---
name: clinical-data-review
description: Review clinical data models and APIs for HL7 FHIR conformance, terminology standards, interoperability, and clinical workflow correctness.
version: "1.0.0"
category: analysis
platforms:
  - CLAUDE_CODE
---

You are in AUTONOMOUS MODE. Do NOT ask questions. Review the entire codebase's clinical data layer systematically.

TARGET:
$ARGUMENTS

If no arguments provided, review all data models, schemas, and APIs in the current
working directory for clinical data standards compliance. If a specific standard is
named (e.g., "FHIR only", "terminology"), focus on that area.

============================================================
PHASE 0: CLINICAL SYSTEM DETECTION
============================================================

Auto-detect the project stack and clinical context:

1. Detect tech stack (package.json, requirements.txt, pom.xml, go.mod, *.csproj, etc.).
2. Identify clinical libraries and dependencies:
   - FHIR: hapi-fhir, fhir.js, fhirclient, pyFHIR, Firely SDK, fhir-net-api
   - HL7v2: node-hl7-complete, python-hl7, HAPI, nHAPI
   - DICOM: dcmjs, pydicom, fo-dicom, cornerstone.js
   - Terminology: SNOMED packages, LOINC libraries, ICD-10 validators
   - CDA: CDA generators/parsers, CCDA templates
3. Identify database and ORM (Prisma, TypeORM, SQLAlchemy, Hibernate, EF Core).
4. Locate data model definitions:
   - Schema files (*.prisma, *.graphql, *.proto)
   - Model/entity classes
   - Migration files
   - OpenAPI/Swagger specs
   - TypeScript/Python types/interfaces

============================================================
PHASE 1: FHIR CONFORMANCE REVIEW
============================================================

Evaluate data models against FHIR R4 resource definitions:

RESOURCE MODELING:
- Map project data models to FHIR resources:
  - Patient: demographics, identifiers, contact, communication preferences
  - Practitioner / PractitionerRole: provider info, specialties, qualifications
  - Organization: facilities, departments, healthcare organizations
  - Encounter: visits, admissions, appointments
  - Condition: diagnoses, problems, health concerns
  - Observation: vitals, lab results, social history, assessments
  - MedicationRequest / MedicationStatement: prescriptions, current meds
  - AllergyIntolerance: allergies, adverse reactions
  - Procedure: surgical, diagnostic, therapeutic procedures
  - DiagnosticReport: lab reports, imaging reports, pathology
  - DocumentReference: clinical documents, notes, external records
  - CarePlan: treatment plans, goals, activities
  - Immunization: vaccination records

For each mapped resource, check:
- Required FHIR elements present (status, subject, code, etc.)
- Correct cardinality (0..1, 0..*, 1..1, 1..*)
- Proper data types (CodeableConcept vs string, Reference vs ID, Period vs DateTime)
- Resource references use proper Reference type with resource type + ID
- Extensions are properly defined (not ad-hoc fields breaking FHIR structure)

SEARCH PARAMETERS:
- Verify FHIR search parameter support on API endpoints.
- Check standard search params: _id, _lastUpdated, _tag, _profile.
- Check resource-specific params: Patient?name, Observation?code, etc.
- Verify search modifiers: :exact, :contains, :missing.
- Check chained search support: Observation?subject:Patient.name
- Verify _include and _revinclude support.

CAPABILITY STATEMENT:
- Check for /metadata endpoint returning CapabilityStatement resource.
- Verify it accurately reflects implemented resources and operations.
- Check for declared profiles and supported search parameters.

BUNDLE SUPPORT:
- Verify transaction Bundle support (POST to root with type: transaction).
- Check for batch Bundle support.
- Verify searchset Bundle response format for search endpoints.
- Check Bundle entry fullUrl and resource consistency.

============================================================
PHASE 2: TERMINOLOGY AND CODING STANDARDS
============================================================

Review clinical terminology implementation:

ICD-10 (DIAGNOSES):
- Search for ICD-10-CM code handling in data models and business logic.
- Verify code format validation (letter + 2 digits + optional decimal + up to 4 digits).
- Check for code versioning (ICD-10 updates annually in October).
- Verify code descriptions are stored or lookable.
- Check for ICD-10-PCS (procedure codes) if surgical/procedural data exists.
- Flag hardcoded ICD-10 codes without version tracking.

CPT / HCPCS (PROCEDURES AND SERVICES):
- Search for CPT code handling in billing, orders, or procedure models.
- Verify CPT code validation (5 digits or 4 digits + letter).
- Check for HCPCS Level II codes (letter + 4 digits) for supplies/equipment.
- Verify modifier support (CPT modifiers: -25, -59, -76, etc.).
- Check for annual code updates handling.

SNOMED CT (CLINICAL TERMS):
- Search for SNOMED concept IDs in data models.
- Verify SNOMED codes use proper SCTID format (6-18 digit numeric).
- Check for concept hierarchy navigation capability.
- Verify SNOMED-to-ICD-10 mapping if cross-coding is needed.
- Check for SNOMED version/edition tracking.

LOINC (LAB AND OBSERVATIONS):
- Search for LOINC codes in observation/lab models.
- Verify LOINC code format validation (numeric with optional dash and check digit).
- Check for proper units of measure (UCUM standard) paired with LOINC codes.
- Verify lab result value sets align with LOINC answer lists.

RxNorm (MEDICATIONS):
- Search for medication coding in prescription/medication models.
- Check for RxNorm concept unique identifiers (RxCUI).
- Verify NDC (National Drug Code) handling if pharmacy integration exists.
- Check for drug-drug interaction checking capability.

TERMINOLOGY SERVICE:
- Check for terminology server integration ($lookup, $validate-code, $expand).
- Verify ValueSet binding on coded fields.
- Check for CodeSystem resources or external terminology service configuration.
- Flag coded fields that accept free text without code validation.

============================================================
PHASE 3: INTEROPERABILITY ASSESSMENT
============================================================

Review data exchange capabilities:

CDA / CCDA DOCUMENTS:
- Search for CDA document generation or parsing.
- Check for CCDA template conformance (CCD, Discharge Summary, Progress Note, etc.).
- Verify required sections: allergies, medications, problems, procedures, results.
- Check for structured vs narrative-only sections.
- Verify XML schema validation on generated documents.

BULK DATA EXPORT:
- Check for FHIR Bulk Data Access ($export) implementation.
- Verify NDJSON output format.
- Check for group-level and system-level export support.
- Verify async export pattern (kick-off, status polling, file download).

ADT MESSAGING:
- Search for HL7v2 ADT (Admit/Discharge/Transfer) message handling.
- Check for A01 (admit), A02 (transfer), A03 (discharge), A04 (register),
  A08 (update) message type support.
- Verify PID, PV1, NK1 segment parsing/generation.

ORU / ORM MESSAGING:
- Search for HL7v2 ORU (results) and ORM (orders) message handling.
- Check for OBR, OBX segment handling in results.
- Verify order/result linking via placer/filler order numbers.

DIRECT MESSAGING:
- Check for Direct protocol support (secure email for clinical data).
- Verify S/MIME encryption compliance.

============================================================
PHASE 4: CLINICAL WORKFLOW VALIDATION
============================================================

Review clinical workflow implementation correctness:

ORDER MANAGEMENT:
- Check order lifecycle: draft -> active -> completed/cancelled.
- Verify order validation (appropriate order for patient context).
- Check for duplicate order detection.
- Verify order modification and cancellation workflows.
- Check for clinical decision support at order entry.

RESULTS MANAGEMENT:
- Verify result status workflow: preliminary -> final -> corrected -> amended.
- Check for abnormal result flagging (reference ranges, critical values).
- Verify result acknowledgment tracking.
- Check for result routing based on ordering provider.

MEDICATION MANAGEMENT:
- Check prescription lifecycle: draft -> active -> stopped/completed.
- Verify drug allergy checking against patient allergies.
- Check for formulary validation.
- Verify medication reconciliation support.
- Check for e-prescribing (NCPDP SCRIPT) readiness.

DOCUMENTATION:
- Check for clinical note types (progress notes, H&P, discharge summary).
- Verify note signing/cosigning workflow.
- Check for addendum support (append, not edit).
- Verify template support for structured documentation.

DATA QUALITY:
- Check for required field enforcement on critical clinical data.
- Verify referential integrity between related clinical records.
- Check for data validation rules (date ranges, numeric ranges, code validation).
- Verify duplicate detection mechanisms (patient matching, record deduplication).

============================================================
OUTPUT
============================================================

## Clinical Data Model Review

**Project:** [name]
**Stack:** [detected technologies]
**Clinical Domain:** [EHR/lab/pharmacy/imaging/billing/etc.]
**Date:** [date]

### Standards Conformance Summary

| Standard | Coverage | Conformance | Issues |
|---|---|---|---|
| FHIR R4 | [N resources mapped] | [FULL/PARTIAL/NONE] | N |
| ICD-10-CM/PCS | [usage found?] | [VALID/PARTIAL/NONE] | N |
| CPT/HCPCS | [usage found?] | [VALID/PARTIAL/NONE] | N |
| SNOMED CT | [usage found?] | [VALID/PARTIAL/NONE] | N |
| LOINC | [usage found?] | [VALID/PARTIAL/NONE] | N |
| RxNorm | [usage found?] | [VALID/PARTIAL/NONE] | N |
| CDA/CCDA | [support found?] | [CONFORMANT/PARTIAL/NONE] | N |
| HL7v2 | [usage found?] | [VALID/PARTIAL/NONE] | N |

### FHIR Resource Mapping

| Project Model | FHIR Resource | Required Elements | Missing Elements | Extensions |
|---|---|---|---|---|
| [model name] | Patient | [present] | [missing] | [non-standard fields] |

### Data Model Findings

| # | Severity | File | Model/Field | Standard | Issue | Fix |
|---|----------|------|-------------|----------|-------|-----|
| 1 | High | path/to/model.ts | Patient.identifier | FHIR R4 | Missing system URI on identifier | Add system field per FHIR Identifier datatype |

### Terminology Gaps

| Coded Field | Current Implementation | Required Standard | Gap |
|---|---|---|---|
| [diagnosis_code] | Free text string | ICD-10-CM CodeableConcept | No code validation, no system URI |

### Interoperability Readiness
- FHIR API: [Ready/Partial/Not implemented]
- Bulk Export: [Ready/Partial/Not implemented]
- CDA/CCDA: [Ready/Partial/Not implemented]
- HL7v2: [Ready/Partial/Not implemented]
- Patient matching: [algorithm used or none]

### Clinical Workflow Assessment
| Workflow | Status | Key Gaps |
|---|---|---|
| Order management | [Complete/Partial/Missing] | [gaps] |
| Results delivery | [Complete/Partial/Missing] | [gaps] |
| Medication mgmt | [Complete/Partial/Missing] | [gaps] |
| Documentation | [Complete/Partial/Missing] | [gaps] |

============================================================
NEXT STEPS
============================================================

After reviewing the findings:
- "Run `/healthcare-api` to scaffold FHIR-compliant API endpoints for missing resources."
- "Run `/healthcare-compliance` to audit regulatory compliance of the clinical data layer."
- "Run `/database-review` to optimize clinical data model performance and indexing."
- "Run `/api-review` to evaluate API design patterns for clinical endpoints."
- "Run `/medical-billing` to review billing code handling and revenue cycle integration."

============================================================
DO NOT
============================================================

- Do NOT modify any code -- this is a review skill, not a build skill.
- Do NOT assume FHIR compliance from library presence alone -- verify actual resource structure.
- Do NOT accept free-text fields as valid coded data -- flag missing terminology binding.
- Do NOT skip checking cardinality and data types against FHIR spec.
- Do NOT ignore custom extensions -- evaluate if standard FHIR elements would suffice.
- Do NOT treat terminology code presence as validation -- verify format and system URI.
- Do NOT overlook data quality rules -- missing validation is a finding.
- Do NOT install external tools or FHIR validators -- analyze schemas and code directly.