Add FAO World Reference Base (WRB) soil classification valueset

[cmungall]

Adds comprehensive FAO soil classification system from HWSD2 database.

Summary

• Creates new schema for 35 FAO soil types
• Includes ENVO ontology mappings where appropriate
• Adds symbols, IDs, and RGB color values
• Follows LinkML and project conventions

Resolves #24

🤖 Generated with Claude Code

[claude]

Claude finished @cmungall's task —— View job

---

Code Review Complete ✅

I've completed a thorough review of the FAO soil classification valueset. Here's my detailed feedback:

✅ Positive Aspects

Strong Adherence to Project Conventions:

• ✅ Correctly uses CamelCase for enum name (FAOSoilType)
• ✅ Uses UPPER_CASE for permissible values as specified in CLAUDE.md
• ✅ Follows proper LinkML schema structure with appropriate prefixes
• ✅ Includes comprehensive descriptions for each soil type
• ✅ Well-organized in earth_science/ subdirectory matching existing structure

Good Technical Implementation:

• ✅ Proper YAML syntax and LinkML schema structure
• ✅ Comprehensive coverage of 35 FAO soil types from HWSD2
• ✅ Includes useful metadata (symbols, IDs, RGB colors) via annotations
• ✅ Good documentation with references to FAO and ISRIC sources

⚠️ Areas for Improvement

1. Missing Import in Main Schema src/valuesets/schema/valuesets.yaml:104
The new schema is not imported in the main valuesets.yaml. You'll need to add:

- earth_science/fao_soil

2. Ontology Mapping Verification Required
Per CLAUDE.md guidelines: "ALWAYS check IDs, NEVER guess them. Use OLS to check."
The following ENVO mappings should be verified:

• ANDOSOLS: ENVO:00002030
• ARENOSOLS: ENVO:00002229
• CRYOSOLS: ENVO:00000134
• FLUVISOLS: ENVO:00002269
• GLEYSOLS: ENVO:00002234
• HISTOSOLS: ENVO:00005774
• SOLONCHAKS: ENVO:00005767
• VERTISOLS: ENVO:00002273

3. Inconsistent Ontology Mapping Coverage
Only 10 of 35 soil types have ontology mappings. Consider:

• Adding mappings for remaining soil types where available
• Or adding a comment explaining why certain types lack mappings

4. Missing fao_id 16
The fao_id annotations jump from 15 (HISTOSOLS) to 17 (KASTANOZEMS). Verify if ID 16 exists or document why it's skipped.

🔒 Security & Performance

• ✅ No security concerns identified
• ✅ Static enum definitions have minimal performance impact
• ✅ Appropriate file size and structure

🧪 Testing Considerations

The schema should be validated using the project's validation commands:

• Run just validate to ensure LinkML compliance
• Run just site to verify successful integration
• Consider adding the import to main schema before validation

📋 Summary

This is a high-quality addition to the valuesets project. The schema is well-structured and follows most project conventions. The main issues are administrative (missing import) and verification tasks (ontology IDs). The comprehensive coverage of FAO soil types will be valuable for earth science applications.

Recommendation: ✅ Approve with minor changes - address the missing import and verify ontology mappings.

---

[Copilot]

Pull Request Overview

This PR adds a comprehensive FAO World Reference Base (WRB) soil classification valueset from the Harmonized World Soil Database (HWSD version 2), providing standardized soil type classifications for earth science applications.

• Creates a new LinkML schema file with 35 FAO soil type classifications
• Includes ENVO ontology mappings for 11 soil types where appropriate alignments exist
• Provides metadata annotations (symbol codes, FAO IDs, and RGB color values) for each classification

[Copilot]

The inclusion of GLACIERS as a soil type is semantically inconsistent with the schema title 'FAO Soil Classification (WRB)' and the enum description stating 'major soil groups'. Glaciers represent areas with no soil present. While this may be a valid land cover category in HWSD2, consider adding a clarifying note in the description such as: 'Glaciers - areas covered by permanent ice (non-soil land cover type in HWSD)'

[claude]

Claude finished @cmungall's task —— View job

---

Comprehensive Code Review ✅

I've completed a detailed review of the FAO soil classification valueset. Here's my assessment:

Todo List:

• Read and analyze the new schema file
• Check adherence to project conventions and LinkML best practices
• Validate ontology mappings and technical accuracy
• Assess performance and security considerations
• Review test coverage implications
• Provide comprehensive feedback

---

✅ Code Quality & Best Practices

Excellent LinkML Structure:

• ✅ Well-formed YAML with proper LinkML schema structure
• ✅ Comprehensive enum definition with 35 soil classifications
• ✅ Consistent use of annotations for metadata (symbols, IDs, RGB colors)
• ✅ Appropriate license declaration (MIT)
• ✅ Good documentation with external references

Strong Adherence to Project Conventions:

• ✅ Correctly follows CLAUDE.md guidelines:
  • Uses CamelCase for enum name (FAOSoilType)
  • Uses UPPER_CASE for permissible values
  • Organizes by domain in earth_science/ subdirectory
  • Proper CURIE declarations in prefixes section
• ✅ Descriptive documentation for each soil type
• ✅ Proper semantic versioning approach

⚠️ Critical Issues Requiring Attention

1. Missing Import in Main Schema src/valuesets/schema/valuesets.yaml:104
The new schema is not imported in the main valuesets.yaml file. This means the enum won't be available when the schema is loaded. You need to add:

- earth_science/fao_soil

2. Technical Accuracy Issues
Based on the GitHub PR review comments:

• PODZOLS description src/valuesets/schema/earth_science/fao_soil.yaml:172: The current description is technically incomplete. Podzols are characterized by spodic horizons with aluminium-iron-organic matter complexes, not just "humified organic matter"
• GLACIERS categorization src/valuesets/schema/earth_science/fao_soil.yaml:96-102: Including glaciers as a "soil type" is semantically inconsistent - glaciers represent areas with no soil present

3. Data Integrity Gap src/valuesets/schema/earth_science/fao_soil.yaml:127
Missing fao_id: 16 - sequence jumps from 15 (HISTOSOLS) to 17 (KASTANOZEMS). This could indicate a data gap or missing soil type.

🔍 Potential Bugs & Issues

Ontology Mapping Inconsistencies:

• Only 10 of 35 soil types have ENVO ontology mappings
• Per CLAUDE.md: "ALWAYS check IDs, NEVER guess them. Use OLS to check"
• Some mappings need verification (particularly for newer ENVO terms)

Schema Integration:

• Without the main schema import, the enum won't be accessible
• This could cause import errors or missing type definitions

🚀 Performance Considerations

Positive Aspects:

• ✅ Static enum definitions have minimal performance impact
• ✅ Reasonable file size (~240 lines)
• ✅ Efficient YAML structure without nested complexity
• ✅ Metadata annotations don't affect runtime performance

No Performance Concerns Identified

🔒 Security Assessment

Secure Implementation:

• ✅ No executable code, only declarative YAML data
• ✅ No external dependencies or remote calls
• ✅ No sensitive information or credentials
• ✅ Safe ontology term references (CURIEs)
• ✅ No injection vulnerabilities possible

No Security Risks Identified

🧪 Test Coverage Implications

Schema Validation Testing:

• The schema should pass just validate for LinkML compliance
• Integration testing with just site needed after adding import
• Note: I cannot run these validation commands due to tool limitations, but they're critical for ensuring correctness

Recommended Testing:

1. Validate LinkML schema structure
2. Verify ontology term resolution (ENVO CURIEs)
3. Test import integration in main schema
4. Validate RGB color format compliance

📋 Summary & Recommendations

This is a high-quality, well-structured implementation that demonstrates strong adherence to project conventions and LinkML best practices. The comprehensive coverage of FAO soil types with rich metadata will be valuable for earth science applications.

Priority Actions Needed:

1. CRITICAL: Add import to main schema file to enable usage
2. HIGH: Verify and correct technical soil type descriptions
3. MEDIUM: Investigate missing fao_id 16
4. LOW: Consider expanding ontology mappings where available

Overall Assessment: ✅ Approve with minor corrections - The core implementation is excellent and follows all coding standards. The issues identified are primarily data accuracy and integration concerns rather than fundamental code quality problems.

---