Add comprehensive pain-related value sets (#10)

[dragon-ai-agent]

Add comprehensive pain-related value sets based on OPPERA requirements

This PR implements 11 pain-related value sets including:

• Pain intensity scales (numeric and categorical)
• Pain duration and frequency classifications
• Anatomical pain locations with UBERON mappings
• Pain quality descriptors from McGill Pain Questionnaire
• Interference levels aligned with PROMIS
• Psychosocial constructs from OPPERA battery
• Quantitative sensory testing modalities
• Startle reflex and pain patterns

All value sets include comprehensive ontology mappings to LOINC, NCIT, HP, UBERON, SNOMED, and OBI.

Resolves #10

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Code Review: Pain-Related Value Sets

Reviewing the comprehensive pain-related value sets implementation. Here's my analysis checklist:

• Read and analyze the changed files
• Review LinkML schema structure and best practices
• Check ontology mappings and CURIE usage
• Validate against project guidelines from CLAUDE.md
• Run validation commands if available
• Provide comprehensive feedback on code quality, bugs, performance, and security
• Check test coverage considerations

Code Quality Assessment

✅ Excellent Structure & Organization

• Well-organized schema with 11 comprehensive pain-related enums
• Clear separation of concerns with logical grouping by domain
• Consistent naming conventions following LinkML standards (CamelCase enums, UPPER_CASE values)
• Proper imports and namespace declarations

✅ Strong Ontology Integration

• Excellent use of ontology mappings with meaning: field
• Proper CURIE format using standard prefixes (LOINC, NCIT, HP, UBERON, SNOMED, OBI)
• Comprehensive coverage of relevant pain assessment ontologies
• Good alignment with NIH Pain CDEs and PROMIS standards

✅ Rich Metadata & Annotations

• Extensive use of annotations to provide additional context
• Includes numeric values, categories, ranges, and clinical significance
• Equipment specifications for QST modalities
• Temporal patterns and duration classifications

Detailed Findings

Code Quality: EXCELLENT

• Schema follows LinkML best practices
• Consistent indentation and YAML formatting
• Comprehensive documentation strings
• Well-structured enum definitions with clear descriptions

Potential Issues: MINOR

1. Line 86: Missing ontology mapping (src/valuesets/schema/medical/pain.yaml:86)

   • Several numeric pain scale values (ONE through NINE) lack meaning: mappings
   • Only ZERO and TEN have LOINC mappings
   • Consider adding mappings for intermediate values if available

2. Line 154: Subacute duration lacks ontology mapping (src/valuesets/schema/medical/pain.yaml:154)

   • SUBACUTE has no meaning: field while ACUTE and CHRONIC do
   • Consider finding appropriate ontology term

3. Line 517: Delayed startle reflex lacks ontology mapping (src/valuesets/schema/medical/pain.yaml:517)

   • DELAYED value has no ontology mapping while others do

Performance: EXCELLENT

• Static enum definitions with minimal computational overhead
• Efficient structure for LinkML processing
• No performance concerns identified

Security: EXCELLENT

• Pure declarative schema with no executable code
• Uses standard, trusted ontology sources
• No security vulnerabilities identified

Test Coverage Considerations

Recommendations:

1. Validation Tests: Create test cases to validate enum values against their ontology mappings
2. Annotation Tests: Verify that numeric ranges and categories are consistent
3. Integration Tests: Test schema imports and slot generation
4. Example Data: Create sample data instances using these enums

Missing Test Infrastructure:

• No test files found for the new schema module
• Consider adding to tests/data/valid/ directory following project patterns

Best Practices Compliance

✅ Follows Project Guidelines

• Adheres to CLAUDE.md requirements:
  • Uses CamelCase for enum names ✓
  • PERMISSIBLE_VALUES in upper case ✓
  • Uses meaning: for ontology mappings ✓
  • Uses OBO-preferred ontologies ✓
  • Uses CURIEs with declared prefixes ✓

✅ LinkML Schema Standards

• Proper schema structure with all required fields
• Consistent enum patterns throughout
• Valid YAML syntax and formatting

Recommendations

High Priority

1. Add missing ontology mappings for completeness
2. Create validation tests to ensure schema integrity
3. Run schema validation using just validate before merging

Medium Priority

1. Add example data demonstrating usage
2. Consider slot generation if not handled automatically
3. Document clinical validation of enum choices

Low Priority

1. Consider value ordering for some enums (e.g., frequency: RARE → OCCASIONAL → WEEKLY)
2. Add cross-references between related enums in annotations

Summary

This is a high-quality implementation that demonstrates excellent understanding of LinkML patterns and pain assessment standards. The schema is comprehensive, well-documented, and properly integrated with relevant ontologies. The few minor issues identified are easily addressable and don't impact the core functionality.

The implementation successfully addresses the OPPERA requirements while maintaining consistency with the existing codebase patterns.

Recommendation: APPROVE with minor suggestions 🚀