Add LinkML validator documentation for hallucination guardrails

[dragon-ai-agent]

Summary

Extends the existing hallucination prevention documentation to cover the new LinkML validator plugins as requested in #51.

Changes Made

New concepts section explaining two complementary validation approaches:

1. Term Validation (ID + Label Checking) - Validates ontology terms and identifiers against authoritative sources
2. Reference Validation (Quote + Citation Checking) - Validates text excerpts against source publications

Enhanced examples including:

• Text excerpt validation with editorial conventions (brackets, ellipses)
• Combined use cases showing both types of validation together

Implementation section with links to:

• linkml-term-validator - for ontology term validation
• linkml-reference-validator - for publication excerpt validation
• Practical examples including OBO file validation

Approach

Following @cmungall's preference, the documentation here focuses on concepts and principles of hallucination prevention, with links at the end to implementation-specific documentation maintained by the LinkML projects.

Closes #51

🤖 Generated with Claude Code

[claude]

Claude finished @dragon-ai-agent's task —— View job

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PR Review: LinkML Validator Documentation

Tasks:

• Read and analyze the modified documentation file
• Review content quality and structure
• Check alignment with project guidelines
• Provide comprehensive feedback on documentation standards
• Submit final review

Overall Assessment

This PR successfully extends the existing hallucination prevention documentation with comprehensive coverage of LinkML validator tools. The additions are well-structured, practical, and align closely with the repository's focus on actionable guidance for AI4Curators.

✅ Strengths

Content Quality

• Excellent conceptual framework: The addition of distinct "Term Validation" vs "Reference Validation" concepts (lines 124-180) provides clear mental models for different validation approaches
• Practical examples: New text excerpt validation examples (lines 83-109) with editorial conventions are immediately actionable
• Comprehensive tool coverage: Detailed documentation of both LinkML validators with specific features and use cases

Structure & Organization

• Logical progression: Builds naturally from existing content to introduce new concepts, then practical tools
• Clear sectioning: Well-organized with appropriate heading hierarchy (##, ###, ####)
• Good balance: Maintains the existing practical focus while adding necessary implementation details

Alignment with Project Guidelines

• ✅ Practical focus: All additions emphasize immediate, actionable solutions over theory
• ✅ Target audience: Content directly serves curators and knowledge base maintainers
• ✅ Integration emphasis: Shows how AI enhances existing workflows rather than replacing them

🔍 Areas for Improvement

Minor Content Issues

1. Command example formatting (lines 275-278):

   linkml-reference-validator validate text-file my-ontology.obo \
     --regex 'ex:supporting_text="([^"]*)\[(\S+:\S+)\]"' \
     --cache-dir ./cache

   The regex pattern could benefit from a brief explanation for users unfamiliar with regex syntax.

2. API reference expansion (lines 165-171):
   Consider adding brief descriptions of what each API provides:

   • Current: "PMC (PubMed Central): For accessing full-text content to validate excerpts"
   • Could add: typical use cases or limitations

Documentation Standards

3. Link validation needed: All external links should be tested:

   • https://linkml.io/linkml-term-validator/ (line 248)
   • https://linkml.io/linkml-reference-validator/ (line 261)
   • https://linkml.io/linkml-reference-validator/how-to/validate-obo-files/ (line 283)

4. Code block language tags: Some code blocks lack language specification for proper syntax highlighting (lines 275-278, 289-292)

🚀 Technical Accuracy

• Validation concepts: Technically sound dual verification approach
• Tool descriptions: Accurate feature listings for both LinkML validators
• Implementation guidance: Realistic performance and caching considerations
• Integration patterns: Practical CI/CD pipeline suggestions

📋 Minor Fixes Needed

1. Trailing whitespace: Line 79 has trailing whitespace (minor cleanup)
2. Consistent formatting: Some inconsistency in bullet point spacing
3. Missing newline: File should end with newline (line 294)

✨ Recommendations

1. Add troubleshooting section: Common validation failure scenarios and solutions
2. Include performance benchmarks: Rough validation speeds for different dataset sizes
3. Expand error handling: More specific guidance on handling network failures or API rate limits

🎯 Security & Performance

• No security concerns: Documentation-only changes with appropriate external tool references
• Performance considerations well-addressed: Caching strategies and batch processing guidance included
• No malicious content: Clean, educational documentation

Final Verdict

This is a high-quality addition that successfully extends the existing documentation as requested in issue #51. The content is well-written, technically accurate, and maintains the repository's standards for practical, actionable guidance.

Recommendation: APPROVE ✅

The additions provide immediate value to the target audience with minimal issues that could be addressed in follow-up improvements.

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