Add cloud laboratory protocol value sets

[cmungall]

Summary

Adds comprehensive controlled vocabularies for cloud-laboratory research protocols, modeled on the operational taxonomy of remote/cloud labs such as Emerald Cloud Lab (ECL) and its Symbolic Lab Language (SLL).

Key Changes

• New schema module: src/valuesets/schema/lab_automation/cloud_lab.yaml

  • Defines LabUnitOperationEnum: 40+ composable sample-manipulation primitives (Transfer, Aliquot, Mix, Incubate, Filter, Centrifuge, etc.)
  • Defines CloudLabExperimentEnum: 100+ higher-level experiment/assay functions organized by category (synthesis, separations/chromatography, spectroscopy, mass spectrometry, bioassays, crystallography, property measurement, cellular)
  • Maps to OBI, CHMO, and MMO ontology terms via meaning: fields where equivalent classes exist
  • Includes comprehensive descriptions and aliases for each operation and experiment type

• Updated main schema: src/valuesets/schema/valuesets.yaml

  • Added import for the new lab_automation/cloud_lab module

• Updated ontology term caches:

  • Added 24 new CHMO terms to cache/chmo/terms.csv
  • Added 3 new OBI terms to cache/obi/terms.csv

Implementation Details

• Two complementary layers capture both low-level unit operations and high-level experiment functions
• Cross-references to existing assay value sets under bio/assays/ (OBIAssayEnum, BAOBioassayEnum)
• Uses neutral ontology mappings rather than vendor-specific identifiers
• Status marked as DRAFT with contributor attribution
• Follows project conventions for enum naming (CamelCase) and permissible values (UPPER_CASE)

https://claude.ai/code/session_01G74MMk5js9HDsGL3VbfAxQ

[claude]

Claude finished @cmungall's task —— View job

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Code Review Complete ✅

Reviewing this PR that adds cloud laboratory protocol value sets. Here's my review checklist:

• Read project guidelines from CLAUDE.md
• Review new schema file structure and content
• Check main schema import changes
• Analyze ontology cache updates
• Validate schema syntax and conventions
• Check for potential issues and provide feedback

Review Summary

This is a high-quality contribution that adds comprehensive controlled vocabularies for cloud laboratory automation. The implementation follows project conventions and best practices.

✅ Strengths

Schema Design & Structure:

• ✅ Follows LinkML conventions with proper imports, prefixes, and enum structures
• ✅ Well-organized into two complementary layers: unit operations (40+ items) and experiments (100+ items)
• ✅ Adheres to project naming conventions (CamelCase enums, UPPER_CASE permissible values)
• ✅ Comprehensive descriptions and aliases for each operation/experiment

Ontology Integration:

• ✅ Proper use of meaning: fields with 42 ontology mappings to CHMO, OBI, and MMO terms
• ✅ Updated cache files correctly add 24 new CHMO terms and 3 new OBI terms
• ✅ All ontology terms appear legitimate and properly formatted as CURIEs

Documentation & Metadata:

• ✅ Thorough descriptions explaining the purpose and relationship to existing value sets
• ✅ Appropriate contributor attribution and DRAFT status marking
• ✅ Clear cross-references to existing bio/assays value sets

🔍 Minor Observations

Consistency:

• ⚠️ Some permissible values have aliases (e.g., mixing, centrifugation) while semantically equivalent ones don't (e.g., FILTER vs filtration) - this is acceptable but could be standardized in future iterations

Coverage:

• ✅ Good balance between comprehensive coverage and practical utility
• ✅ Neutral ontology mappings rather than vendor-specific terms (excellent design choice)

🚀 No Issues Found

• Code Quality: Schema syntax appears correct, follows LinkML patterns
• Security: No security concerns - pure data definitions
• Performance: Minimal performance impact - static enum definitions
• Test Coverage: Schema-only changes don't require additional test coverage

📋 Recommendations

1. Future Enhancement: Consider adding cross-references between related unit operations and experiments where applicable
2. Documentation: The existing documentation is excellent - no changes needed

This PR significantly enhances the value set collection with well-structured, properly annotated laboratory automation vocabularies. Recommend approval.