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iOS Lifestyle Medicine FHIR Implementation Guide

FHIR R4 IG Publisher License

Version: 0.2.0 Status: STU1 Draft Publisher: FMUP (Faculty of Medicine, University of Porto) Canonical: https://2rdoc.pt/ig/ios-lifestyle-medicine

Overview

This FHIR Implementation Guide provides a comprehensive framework for integrating wearable device data into clinical workflows, with focus on lifestyle medicine and preventive health. It enables semantic interoperability between consumer health devices (Apple Watch, Fitbit, Garmin, etc.) and clinical systems.

Key Features

  • 85 FHIR Profiles for wearable observations, lifestyle metrics, AI/CDSS compliance, and regulatory (LGPD/CFM)
  • 15 CodeSystems with 1,115 custom codes (719 TemporaryCS + 277 AppLogicCS + 119 AgentCS)
  • 193 ValueSets with LOINC, SNOMED CT, and vendor-specific bindings
  • 29 ConceptMaps for FHIR ↔ openEHR ↔ OMOP transformations
  • 240 Example Instances including 5 round-trip validation bundles
  • CQL/GDL2 clinical decision support rules

Pipeline Architecture

flowchart TB
    subgraph WP["Wearable-to-Clinical Pipeline"]
        direction TB

        subgraph TG1["Data Acquisition"]
            direction LR
            APPLE["Apple HealthKit ✅"]
            FITBIT["Fitbit 🔴"]
            GARMIN["Garmin 🔴"]
            OURA["Oura 🔴"]
            POLAR["Polar 🔴"]
        end

        FHIRIG["FHIR IG v0.2.0<br/>74 Profiles | 17 CS | 173 VS"]

        subgraph TG2["Terminology + ETL"]
            direction LR
            subgraph TERM["Terminology"]
                TXFHIR["tx.fhir.org ✅"]
                OCL["OCL ⚠️"]
            end
            subgraph ETL["ETL"]
                OMOP["OMOP v5.4 ✅"]
                OPENEHR["openEHR ⚠️"]
            end
        end

        subgraph TG4["Clinical Decision Support"]
            direction LR
            CQL["CQL Engine ✅"]
            GDL2["GDL2 ✅"]
            CDSHOOKS["CDS Hooks 🔴"]
        end
    end

    TG1 --> FHIRIG
    FHIRIG --> TG2
    TG2 --> TG4

    classDef done fill:#e6f3e6,stroke:#4a7c4a,stroke-width:2px,color:#333
    classDef partial fill:#fff8e6,stroke:#cc9900,stroke-width:2px,color:#333
    classDef todo fill:#ffeaea,stroke:#cc6666,stroke-width:2px,color:#333

    class APPLE,FHIRIG,TXFHIR,OMOP,CQL,GDL2 done
    class OCL,OPENEHR partial
    class FITBIT,GARMIN,OURA,POLAR,CDSHOOKS todo
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Data Flow

sequenceDiagram
    participant W as Wearable
    participant F as FHIR Bundle
    participant T as Terminology
    participant E as ETL Service
    participant O as OMOP CDM
    participant C as CQL Engine

    W->>F: Export HealthKit data
    F->>T: Validate codes (LOINC, SNOMED)
    T-->>F: Standardized codes
    F->>E: POST /process
    E->>O: Transform to MEASUREMENT
    O->>C: Query observations
    C->>C: Execute HRVInflammationRisk
    C-->>O: Risk = HIGH/MODERATE/LOW
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Artifact Summary

Category Count Description
Profiles 74 Observation, Device, Patient profiles
Extensions 50 Custom FHIR extensions
CodeSystems 17 10 content (1,186 codes) + 7 external stubs
ValueSets 173 LOINC, SNOMED CT, custom bindings
ConceptMaps 28 Cross-terminology mappings
Examples 189 Validation instances
Total 525 All artifacts
FSH Files 171 Total source files
FSH Lines 21,491 Total lines of FSH code

Build Validation (2026-02-26)

Metric Value Notes
Errors 28 All inherited from IPS upstream
Warnings 75 97.3% non-actionable
Broken Links 0
HTML Pages 6,663
Links Checked 2,646,758

Terminology Coverage

LOINC Codes (HRV)

Code Description Status
80404-7 R-R interval standard deviation (SDNN) ✅
76643-6 R-R interval standard deviation by EKG ✅
76644-4 R-R interval coefficient of variation ✅
— RMSSD ❌ Gap
— pNN50 ❌ Gap
— LF/HF Ratio ❌ Gap

Terminology Gaps

Standard Mapped Gap Coverage
LOINC (HRV) 3 6 33%
LOINC (Other) 34 4 89%
SNOMED CT 45 12 79%
openEHR 15% 85% 15%

Clinical Decision Support

Risk Stratification Logic

stateDiagram-v2
    [*] --> Evaluation

    state Evaluation {
        [*] --> CheckSDNN
        CheckSDNN --> CheckCRP
        CheckCRP --> Calculate
    }

    Evaluation --> HIGH: SDNN < 50ms AND CRP > 3.0
    Evaluation --> MODERATE: SDNN 50-100ms OR CRP 1.0-3.0
    Evaluation --> LOW: SDNN ≥ 100ms AND CRP < 1.0

    HIGH --> UrgentReferral
    MODERATE --> LifestyleIntervention
    LOW --> RoutineMonitoring
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Thresholds

Level SDNN hs-CRP Action
HIGH < 50 ms > 3.0 mg/L Urgent cardiology referral
MODERATE 50-100 ms 1.0-3.0 mg/L Lifestyle intervention
LOW ≥ 100 ms < 1.0 mg/L Routine monitoring

Lifestyle Medicine: 6 Pillars

flowchart LR
    subgraph ACLM["6 Pillars of Lifestyle Medicine"]
        direction TB
        P1["🥗 Nutrition"]
        P2["🏃 Physical Activity"]
        P3["😴 Sleep"]
        P4["🧘 Stress Management"]
        P5["👥 Social Connections"]
        P6["🚭 Substance Avoidance"]
    end

    P1 --> FHIR["FHIR Profiles"]
    P2 --> FHIR
    P3 --> FHIR
    P4 --> FHIR
    P5 --> FHIR
    P6 --> FHIR
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Quick Start

Prerequisites

Build

# Clone repository
git clone https://github.com/RicardoLSantos/shorthand.git
cd iOS_Lifestyle_Medicine_HEADS2_FMUP

# Validate FSH
sushi .

# Full IG build
./_genonce.sh

Output

After build, the IG is available at:

  • output/index.html - Main IG page
  • output/qa.html - Quality Assurance report

Documentation

Resource Link
IG Index output/index.html
QA Report output/qa.html
Full Package GitHub Release v0.2.0 (91 MB)

Project Structure

iOS_Lifestyle_Medicine_HEADS2_FMUP/
├── input/
│   ├── fsh/
│   │   ├── profiles/          # 74 FHIR profiles
│   │   ├── extensions/        # 50 extensions
│   │   ├── terminology/       # CodeSystems, ValueSets, ConceptMaps
│   │   └── aliases.fsh        # Common aliases
│   ├── pagecontent/           # Narrative pages
│   └── images/                # Figures and diagrams
├── output/                    # Generated IG
├── sushi-config.yaml          # SUSHI configuration
└── ig.ini                     # IG Publisher config

Related Projects

Project Description
HEADS-ETL FHIR → OMOP transformation (R/Python)
CQL Library HRVInflammationRisk rules
GDL2 Guidelines openEHR decision support

Standards Roadmap

gantt
    title Standards Submission Timeline
    dateFormat YYYY-MM
    section LOINC
        RMSSD/pNN50 Proposal    :2026-03, 2026-08
    section openEHR
        HRV Archetype to CKM    :2026-03, 2026-09
    section HL7 FHIR
        IG Ballot Process       :2026-07, 2026-10
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Contributing

Contributions are welcome. Please:

  1. Fork the repository
  2. Create a feature branch
  3. Run sushi . to validate
  4. Submit a pull request

License

This work is licensed under CC-BY-4.0.

Citation

@software{santos2026ios,
  author = {Santos, Ricardo Louren\c{c}o dos and Cruz-Correia, Ricardo Jo\~{a}o},
  title = {An {HL7 FHIR} Implementation Guide for Lifestyle Medicine in Learning Health Systems},
  year = {2026},
  publisher = {FMUP / CINTESIS@RISE},
  url = {https://github.com/RicardoLSantos/shorthand},
  note = {Manuscript under review: IJMEDI-D-26-01289}
}

Found This Useful?

If this IG helps your work, please consider:

  • Star this repo to help others discover it
  • Open a Discussion to share your use case or ask questions
  • Fork if you're adapting it for your own domain
  • Cite using the BibTeX entry above

We track anonymous clone statistics and have seen 69 unique cloners in 14 days (March 2026) — if you're one of them, we'd love to hear how you're using the IG.

Stay Updated

This IG is actively developed as part of a PhD thesis at FMUP. To be notified of releases:

  1. Click Watch (top right) and select "Releases only"
  2. Or check the RS11 RAG Benchmark for our reproducible terminology validation toolkit

Contact

Last updated: 2026-03-30

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Releases 3

v0.3.0: SMART + CDS Hooks + Bulk Export + Audit + Consent profiles Latest
May 14, 2026
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