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Summary

This PR adds comprehensive value sets for MRI/fMRI neuroimaging and significantly expands the nuclear energy and business domains. The neuroimaging value sets provide standardized terminology for research data management, BIDS compliance, and clinical applications.

MRI/fMRI Neuroimaging Value Sets (New)

New Schema: medical/neuroimaging.yaml

  • MRIModalityEnum: 13 imaging modalities including:
    • Structural MRI: T1-weighted, T2-weighted, FLAIR
    • Functional MRI: BOLD, task-based, resting-state, connectivity
    • Advanced techniques: DTI, ASL, SWI, perfusion (DSC/DCE)
  • MRISequenceTypeEnum: 6 pulse sequence types (GRADIENT_ECHO, SPIN_ECHO, EPI, MPRAGE, SPACE, TRUFI)
  • MRIContrastTypeEnum: 6 contrast mechanisms (T1_WEIGHTED, T2_WEIGHTED, T2_STAR, etc.)
  • FMRIParadigmTypeEnum: 5 experimental paradigms (BLOCK_DESIGN, EVENT_RELATED, MIXED_DESIGN, etc.)

Comprehensive Ontology Integration

  • NCIT mappings for medical imaging terms
  • EDAM mappings for experimental design concepts
  • CHMO mappings for NMR/chemical concepts
  • STATO mappings for statistical design terms
  • mesh mappings for additional biomedical concepts
  • Rich metadata with technical parameters, clinical applications, and domain expertise

Nuclear Energy Domain Expansion

6 New Nuclear Schema Files with 33 Enums Total

  • reactor_types.yaml: Reactor classifications, generations, coolants, moderators, neutron spectra, sizes
  • nuclear_fuels.yaml: Fuel types, enrichment levels, forms, and cycle stages
  • nuclear_waste.yaml: Waste classifications, storage, disposal, and processing methods
  • nuclear_safety.yaml: Safety systems, protection systems, emergency response, radiation protection
  • nuclear_facilities.yaml: Facility types, operational status, licensing, vessel/containment designs
  • nuclear_operations.yaml: Operational states, maintenance, fuel handling, lifecycle phases

Business Domain Addition

6 New Business Schema Files

  • organizational_structures.yaml: 7 organizational enums covering business structures and roles
  • industry_classifications.yaml: 4 industry classification systems (NAICS, SIC, etc.)
  • management_operations.yaml: 6 management-focused enums for business processes
  • quality_management.yaml: 5 quality system enums (ISO standards, methodologies)
  • supply_chain.yaml: 6 supply chain and logistics enums
  • human_resources.yaml: 8 HR-related enums for workforce management

Biology Domain Updates

  • Enhanced UniProt species support with proteome ID mappings
  • New sync script: scripts/sync_uniprot_species.py
  • Added Gene Ontology aspect classifications (go_aspect.yaml)

Technical Improvements

  • Updated main schema with all new imports
  • Added ontology prefixes (CHMO, STATO) for enhanced semantic integration
  • Generated 426 total rich Python enums with metadata access
  • All schemas validated successfully via LinkML
  • Comprehensive ontology term verification using OLS

Use Cases

These value sets support:

  • Neuroimaging research: BIDS-compliant data organization, meta-analyses
  • Clinical applications: Standardized imaging protocols, EHR integration
  • Nuclear industry: Regulatory compliance, technical documentation
  • Business applications: Enterprise data management, industry reporting
  • Data sharing platforms: OpenNeuro, XNAT, research databases

Test Plan

  • Schema validation passes (just validate)
  • Rich enum generation successful (just site)
  • Ontology mappings verified via OLS
  • All imports resolve correctly
  • Generated Python datamodels functional
  • Integration testing with downstream applications
  • Documentation review

🤖 Generated with Claude Code

…ness domains

## MRI/fMRI Neuroimaging Value Sets

### New Schema: medical/neuroimaging.yaml
- **MRIModalityEnum**: 13 imaging modalities including structural (T1, T2, FLAIR),
  functional (BOLD, task-based, resting-state), and advanced techniques (DTI, ASL, SWI, perfusion)
- **MRISequenceTypeEnum**: 6 pulse sequence types (GRADIENT_ECHO, SPIN_ECHO, EPI, MPRAGE, SPACE, TRUFI)
- **MRIContrastTypeEnum**: 6 contrast mechanisms (T1_WEIGHTED, T2_WEIGHTED, T2_STAR, etc.)
- **FMRIParadigmTypeEnum**: 5 experimental paradigms (BLOCK_DESIGN, EVENT_RELATED, MIXED_DESIGN, etc.)

### Comprehensive Ontology Mappings
- NCIT mappings for medical imaging terms
- EDAM mappings for experimental design concepts
- CHMO mappings for NMR/chemical concepts
- STATO mappings for statistical design terms
- mesh mappings for biomedical concepts
- Rich metadata with technical parameters and clinical applications

## Nuclear Energy Domain Expansion

### New Nuclear Schema Files
- **reactor_types.yaml**: 6 comprehensive enums for reactor classifications
  - ReactorTypeEnum: 15 reactor types (PWR, BWR, PHWR, etc.)
  - ReactorGenerationEnum: 5 generational classifications
  - ReactorCoolantEnum: 8 primary coolant types
  - ReactorModeratorEnum: 5 neutron moderator types
  - ReactorNeutronSpectrumEnum: 3 neutron energy classifications
  - ReactorSizeCategoryEnum: 5 size categories

- **nuclear_fuels.yaml**: 4 fuel-related enums
  - NuclearFuelTypeEnum: 14 fuel types with enrichment levels
  - UraniumEnrichmentLevelEnum: 6 enrichment classifications
  - FuelFormEnum: 4 physical fuel forms
  - FuelCycleStageEnum: 8 fuel cycle stages

- **nuclear_waste.yaml**: 4 waste management enums
  - RadioactiveWasteClassEnum: 5 waste classifications
  - WasteStorageMethodEnum: 8 storage approaches
  - WasteDisposalMethodEnum: 6 disposal strategies
  - WasteProcessingMethodEnum: 8 processing techniques

- **nuclear_safety.yaml**: 4 safety-focused enums
  - NuclearSafetySystemEnum: 12 safety systems
  - ReactorProtectionSystemEnum: 8 protection systems
  - EmergencyResponseLevelEnum: 7 emergency classifications
  - RadiationProtectionLevelEnum: 5 protection categories

- **nuclear_facilities.yaml**: 6 facility type enums
  - NuclearFacilityTypeEnum: 12 facility categories
  - PowerPlantStatusEnum: 8 operational states
  - NuclearLicenseTypeEnum: 6 licensing categories
  - ReactorVesselTypeEnum: 4 vessel designs
  - ContainmentTypeEnum: 5 containment structures
  - CoolingSystemTypeEnum: 6 cooling approaches

- **nuclear_operations.yaml**: 6 operational enums
  - ReactorOperationalStateEnum: 9 operational states
  - MaintenanceTypeEnum: 8 maintenance categories
  - FuelHandlingOperationEnum: 8 fuel operations
  - PlantLifecyclePhaseEnum: 7 lifecycle phases
  - OperationalModeEnum: 6 operating modes
  - EmergencyProcedureTypeEnum: 9 emergency procedures

## Business Domain Addition

### New Business Schema Files
- **organizational_structures.yaml**: 7 organizational enums
- **industry_classifications.yaml**: 4 industry classification systems
- **management_operations.yaml**: 6 management-focused enums
- **quality_management.yaml**: 5 quality system enums
- **supply_chain.yaml**: 6 supply chain enums
- **human_resources.yaml**: 8 HR-related enums

## Biology Domain Updates

### Enhanced UniProt Species Support
- **uniprot_species.yaml**: Enhanced with proteome mappings
- **scripts/sync_uniprot_species.py**: New sync script for UniProt data
- **go_aspect.yaml**: New Gene Ontology aspect classifications

## Technical Improvements

### Schema Integration
- Updated main valuesets.yaml with all new imports
- Added new ontology prefixes (CHMO, STATO) for enhanced mappings
- Maintained consistent naming conventions and structure

### Generated Artifacts
- Updated Python datamodel classes (valuesets.py, valuesets_pydantic.py)
- Regenerated rich enum classes with metadata access
- Updated enum exports in __init__.py (426 total enums)
- Refreshed documentation schema

### Quality Assurance
- All schemas validated successfully
- Comprehensive ontology term verification via OLS
- Rich metadata annotations for domain expertise
- Consistent CURIE-based ontology mappings

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-Authored-By: Claude <[email protected]>
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