Add environmental_context field to ingredient schema for cross-repo environmental linking

## Summary

Add `environmental_context` field to MediaIngredientMech ingredient records to enable environmental linking with CommunityMech and CultureMech.

## Background

**Triggered by**: CommunityMech issue #24 (SPRUCE Peatland Community addition)

Currently:
- **CommunityMech** has `environment_term` field with ENVO terms
- **CultureMech** is adding `source_environment` field (see CultureBotAI/CultureMech#2)
- **MediaIngredientMech** has ENVO prefix defined but no environmental fields

This creates a gap where ingredients cannot be linked to environmental contexts.

## Proposed Schema Addition

Add `environmental_context` field to ingredient records:

```yaml
# In mapped_ingredients_schema.yaml
environmental_context:
  description: Environmental contexts where this ingredient is relevant
  range: EnvironmentContext
  multivalued: true
  inlined_as_list: true

EnvironmentContext:
  description: Environmental context for ingredient usage
  attributes:
    environment_term:
      description: ENVO term for environment (CURIE format)
      range: string
      required: true
      pattern: "^ENVO:\\d{7,8}$"
    
    relevance:
      description: Why this ingredient is relevant to this environment
      range: EnvironmentRelevanceEnum
      required: true
    
    notes:
      description: Additional context
      range: string

EnvironmentRelevanceEnum:
  permissible_values:
    NATURAL_SOURCE:
      description: Ingredient is naturally sourced from this environment
    REQUIRED_FOR_ORGANISM:
      description: Required for cultivating organisms from this environment  
    SELECTIVE_AGENT:
      description: Selectively promotes organisms from this environment
    ENVIRONMENT_MIMIC:
      description: Mimics chemical conditions of this environment
    COMMONLY_USED:
      description: Commonly used for this environment (general association)
```

## Example Usage

### Example 1: Peatland-Specific Ingredient
```yaml
ontology_id: CHEBI:27385
preferred_term: Humic acid
ontology_mapping:
  ontology_id: CHEBI:27385
  ontology_label: humic acid
  ontology_source: CHEBI

environmental_context:
  - environment_term: ENVO:00000044  # peatland
    relevance: NATURAL_SOURCE
    notes: "Major component of peat organic matter, provides carbon source for peat microbes"
  
  - environment_term: ENVO:00005773  # peat bog  
    relevance: REQUIRED_FOR_ORGANISM
    notes: "Required for cultivation of humic acid-degrading bacteria from peat bogs"

occurrence_statistics:
  total_occurrences: 45
  media_count: 12
```

### Example 2: Multi-Environment Ingredient
```yaml
ontology_id: CHEBI:26710
preferred_term: NaCl
ontology_mapping:
  ontology_id: CHEBI:26710
  ontology_label: sodium chloride

environmental_context:
  - environment_term: ENVO:00002149  # sea water
    relevance: ENVIRONMENT_MIMIC
    notes: "Provides salinity for marine organism cultivation"
  
  - environment_term: ENVO:00002044  # saline lake
    relevance: ENVIRONMENT_MIMIC
    notes: "High concentrations for halophilic organisms"
  
  - environment_term: ENVO:00000044  # peatland
    relevance: COMMONLY_USED
    notes: "Low concentrations as mineral source"
```

### Example 3: Environment-Specific Extract
```yaml
ontology_id: CHEBI:NNNNNN  # To be assigned
preferred_term: Sphagnum moss extract
ontology_mapping:
  ontology_id: CHEBI:NNNNNN
  ontology_label: plant extract

environmental_context:
  - environment_term: ENVO:00000044  # peatland
    relevance: NATURAL_SOURCE
    notes: "Extracted from Sphagnum moss, dominant peatland plant"
  
  - environment_term: ENVO:00005773  # peat bog
    relevance: REQUIRED_FOR_ORGANISM
    notes: "Essential for cultivating Sphagnum-associated bacteria"
```

## Benefits

1. **Cross-repository discovery**: Find ingredients relevant to specific environments
2. **Community curation**: Auto-suggest ingredients when adding environment-specific communities
3. **Media formulation**: Identify environment-appropriate ingredients when designing new media
4. **Environmental coverage**: Track which environments have specialized ingredients
5. **Knowledge linking**: Connect ingredient chemistry to ecological context

## Use Cases

### Use Case 1: Adding Peatland Community
When curating SPRUCE peatland community:
```python
# Search for peatland-relevant ingredients
ingredients = search_ingredients(environment="ENVO:00000044")
# Returns: humic acid, Sphagnum extract, organic acids, etc.
```

### Use Case 2: Formulating Environment-Specific Media
```python
# Design medium for deep-sea organisms
ingredients = get_ingredients_by_environment("ENVO:01000030")  # hydrothermal vent
# Suggests: high-pressure tolerant components, sulfur compounds, etc.
```

### Use Case 3: Environmental Coverage Analysis
```
Environment: Peatland (ENVO:00000044)
- Communities: 3
- Media: 15
- Specialized Ingredients: 8 ✅ (humic acid, Sphagnum extract, etc.)

Environment: Permafrost (ENVO:00000134)
- Communities: 2  
- Media: 1
- Specialized Ingredients: 0 ⚠️ GAP IDENTIFIED
```

### Use Case 4: Cross-Repository Query
```sparql
# Find complete environment profile
SELECT ?community ?media ?ingredient
WHERE {
  # Peatland communities
  ?community communitymech:environment_term ENVO:00000044 .
  
  # Peatland media
  ?media culturemech:source_environment ENVO:00000044 .
  
  # Peatland ingredients  
  ?ingredient mediaingredientmech:environmental_context ?ctx .
  ?ctx mediaingredientmech:environment_term ENVO:00000044 .
}
```

## Implementation Plan

### Phase 1: Schema Design
- [ ] Review and refine `EnvironmentContext` class and `EnvironmentRelevanceEnum`
- [ ] Define validation rules for ENVO terms
- [ ] Decide on required vs. recommended fields

### Phase 2: Schema Migration
- [ ] Update `mapped_ingredients_schema.yaml`
- [ ] Regenerate Python dataclasses  
- [ ] Update validation pipelines
- [ ] Create migration documentation

### Phase 3: Data Curation

#### Automated Inference
- Analyze ingredient names for environment keywords ("marine", "soil", "gut")
- Check occurrence in environment-tagged media (if CultureMech implemented)
- Infer from chemical properties (pH, salinity, etc.)

#### LLM-Assisted Curation
```python
# Use Claude to suggest environmental contexts
for ingredient in unmapped_ingredients:
    suggestion = llm.suggest_environment_context(
        name=ingredient.name,
        chebi_term=ingredient.ontology_id,
        occurrences=ingredient.media_count
    )
    # Returns: {environment_term, relevance, notes, confidence}
```

#### Prioritization
1. **High Priority**: 
   - Specialized extracts (Sphagnum, seaweed, etc.)
   - Environment-specific compounds (humic acid → peatland)
   - Selective agents (high salt → marine)

2. **Medium Priority**:
   - Common ingredients used differently across environments
   - pH-specific buffers and compounds

3. **Low Priority** (Can skip):
   - Ubiquitous ingredients (water, glucose) unless specific relevance

## Migration Strategy

### Backward Compatibility
- Field is **optional** - existing records remain valid
- No breaking changes to API or validation

### Gradual Rollout
1. Schema update (non-breaking)
2. Add to new ingredient records  
3. Backfill high-priority ingredients
4. Full coverage over 6-12 months

## Notes

- ENVO prefix already exists in schema: `ENVO: http://purl.obolibrary.org/obo/ENVO_`
- Field is **multivalued** (ingredients can be relevant to multiple environments)
- Field is **optional** (many ubiquitous ingredients may not need environmental context)
- Coordinated with CultureMech issue #2 for `source_environment` field

## Related Issues

- **CultureMech**: https://github.com/CultureBotAI/CultureMech/issues/2
- **CommunityMech**: Issue #24 (SPRUCE) + cross-repo coordination issue
- **Orchestration**: Enhanced `add_community` skill to use environmental linking

## References

- **Full Proposal**: `culturebotai-claw/workspace/reports/Cross_Repo_Environment_Linking_Proposal.md`
- **ENVO Ontology**: http://www.obofoundry.org/ontology/envo.html
- **MIxS Environmental Packages**: https://press3.mcs.anl.gov/gensc/mixs/

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Add environmental_context field to ingredient schema for cross-repo environmental linking #1

Summary

Background

Proposed Schema Addition

Example Usage

Example 1: Peatland-Specific Ingredient

Example 2: Multi-Environment Ingredient

Example 3: Environment-Specific Extract

Benefits

Use Cases

Use Case 1: Adding Peatland Community

Use Case 2: Formulating Environment-Specific Media

Use Case 3: Environmental Coverage Analysis

Use Case 4: Cross-Repository Query

Implementation Plan

Phase 1: Schema Design

Phase 2: Schema Migration

Phase 3: Data Curation

Automated Inference

LLM-Assisted Curation

Prioritization

Migration Strategy

Backward Compatibility

Gradual Rollout

Notes

Related Issues

References

Metadata

Assignees

Labels

Type

Projects

Milestone

Relationships

Development

Add environmental_context field to ingredient schema for cross-repo environmental linking #1

Description

Summary

Background

Proposed Schema Addition

Example Usage

Example 1: Peatland-Specific Ingredient

Example 2: Multi-Environment Ingredient

Example 3: Environment-Specific Extract

Benefits

Use Cases

Use Case 1: Adding Peatland Community

Use Case 2: Formulating Environment-Specific Media

Use Case 3: Environmental Coverage Analysis

Use Case 4: Cross-Repository Query

Implementation Plan

Phase 1: Schema Design

Phase 2: Schema Migration

Phase 3: Data Curation

Automated Inference

LLM-Assisted Curation

Prioritization

Migration Strategy

Backward Compatibility

Gradual Rollout

Notes

Related Issues

References

Metadata

Metadata

Assignees

Labels

Type

Projects

Milestone

Relationships

Development

Issue actions