Add comprehensive enum metadata and stewardship framework

[cmungall]

Summary

This PR enhances the value sets project with comprehensive metadata and stewardship tracking for all 516 enums across 109 schema files.

Key Features

🏛️ Custom Metamodel for Validation

Created src/valuesets/metamodel/valuesets_meta.yaml with metaclasses:

• ValueSetEnumDefinition: Requires title, description, status, contributors
• ValueSetEnumDefinitionWithStewardship: Adds stewards, publishers, endorsers
• ReferenceEnumDefinition: For reference/controlled vocabulary enums
• Additional specialized metaclasses for sources and conformance

🌐 Stewardship Value Set

New stewardship.yaml with 15 recognized organizations:

• GA4GH, Gene Ontology Consortium, Genomic Standards Consortium
• Phenopackets, EMBL-EBI, NCBI, CDISC, HL7, ISO, W3C
• Uses ROR IDs for authoritative organization identification

📋 Complete Metadata Coverage

Updated all 516 enums with:

• ✅ Human-readable titles
• ✅ Descriptions
• ✅ Status (DRAFT, STANDARD, etc. using StandardsMaturityLevel)
• ✅ Contributors (default: ORCID + claude-code)
• ✅ Metaclass instantiation references

🎯 Conservative Stewardship Application

Applied stewardship metadata to well-established value sets:

Gene Ontology (4 enums):

• go_aspect.yaml, go_causality.yaml, go_evidence.yaml
• Stewards/Publishers: https://geneontology.org

Phenopackets (11 enums):

• KaryotypicSexEnum, PhenotypicSexEnum, AllelicStateEnum, ACMGPathogenicityEnum, etc.
• Stewards: https://phenopackets.org | Publishers: https://ga4gh.org

INSDC/GSC (2 enums):

• insdc_geographic_locations.yaml, insdc_missing_values.yaml
• Stewards: https://gensc.org | Publishers: https://www.insdc.org

📖 Governance Documentation

Created docs/governance.md covering:

• Source of Truth model (mirrored vs community value sets)
• Maturity levels and lifecycle management
• Stewardship roles and responsibilities
• Contributing process and quality standards
• Working group structure (placeholder for community expansion)

🐛 Bug Fix

Fixed pre-existing venv issue with stale shebangs pointing to old project location:

• ✅ just site now succeeds
• ✅ just test passes (63 tests)
• ✅ All LinkML generators work correctly

Technical Notes

Stewardship metadata uses annotations: block because LinkML's EnumDefinition doesn't support custom slots directly:

enums:
  GOAspect:
    instantiates:
    - valuesets_meta:ValueSetEnumDefinitionWithStewardship
    annotations:
      stewards: https://geneontology.org
      publishers: https://geneontology.org

Testing

• ✅ All 63 tests pass
• ✅ just site generates documentation
• ✅ just validate runs without errors
• ✅ Schema validation passes

Impact

• All enums now have complete, consistent metadata
• Foundation for community governance and stewardship tracking
• Validation framework via custom metamodel
• Clear path for expanding stewardship annotations

Next Steps

Future work could include:

• Expanding stewardship annotations to additional value sets
• Setting up working groups for domain-specific governance
• Creating automated validation for metadata completeness

🤖 Generated with Claude Code

Co-Authored-By: Claude [email protected]

[claude]

Claude finished @cmungall's task —— View job

---

PR Review: Add comprehensive enum metadata and stewardship framework

Review Checklist:

• Analyze metamodel design and validation approach
• Review enum metadata consistency across sample files
• Examine stewardship implementation and organization data
• Review governance documentation structure
• Check for potential bugs and security issues
• Assess performance implications
• Evaluate test coverage and validation
• Provide comprehensive feedback and recommendations

🔍 Review Summary

This is an excellent foundational PR that adds crucial governance infrastructure to the valuesets project. The implementation demonstrates thoughtful design and comprehensive coverage.

✅ Strengths

1. Well-Designed Metamodel Architecture

• Clean separation of concerns: The metamodel (src/valuesets/metamodel/valuesets_meta.yaml) properly separates validation rules from the main schema
• Hierarchical inheritance: Smart use of is_a relationships (ValueSetEnumDefinition → ValueSetEnumDefinitionWithStewardship)
• FHIR alignment: Stewardship roles (stewards/publishers/endorsers) follow established HL7 FHIR MetadataResource patterns
• Future-proof design: Uses instantiates for declarative conformance that can enable validation when LinkML supports it

2. Comprehensive Metadata Coverage

• 516 enums updated: All enums now have complete metadata (title, description, status, contributors)
• Consistent application: Excellent consistency across all domain files I sampled
• Proper ontology mappings: Good use of meaning: fields with valid CURIEs (GO:, NCIT:, etc.)
• Conservative stewardship: Appropriately applied only to well-established standards

3. Robust Stewardship Implementation

The stewardship.yaml design is particularly well done:

• ROR IDs preferred: Uses Research Organization Registry IDs for authoritative identification
• Comprehensive coverage: 15 key organizations spanning bioinformatics, standards bodies, and research institutions
• Rich metadata: Each organization includes establishment dates, websites, and contextual annotations

4. Excellent Governance Documentation

The governance.md provides:

• Clear stewardship model: Good distinction between mirrored vs. community value sets
• Maturity progression: Well-defined advancement path from DRAFT to STANDARD
• Future-oriented: Placeholder structure for working groups and steering committee

🐛 Issues Found

1. Minor Schema Inconsistencies

• ID namespace inconsistency: Some files use https://w3id.org/linkml/valuesets/ while others use https://w3id.org/valuesets/ or https://w3id.org/common-value-sets/ (seen in maturity_levels.yaml:5)
• Missing source attribution: Some enums with external origins lack source: fields

2. Validation Gaps

• No metamodel validation enforcement: Current LinkML doesn't validate instantiates constraints
• Missing status validation: No validation that status values match StandardsMaturityLevel enum
• Stewardship requirements unclear: ValueSetEnumDefinitionWithStewardship requires "at least one steward OR publisher" but this isn't enforceable

3. Documentation Issues

• Placeholder URLs: governance.md contains placeholder URLs (https://example.org/valuesets-stewardship-signup)
• Missing validation commands: Should mention running just validate after changes per CLAUDE.md guidelines

🔒 Security Assessment

• No security issues identified: All changes are schema/metadata updates
• Safe external references: All stewardship URLs point to legitimate organizations
• No credentials exposed: No secrets or sensitive information in the changes

⚡ Performance Considerations

• Minimal performance impact: Metadata additions don't affect runtime performance
• Large file count: 100 changed files is significant but well-organized
• Generation efficiency: Should verify just site generation time isn't significantly impacted

🧪 Test Coverage Assessment

Reviewed existing test suite:

• Good enum functionality tests: /tests/test_rich_enums.py provides comprehensive coverage
• Missing metamodel tests: No tests for new validation metaclasses
• No governance validation tests: Should add tests for stewardship metadata validation

📋 Recommendations

High Priority

1. Standardize ID namespaces: Choose one pattern and apply consistently across all schema files
2. Add metamodel tests: Create tests validating that enums properly instantiate their declared metaclasses
3. Fix placeholder URLs: Replace example.org URLs in governance.md with real endpoints or mark as "TBD"

Medium Priority

4. Add validation helper: Create just validate-stewardship command to check stewardship metadata completeness
5. Document stewardship criteria: Add guidelines for when to apply stewardship annotations
6. Consider status validation: Add validation that status values are from StandardsMaturityLevel enum

Low Priority

7. Enhance test coverage: Add tests for new governance features
8. Performance baseline: Measure and document site generation time impact
9. Working group structure: Begin organizing domain-specific working groups mentioned in governance.md

💡 Architecture Praise

The annotation-based stewardship approach is particularly clever:

annotations:
  stewards: https://geneontology.org
  publishers: https://geneontology.org

This works around LinkML's current limitation where EnumDefinition doesn't support custom slots directly, while maintaining clean semantics and future extensibility.

🎯 Conclusion

This PR represents exceptional work that establishes crucial governance foundations. The metamodel design is sophisticated, the metadata coverage is comprehensive, and the stewardship model is well-architected. The minor issues identified are easily addressable and don't detract from the overall quality.

Recommendation: Approve with minor fixes

The identified namespace inconsistencies and placeholder URLs should be addressed, but the core contribution is excellent and ready for adoption.

[claude]

Claude finished @cmungall's task —— View job

---

PR Review: Add comprehensive enum metadata and stewardship framework

Review Checklist:

• Analyze metamodel design and validation approach
• Review enum metadata consistency across sample files
• Examine stewardship implementation and organization data
• Review governance documentation structure
• Check for potential bugs and security issues
• Assess performance implications
• Evaluate test coverage and validation
• Provide comprehensive feedback and recommendations

🔍 Review Summary

This is an excellent foundational PR that adds crucial governance infrastructure to the valuesets project. The implementation demonstrates thoughtful design and comprehensive coverage.

✅ Strengths

1. Well-Designed Metamodel Architecture

• Clean separation of concerns: The metamodel (src/valuesets/metamodel/valuesets_meta.yaml) properly separates validation rules from the main schema
• Hierarchical inheritance: Smart use of is_a relationships (ValueSetEnumDefinition → ValueSetEnumDefinitionWithStewardship)
• FHIR alignment: Stewardship roles (stewards/publishers/endorsers) follow established HL7 FHIR MetadataResource patterns
• Future-proof design: Uses instantiates for declarative conformance that can enable validation when LinkML supports it

2. Comprehensive Metadata Coverage

• 516 enums updated: All enums now have complete metadata (title, description, status, contributors)
• Consistent application: Excellent consistency across all domain files I sampled
• Proper ontology mappings: Good use of meaning: fields with valid CURIEs (GO:, NCIT:, etc.)
• Conservative stewardship: Appropriately applied only to well-established standards

3. Robust Stewardship Implementation

The stewardship.yaml design is particularly well done:

• ROR IDs preferred: Uses Research Organization Registry IDs for authoritative identification
• Comprehensive coverage: 15 key organizations spanning bioinformatics, standards bodies, and research institutions
• Rich metadata: Each organization includes establishment dates, websites, and contextual annotations

4. Excellent Governance Documentation

The governance.md provides:

• Clear stewardship model: Good distinction between mirrored vs. community value sets
• Maturity progression: Well-defined advancement path from DRAFT to STANDARD
• Future-oriented: Placeholder structure for working groups and steering committee

🐛 Issues Found

1. Minor Schema Inconsistencies

• ID namespace inconsistency: Some files use https://w3id.org/linkml/valuesets/ while others use https://w3id.org/valuesets/ or https://w3id.org/common-value-sets/ (seen in maturity_levels.yaml:5)
• Missing source attribution: Some enums with external origins lack source: fields

2. Validation Gaps

• No metamodel validation enforcement: Current LinkML doesn't validate instantiates constraints
• Missing status validation: No validation that status values match StandardsMaturityLevel enum
• Stewardship requirements unclear: ValueSetEnumDefinitionWithStewardship requires "at least one steward OR publisher" but this isn't enforceable

3. Documentation Issues

• Placeholder URLs: governance.md contains placeholder URLs (https://example.org/valuesets-stewardship-signup)
• Missing validation commands: Should mention running just validate after changes per CLAUDE.md guidelines

🔒 Security Assessment

• No security issues identified: All changes are schema/metadata updates
• Safe external references: All stewardship URLs point to legitimate organizations
• No credentials exposed: No secrets or sensitive information in the changes

⚡ Performance Considerations

• Minimal performance impact: Metadata additions don't affect runtime performance
• Large file count: 100 changed files is significant but well-organized
• Generation efficiency: Should verify just site generation time isn't significantly impacted

🧪 Test Coverage Assessment

Reviewed existing test suite:

• Good enum functionality tests: /tests/test_rich_enums.py provides comprehensive coverage
• Missing metamodel tests: No tests for new validation metaclasses
• No governance validation tests: Should add tests for stewardship metadata validation

📋 Recommendations

High Priority

1. Standardize ID namespaces: Choose one pattern and apply consistently across all schema files
2. Add metamodel tests: Create tests validating that enums properly instantiate their declared metaclasses
3. Fix placeholder URLs: Replace example.org URLs in governance.md with real endpoints or mark as "TBD"

Medium Priority

4. Add validation helper: Create just validate-stewardship command to check stewardship metadata completeness
5. Document stewardship criteria: Add guidelines for when to apply stewardship annotations
6. Consider status validation: Add validation that status values are from StandardsMaturityLevel enum

Low Priority

7. Enhance test coverage: Add tests for new governance features
8. Performance baseline: Measure and document site generation time impact
9. Working group structure: Begin organizing domain-specific working groups mentioned in governance.md

💡 Architecture Praise

The annotation-based stewardship approach is particularly clever:

annotations:
  stewards: https://geneontology.org
  publishers: https://geneontology.org

This works around LinkML's current limitation where EnumDefinition doesn't support custom slots directly, while maintaining clean semantics and future extensibility.

🎯 Conclusion

This PR represents exceptional work that establishes crucial governance foundations. The metamodel design is sophisticated, the metadata coverage is comprehensive, and the stewardship model is well-architected. The minor issues identified are easily addressable and don't detract from the overall quality.

Recommendation: Approve with minor fixes

The identified namespace inconsistencies and placeholder URLs should be addressed, but the core contribution is excellent and ready for adoption.

[Copilot]

Pull request overview

This PR enhances the valuesets project by adding comprehensive metadata and stewardship tracking for all 516 enums across 109 schema files. The changes establish a custom metamodel for validation, define stewardship organizations, and apply metadata to all enums in the repository.

Key changes:

• Created a custom metamodel (valuesets_meta.yaml) with metaclasses for enum validation
• Introduced stewardship.yaml defining 15 recognized organizations for value set governance
• Updated all 516 enums with title, description, status, contributors, and instantiates references
• Applied stewardship metadata to 17 well-established value sets (GO, Phenopackets, INSDC/GSC)
• Fixed pre-existing venv issue with stale shebangs
• Created governance documentation

Reviewed changes

Copilot reviewed 132 out of 136 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
src/valuesets/metamodel/valuesets_meta.yaml	Defines metaclasses for enum validation and stewardship tracking
src/valuesets/schema/stewardship.yaml	New enum defining 15 stewardship organizations with ROR IDs
src/valuesets/schema/**/*.yaml	109 schema files updated with enum metadata (title, status, contributors, instantiates)
src/valuesets/schema/clinical/phenopackets.yaml	Added stewardship annotations to 11 Phenopackets enums
docs/governance.md	New governance documentation
justfile	Added gen-slides to site target