design-fhir-loinc-questionnaires

Helps creating FHIR conforming questionnaire definitions from plain requirement ideation docs. Contains scripts to look up LOINC and SNOMED CT codes for medical conditions, findings, observations, medications, procedures from a official coding APIs. No API keys required at the moment.

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Install skill "design-fhir-loinc-questionnaires" with this command: npx skills add elmariachi111/fhir-questionnaire

FHIR Questionnaire Skill

⚠️ CRITICAL RULES - READ FIRST

NEVER suggest LOINC or SNOMED CT codes from memory or training data. ALWAYS use the search and query scripts in this skill.

When any clinical code is needed:

  1. For clinical questions/observations: ALWAYS run python scripts/search_loinc.py "search term" FIRST
  2. For clinical concepts/conditions: ALWAYS run python scripts/search_snomed.py "search term" FIRST
  3. ONLY use codes returned by the scripts
  4. If search fails or returns no results, DO NOT make up codes

Clinical codes from AI memory are highly unreliable and will cause incorrect clinical coding.

Network Access Requirements

Requires whitelisted network access:

  • clinicaltables.nlm.nih.gov (LOINC search)
  • tx.fhir.org (FHIR terminology server for LOINC answer lists and SNOMED CT search)

If network access fails, STOP. Do not suggest codes.

Essential Scripts (Use These Every Time)

1. Search LOINC Codes

ALWAYS run this before suggesting any LOINC code (clinical questions/observations):

python scripts/search_loinc.py "depression screening"
python scripts/search_loinc.py "blood pressure" --format fhir

2. Search SNOMED CT Codes

ALWAYS run this before suggesting any SNOMED CT code (clinical concepts/conditions):

python scripts/search_snomed.py "diabetes"
python scripts/search_snomed.py "hypertension" --format fhir
python scripts/search_snomed.py "diabetes mellitus" --semantic-tag "disorder"

Note: The --semantic-tag filter works best when the semantic tag appears in the display name (e.g., "Diabetes mellitus (disorder)").

3. Find Answer Options

For questions with standardized answers:

python scripts/query_valueset.py --loinc-code "72166-2"
python scripts/query_valueset.py --loinc-code "72166-2" --format fhir

4. Validate Questionnaire

Before finalizing:

python scripts/validate_questionnaire.py questionnaire.json

Templates

Start with assets/templates/:

  • minimal.json - Bare bones structure
  • basic.json - Simple questionnaire
  • advanced.json - Complex with conditional logic

Workflows

Standardized Clinical Instruments (PHQ-9, GAD-7, etc.)

# Step 1: Find panel code (NEVER skip this)
python scripts/search_loinc.py "PHQ-9 panel"

# Step 2: Find answer options
python scripts/query_valueset.py --loinc-code "FOUND-CODE" --format fhir

# Step 3: See examples/templates
# Check references/examples.md for complete implementations

Custom Organizational Questionnaires

# Step 1: Start with template
cp assets/templates/advanced.json my-questionnaire.json

# Step 2: For any clinical questions, search LOINC
python scripts/search_loinc.py "body weight"

# Step 3: Add answer options if available
python scripts/query_valueset.py --loinc-code "FOUND-CODE"

# Step 4: For custom questions without LOINC results, use inline answerOptions
# (no coding system needed - just code + display)

# Step 5: Validate
python scripts/validate_questionnaire.py my-questionnaire.json

Custom Answer Lists (When LOINC Has No Match)

When LOINC search returns no suitable answer list, use inline answerOption with system-less valueCoding by default. This is the simplest, spec-compliant approach for custom answer lists:

{
  "linkId": "sleep-quality",
  "type": "choice",
  "text": "How would you rate your sleep quality?",
  "answerOption": [
    {"valueCoding": {"code": "good", "display": "Good"}},
    {"valueCoding": {"code": "fair", "display": "Fair"}},
    {"valueCoding": {"code": "poor", "display": "Poor"}}
  ]
}

Do NOT invent a coding system URI. Omitting system is valid FHIR and signals that these are local, questionnaire-scoped codes.

Opt-in: Reusable Welshare Coding System

If the user explicitly requests reusable codes that can be shared across questionnaires, use the Welshare namespace (http://codes.welshare.app) via the helper script:

python scripts/create_custom_codesystem.py --interactive

This creates a CodeSystem + ValueSet pair. To convert an inline answer list to the reusable format, add "system": "http://codes.welshare.app/CodeSystem/<category>/<id>.json" to each valueCoding and optionally reference the ValueSet via answerValueSet. See references/loinc_guide.md for details.

Common Patterns

  • Conditional display: Use enableWhen to show/hide questions
  • Repeating groups: Set "repeats": true for medications, allergies, etc.
  • Standardized answers: Use query_valueset.py --loinc-code "CODE" for LOINC-backed answer lists
  • Custom answers: Use inline answerOption with valueCoding (no system) for non-standardized choices

See references/examples.md for complete working examples.

Script Reference

search_loinc.py - Find LOINC Codes

python scripts/search_loinc.py "blood pressure"
python scripts/search_loinc.py "depression" --limit 10 --format fhir

search_snomed.py - Find SNOMED CT Codes

python scripts/search_snomed.py "diabetes"
python scripts/search_snomed.py "hypertension" --limit 10 --format fhir
python scripts/search_snomed.py "asthma" --format table
python scripts/search_snomed.py "diabetes mellitus" --semantic-tag "disorder"

Formats: json (default), table, fhir Semantic tags (when present in results): disorder, finding, procedure, body structure, substance, organism Note: Semantic tag filtering only works when tags are included in the display name from the terminology server.

query_valueset.py - Find Answer Options

python scripts/query_valueset.py --loinc-code "72166-2"
python scripts/query_valueset.py --loinc-code "72166-2" --format fhir
python scripts/query_valueset.py --search "smoking"

Alternative servers (if tx.fhir.org fails):

  • --server https://hapi.fhir.org/baseR4
  • --server https://r4.ontoserver.csiro.au/fhir

validate_questionnaire.py - Validate Structure

python scripts/validate_questionnaire.py questionnaire.json
python scripts/validate_questionnaire.py questionnaire.json --verbose

extract_loinc_codes.py - Analyze Codes

python scripts/extract_loinc_codes.py questionnaire.json
python scripts/extract_loinc_codes.py questionnaire.json --validate

create_custom_codesystem.py - Reusable Custom Codes (Opt-in)

python scripts/create_custom_codesystem.py --interactive

Only use when the user explicitly requests reusable codes across questionnaires. Uses the Welshare namespace: http://codes.welshare.app. Default for custom answers is inline answerOption without a coding system.

Troubleshooting

  • No LOINC results: Use broader search terms (e.g., "depression" not "PHQ-9 question 1")
  • Network errors: Try alternative servers with --server flag
  • Validation errors: Check references/fhir_questionnaire_spec.md for requirements
  • No answer list found: Use inline answerOption with system-less valueCoding (code + display only). Do NOT fall back to a custom coding system unless the user explicitly requests it

Deep Knowledge References

We've assembled deep knowledge for you to consult on specific topics. Checkout the index file on See REFERENCE.md and drill down the knowledge path for highly detailed instructions on modelling questionnaires.

Reference Links

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