fhir-generator

Name: fhir-generator
Rating: 55
Author: Fadil369

by Fadil369

AI-powered OCR pipeline for healthcare document processing with automated PowerPoint generation

⭐ 0🍴 0📅 2025年11月23日

ai fhir google-vision healthcare hipaa langchain medical nodejs

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SKILL.md

name: fhir-generator description: FHIR R4 resource generation and validation for healthcare interoperability. Converts medical data into FHIR-compliant JSON resources (Patient, Observation, MedicationRequest, Condition, etc.). Use when creating FHIR resources, validating healthcare data structures, or preparing data for EHR integration. license: MIT allowed-tools:

python
bash metadata: version: "1.0.0" category: healthcare fhir-version: "R4" standard: "HL7 FHIR"

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

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fhir-generator

SKILL.md

FHIR R4 Resource Generator Skill

Overview

When to Use This Skill

Core FHIR Resources

1. Patient Resource

2. MedicationRequest Resource

3. Observation Resource (Lab Results, Vitals)

4. Condition/Diagnosis Resource

5. DiagnosticReport Resource

FHIR Bundle Creation

Medical Coding Systems

Common Code Systems

Common LOINC Codes

FHIR Validation

Complete Medical Document → FHIR Pipeline

Example Workflows

Example 1: Prescription → FHIR

Example 2: Lab Results → FHIR

Best Practices

Integration with Agents

Resources

スコア

レビュー

prompt-lookup

skill-lookup

create-pr

orpc-contract-first

component-refactoring

web-design-guidelines

fhir-generator

SKILL.md

FHIR R4 Resource Generator Skill

Overview

When to Use This Skill

Core FHIR Resources

1. Patient Resource

2. MedicationRequest Resource

3. Observation Resource (Lab Results, Vitals)

4. Condition/Diagnosis Resource

5. DiagnosticReport Resource

FHIR Bundle Creation

Medical Coding Systems

Common Code Systems

Common LOINC Codes

FHIR Validation

Complete Medical Document → FHIR Pipeline

Example Workflows

Example 1: Prescription → FHIR

Example 2: Lab Results → FHIR

Best Practices

Integration with Agents

Resources

スコア

レビュー

関連

関連スキル

prompt-lookup

skill-lookup

create-pr

orpc-contract-first

component-refactoring

web-design-guidelines