get('last_name', ''),
"given": [patient_data.get('first_name', '')]
}],
"gender": patient_data.get('gender', 'unknown'),
"birthDate": patient_data.get('birth_date', ''),
"address": [{
"use": "home",
"line": [patient_data.get('address_line', '')],
"city": patient_data.get('city', ''),
"state": patient_data.get('state', ''),
"postalCode": patient_data.get('zip', ''),
"country": patient_data.get('country', 'US')
}],
"telecom": [{
"system": "phone",
"value": patient_data.get('phone', ''),
"use": "mobile"
}]
}
2. MedicationRequest Resource
def create_medication_request(medication_data, patient_reference):
"""Generate FHIR R4 MedicationRequest"""
return {
"resourceType": "MedicationRequest",
"id": medication_data.get('id', 'med-request-1'),
"status": "active",
"intent": "order",
"medicationCodeableConcept": {
"coding": [{
"system": "http://www.nlm.nih.gov/research/umls/rxnorm",
"code": medication_data.get('rxnorm_code', ''),
"display": medication_data.get('name', '')
}],
"text": medication_data.get('name', '')
},
"subject": {
"reference": patient_reference,
"display": "Patient"
},
"authoredOn": medication_data.get('date', ''),
"dosageInstruction": [{
"text": medication_data.get('sig', ''),
"timing": {
"repeat": {
"frequency": medication_data.get('frequency', 1),
"period": 1,
"periodUnit": "d",
"when": [medication_data.get('timing', 'MORN')]
}
},
"route": {
"coding": [{
"system": "http://snomed.info/sct",
"code": medication_data.get('route_code', '26643006'),
"display": medication_data.get('route', 'Oral')
}]
},
"doseAndRate": [{
"doseQuantity": {
"value": medication_data.get('dose_value', 0),
"unit": medication_data.get('dose_unit', 'mg'),
"system": "http://unitsofmeasure.org",
"code": medication_data.get('ucum_code', 'mg')
}
}]
}],
"dispenseRequest": {
"quantity": {
"value": medication_data.get('quantity', 30),
"unit": "tablet"
},
"expectedSupplyDuration": {
"value": medication_data.get('days_supply', 30),
"unit": "days"
}
}
}
3. Observation Resource (Lab Results, Vitals)
def create_observation(obs_data, patient_reference):
"""Generate FHIR R4 Observation for lab results or vitals"""
return {
"resourceType": "Observation",
"id": obs_data.get('id', 'obs-1'),
"status": "final",
"category": [{
"coding": [{
"system": "http://terminology.hl7.org/CodeSystem/observation-category",
"code": obs_data.get('category', 'laboratory'),
"display": obs_data.get('category_display', 'Laboratory')
}]
}],
"code": {
"coding": [{
"system": "http://loinc.org",
"code": obs_data.get('loinc_code', ''),
"display": obs_data.get('test_name', '')
}],
"text": obs_data.get('test_name', '')
},
"subject": {
"reference": patient_reference
},
"effectiveDateTime": obs_data.get('date', ''),
"valueQuantity": {
"value": obs_data.get('value', 0),
"unit": obs_data.get('unit', ''),
"system": "http://unitsofmeasure.org",
"code": obs_data.get('ucum_code', '')
},
"referenceRange": [{
"low": {
"value": obs_data.get('ref_low', 0),
"unit": obs_data.get('unit', '')
},
"high": {
"value": obs_data.get('ref_high', 0),
"unit": obs_data.get('unit', '')
}
}]
}
4. Condition/Diagnosis Resource
def create_condition(diagnosis_data, patient_reference):
"""Generate FHIR R4 Condition resource"""
return {
"resourceType": "Condition",
"id": diagnosis_data.get('id', 'condition-1'),
"clinicalStatus": {
"coding": [{
"system": "http://terminology.hl7.org/CodeSystem/condition-clinical",
"code": diagnosis_data.get('clinical_status', 'active')
}]
},
"verificationStatus": {
"coding": [{
"system": "http://terminology.hl7.org/CodeSystem/condition-ver-status",
"code": "confirmed"
}]
},
"category": [{
"coding": [{
"system": "http://terminology.hl7.org/CodeSystem/condition-category",
"code": "encounter-diagnosis",
"display": "Encounter Diagnosis"
}]
}],
"severity": {
"coding": [{
"system": "http://snomed.info/sct",
"code": diagnosis_data.get('severity_code', '24484000'),
"display": diagnosis_data.get('severity', 'Severe')
}]
},
"code": {
"coding": [{
"system": "http://snomed.info/sct",
"code": diagnosis_data.get('snomed_code', ''),
"display": diagnosis_data.get('diagnosis_name', '')
}, {
"system": "http://hl7.org/fhir/sid/icd-10-cm",
"code": diagnosis_data.get('icd10_code', ''),
"display": diagnosis_data.get('diagnosis_name', '')
}],
"text": diagnosis_data.get('diagnosis_name', '')
},
"subject": {
"reference": patient_reference
},
"onsetDateTime": diagnosis_data.get('onset_date', ''),
"recordedDate": diagnosis_data.get('recorded_date', '')
}
5. DiagnosticReport Resource
def create_diagnostic_report(report_data, patient_reference, observations):
"""Generate FHIR R4 DiagnosticReport"""
return {
"resourceType": "DiagnosticReport",
"id": report_data.get('id', 'report-1'),
"status": "final",
"category": [{
"coding": [{
"system": "http://terminology.hl7.org/CodeSystem/v2-0074",
"code": "LAB",
"display": "Laboratory"
}]
}],
"code": {
"coding": [{
"system": "http://loinc.org",
"code": report_data.get('loinc_code', ''),
"display": report_data.get('report_name', '')
}],
"text": report_data.get('report_name', '')
},
"subject": {
"reference": patient_reference
},
"effectiveDateTime": report_data.get('date', ''),
"issued": report_data.get('issued_date', ''),
"result": [
{"reference": f"Observation/{obs_id}"}
for obs_id in observations
],
"conclusion": report_data.get('conclusion', '')
}
FHIR Bundle Creation
def create_fhir_bundle(entries, bundle_type="transaction"):
"""Create FHIR Bundle to group multiple resources"""
return {
"resourceType": "Bundle",
"type": bundle_type,
"entry": [
{
"fullUrl": f"urn:uuid:{entry.get('id', '')}",
"resource": entry,
"request": {
"method": "POST",
"url": entry.get('resourceType', '')
}
}
for entry in entries
]
}
Medical Coding Systems
Common Code Systems
CODE_SYSTEMS = {
"rxnorm": {
"system": "http://www.nlm.nih.gov/research/umls/rxnorm",
"description": "RxNorm - Medication names"
},
"snomed": {
"system": "http://snomed.info/sct",
"description": "SNOMED CT - Clinical terms"
},
"loinc": {
"system": "http://loinc.org",
"description": "LOINC - Lab tests and observations"
},
"icd10": {
"system": "http://hl7.org/fhir/sid/icd-10-cm",
"description": "ICD-10-CM - Diagnoses"
},
"cpt": {
"system": "http://www.ama-assn.org/go/cpt",
"description": "CPT - Procedures"
},
"ucum": {
"system": "http://unitsofmeasure.org",
"description": "UCUM - Units of measure"
}
}
Common LOINC Codes
COMMON_LOINC_CODES = {
"glucose": "2345-7", # Glucose [Mass/volume] in Serum or Plasma
"hba1c": "4548-4", # Hemoglobin A1c/Hemoglobin.total in Blood
"cholesterol": "2093-3", # Cholesterol [Mass/volume] in Serum or Plasma
"hdl": "2085-9", # HDL Cholesterol [Mass/volume] in Serum or Plasma
"ldl": "2089-1", # LDL Cholesterol [Mass/volume] in Serum or Plasma
"triglycerides": "2571-8", # Triglyceride [Mass/volume] in Serum or Plasma
"creatinine": "2160-0", # Creatinine [Mass/volume] in Serum or Plasma
"hemoglobin": "718-7", # Hemoglobin [Mass/volume] in Blood
"wbc": "6690-2", # Leukocytes [#/volume] in Blood
"platelets": "777-3", # Platelets [#/volume] in Blood
"bp_systolic": "8480-6", # Systolic blood pressure
"bp_diastolic": "8462-4", # Diastolic blood pressure
"heart_rate": "8867-4", # Heart rate
"temperature": "8310-5", # Body temperature
"weight": "29463-7", # Body weight
"height": "8302-2" # Body height
}
FHIR Validation
def validate_fhir_resource(resource):
"""Basic FHIR resource validation"""
errors = []
# Required fields
if 'resourceType' not in resource:
errors.append("Missing required field: resourceType")
# Resource-specific validation
resource_type = resource.get('resourceType')
if resource_type == 'Patient':
if 'name' not in resource or not resource['name']:
errors.append("Patient must have at least one name")
elif resource_type == 'MedicationRequest':
if 'status' not in resource:
errors.append("MedicationRequest must have status")
if resource.get('status') not in ['active', 'on-hold', 'cancelled', 'completed']:
errors.append(f"Invalid status: {resource.get('status')}")
elif resource_type == 'Observation':
if 'status' not in resource:
errors.append("Observation must have status")
if 'code' not in resource:
errors.append("Observation must have code")
return {
"valid": len(errors) == 0,
"errors": errors
}
Complete Medical Document → FHIR Pipeline
def medical_data_to_fhir_bundle(medical_data):
"""Convert complete medical document to FHIR Bundle"""
# Create Patient resource
patient = create_fhir_patient(medical_data.get('patient', {}))
patient_ref = f"Patient/{patient['id']}"
resources = [patient]
# Add MedicationRequests
for med in medical_data.get('medications', []):
med_request = create_medication_request(med, patient_ref)
resources.append(med_request)
# Add Observations (lab results, vitals)
for obs in medical_data.get('observations', []):
observation = create_observation(obs, patient_ref)
resources.append(observation)
# Add Conditions (diagnoses)
for dx in medical_data.get('diagnoses', []):
condition = create_condition(dx, patient_ref)
resources.append(condition)
# Create Bundle
bundle = create_fhir_bundle(resources, bundle_type="transaction")
# Validate all resources
validation_results = [
validate_fhir_resource(res) for res in resources
]
return {
"bundle": bundle,
"validation": validation_results,
"resource_count": len(resources)
}
Example Workflows
Example 1: Prescription → FHIR
# Input: OCR extracted prescription data
prescription_data = {
"patient": {
"id": "pat-001",
"first_name": "John",
"last_name": "Doe",
"mrn": "MRN123456",
"birth_date": "1980-01-15"
},
"medications": [{
"id": "med-001",
"name": "Metformin",
"rxnorm_code": "860975",
"dose_value": 500,
"dose_unit": "mg",
"frequency": 2,
"route": "Oral",
"quantity": 60,
"days_supply": 30,
"sig": "Take 500mg by mouth twice daily with meals"
}]
}
# Generate FHIR Bundle
result = medical_data_to_fhir_bundle(prescription_data)
print(f"Created {result['resource_count']} FHIR resources")
Example 2: Lab Results → FHIR
# Input: OCR extracted lab results
lab_data = {
"patient": {
"id": "pat-001",
"mrn": "MRN123456"
},
"observations": [
{
"id": "obs-glucose",
"test_name": "Glucose",
"loinc_code": "2345-7",
"value": 126,
"unit": "mg/dL",
"ucum_code": "mg/dL",
"ref_low": 70,
"ref_high": 99,
"category": "laboratory",
"date": "2024-11-22T10:30:00Z"
},
{
"id": "obs-hba1c",
"test_name": "Hemoglobin A1c",
"loinc_code": "4548-4",
"value": 7.2,
"unit": "%",
"ucum_code": "%",
"ref_low": 4.0,
"ref_high": 5.6,
"category": "laboratory",
"date": "2024-11-22T10:30:00Z"
}
]
}
# Generate FHIR Bundle
result = medical_data_to_fhir_bundle(lab_data)
Best Practices
- Always validate FHIR resources before submission
- Use standard code systems (LOINC, SNOMED, RxNorm, ICD-10)
- Include meaningful text alongside coded values
- Provide reference ranges for observations
- Use appropriate status codes (active, final, entered-in-error, etc.)
- Include timestamps (effectiveDateTime, authoredOn, etc.)
- Link resources properly using references
- Document source of data (OCR extraction, manual entry, etc.)
Integration with Agents
This skill integrates with:
- HEALTHCARELINC: Receives structured medical data
- COMPLIANCELINC: Validates HIPAA compliance
- Medical-OCR: Receives OCR-extracted data
Resources
Version: 1.0.0
Last Updated: 2024-11-22
FHIR Version: R4
Maintainer: Doctors-Linc Development Team