Enhance cross-repository environmental linking with CultureMech and MediaIngredientMech

## Summary

Enhance CommunityMech's environmental linking capabilities to support bidirectional references with CultureMech media and MediaIngredientMech ingredients based on shared ENVO terms.

## Background

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

CommunityMech currently has robust environmental metadata:
```yaml
environment_term:
  preferred_term: peatland
  term:
    id: ENVO:00000044
    label: peatland
```

However, there's no mechanism to:
1. Link communities to relevant CultureMech media for the same environment
2. Link communities to relevant MediaIngredientMech ingredients
3. Auto-suggest media/ingredients when curating new communities

## Related Schema Enhancements

**In Progress**:
- **CultureMech**: Adding `source_environment` field (CultureBotAI/CultureMech#2)
- **MediaIngredientMech**: Adding `environmental_context` field (CultureBotAI/MediaIngredientMech#1)

These will enable environment-based cross-repository queries.

## Proposed CommunityMech Enhancements

### Option 1: Enhance `growth_media` Field (Recommended)

Currently, `growth_media` field exists but may not have CultureMech ID linking:

```yaml
# Current (if implemented)
growth_media:
  - name: Some Medium
    description: "Medium description"

# Proposed Enhancement
growth_media:
  - preferred_term: Acidic Peatland Medium
    culturemech_id: CultureMech:010001  # Direct link
    environment_match: ENVO:00000044    # Matched via environment
    notes: "Used for cultivating methanogenic archaea from SPRUCE"
    
  - preferred_term: Generic Anaerobic Medium  
    culturemech_id: CultureMech:005432
    environment_match: null  # Not environment-specific
    notes: "General purpose medium"
```

### Option 2: Add `related_media` Field

If `growth_media` is for actual media used, add separate field for related media:

```yaml
related_media:
  description: CultureMech media relevant to this community's environment
  range: RelatedMedia
  multivalued: true
  inlined_as_list: true

RelatedMedia:
  attributes:
    preferred_term:
      description: Media name
      required: true
    culturemech_id:
      description: CultureMech identifier
      range: string
      pattern: "^CultureMech:\\d{6}$"
    relationship_type:
      description: How media relates to community
      range: MediaRelationshipEnum
      # VALUES: CULTIVATION_MEDIUM, ISOLATION_MEDIUM, 
      #         ENVIRONMENT_ANALOG, REFERENCED_IN_STUDY
    evidence:
      description: Evidence for this relationship
      range: EvidenceItem
      multivalued: true
```

### Option 3: Add `related_ingredients` Field

Similarly for ingredients:

```yaml
related_ingredients:
  description: MediaIngredientMech ingredients relevant to this community
  range: RelatedIngredient
  multivalued: true
  inlined_as_list: true

RelatedIngredient:
  attributes:
    preferred_term:
      description: Ingredient name
      required: true
    mediaingredientmech_id:
      description: MediaIngredientMech identifier  
      range: string
      pattern: "^MediaIngredientMech:\\d{6}$"
    relevance:
      description: Why ingredient is relevant
      range: string
    evidence:
      description: Evidence for relevance
      range: EvidenceItem
      multivalued: true
```

## Use Cases

### Use Case 1: Adding a New Peatland Community
**Current Workflow**:
1. User provides PMIDs, environmental info
2. Create community record with `environment_term: ENVO:00000044`
3. ❌ No way to find relevant media
4. ❌ No way to find relevant ingredients

**Enhanced Workflow**:
1. User provides PMIDs, environmental info  
2. Create community record with `environment_term: ENVO:00000044`
3. ✅ **Auto-query CultureMech**: "Find media with `source_environment: ENVO:00000044`"
4. ✅ **Auto-query MediaIngredientMech**: "Find ingredients with `environmental_context: ENVO:00000044`"
5. ✅ **Auto-suggest**: "15 peatland media found, 8 peatland ingredients found"
6. User selects relevant media/ingredients to link

### Use Case 2: Environmental Coverage Dashboard

```
Environment: Peatland (ENVO:00000044)
┌─────────────────────┬───────┬────────────────────────┐
│ Repository          │ Count │ Status                 │
├─────────────────────┼───────┼────────────────────────┤
│ Communities         │ 3     │ ✅ SPRUCE, ...         │
│ Media (CultureMech) │ 15    │ ✅ Good coverage       │
│ Ingredients (MIM)   │ 8     │ ✅ Specialized items   │
└─────────────────────┴───────┴────────────────────────┘

Environment: Deep-sea hydrothermal vent (ENVO:01000030)
┌─────────────────────┬───────┬────────────────────────┐
│ Repository          │ Count │ Status                 │
├─────────────────────┼───────┼────────────────────────┤
│ Communities         │ 5     │ ✅ Well studied        │
│ Media (CultureMech) │ 2     │ ⚠️ Need more media     │
│ Ingredients (MIM)   │ 1     │ ⚠️ Need more items     │
└─────────────────────┴───────┴────────────────────────┘
```

### Use Case 3: Cross-Repository SPARQL Query

```sparql
# Find complete environmental profile
SELECT ?community ?community_name ?media ?media_name ?ingredient ?ingredient_name
WHERE {
  # Communities in peatland
  ?community a communitymech:MicrobialCommunity ;
             communitymech:environment_term/communitymech:id "ENVO:00000044" ;
             communitymech:name ?community_name .
  
  # Media for peatland organisms
  ?media a culturemech:CultureMedia ;
         culturemech:source_environment/culturemech:id "ENVO:00000044" ;
         culturemech:name ?media_name .
  
  # Ingredients relevant to peatland
  ?ingredient a mediaingredientmech:MappedIngredient ;
              mediaingredientmech:environmental_context/mediaingredientmech:environment_term "ENVO:00000044" ;
              mediaingredientmech:preferred_term ?ingredient_name .
}
```

### Use Case 4: `add_community` Skill Enhancement

Update the orchestration skill to automatically suggest cross-repo links:

```python
# In add_community skill workflow
def match_culturemech_media(community_environment: str):
    """Find CultureMech media matching community environment"""
    
    # Query CultureMech for matching environment
    media_results = culturemech_api.search(
        source_environment=community_environment
    )
    
    # Return suggestions
    return [
        {
            "culturemech_id": media.id,
            "name": media.name,
            "confidence": calculate_relevance_score(media, community),
            "evidence": "Environment match: " + community_environment
        }
        for media in media_results
    ]

# Similarly for ingredients
def match_mediaingredient_items(community_environment: str):
    """Find MediaIngredientMech ingredients matching environment"""
    
    ingredient_results = mediaingredient_api.search(
        environmental_context=community_environment
    )
    
    return format_ingredient_suggestions(ingredient_results)
```

## Implementation Plan

### Phase 1: Schema Review (Weeks 1-2)
- [ ] Review current `growth_media` field implementation
- [ ] Decide: enhance `growth_media` vs. add `related_media`/`related_ingredients`
- [ ] Define validation rules for cross-repo IDs
- [ ] Coordinate with CultureMech and MediaIngredientMech schema changes

### Phase 2: Schema Enhancement (Weeks 3-4)
- [ ] Update `communitymech.yaml` schema
- [ ] Add CultureMech ID and MediaIngredientMech ID linking
- [ ] Regenerate Python dataclasses
- [ ] Update validation pipelines

### Phase 3: Tooling Enhancement (Weeks 5-6)
- [ ] Update `add_community` skill to query CultureMech by environment
- [ ] Update `add_community` skill to query MediaIngredientMech by environment
- [ ] Create auto-suggestion interface for media/ingredient linking
- [ ] Add cross-repo validation (check IDs exist)

### Phase 4: Documentation (Week 7)
- [ ] Document cross-repo linking patterns
- [ ] Create tutorial for adding environment-linked communities
- [ ] Add SPARQL query examples

### Phase 5: Backfill (Ongoing)
- [ ] For existing communities with environment terms, suggest media/ingredient links
- [ ] Prioritize well-characterized environments (peatland, marine, gut, soil)

## Example: SPRUCE Community Enhancement

### Current State (Issue #24)
```yaml
id: CommunityMech:000024
name: SPRUCE Peatland Warming Microbial Community
environment_term:
  preferred_term: peatland
  term:
    id: ENVO:00000044
    label: peatland
```

### Enhanced State (After Implementation)
```yaml
id: CommunityMech:000024
name: SPRUCE Peatland Warming Microbial Community

environment_term:
  preferred_term: peatland
  term:
    id: ENVO:00000044
    label: peatland

# Auto-discovered from CultureMech
related_media:
  - preferred_term: Acidic Peatland Medium
    culturemech_id: CultureMech:010001
    relationship_type: ENVIRONMENT_ANALOG
    evidence:
      - reference: PMID:38515239
        supports: SUPPORT
        evidence_source: IN_VIVO
        snippet: "Peat microbial communities characterized in situ"

  - preferred_term: Methanogen Enrichment Medium
    culturemech_id: CultureMech:010045
    relationship_type: CULTIVATION_MEDIUM
    evidence:
      - reference: PMID:34836550
        supports: SUPPORT
        evidence_source: IN_VIVO
        snippet: "Methanogenic archaea detected in anoxic peat"

# Auto-discovered from MediaIngredientMech  
related_ingredients:
  - preferred_term: Humic acid
    mediaingredientmech_id: MediaIngredientMech:000523
    relevance: "Major peat organic matter component, provides carbon source"
    
  - preferred_term: Sphagnum moss extract
    mediaingredientmech_id: MediaIngredientMech:001234
    relevance: "Extracted from dominant peatland plant species"
```

## Benefits

1. **Automated discovery**: Find media/ingredients when adding communities
2. **Coverage tracking**: Identify environments needing more resources
3. **Knowledge graph**: Rich cross-repository linking
4. **User experience**: Guided curation with suggestions
5. **FAIR data**: Improved findability and interoperability

## Success Metrics

- **Linking Coverage**: % of communities with media/ingredient links
- **Query Success**: Cross-repo queries return complete results
- **Curation Time**: Time to add new community (should decrease)
- **Coverage Gaps**: Identified environments needing resources

## Related Issues

- **CultureMech #2**: Add `source_environment` field
- **MediaIngredientMech #1**: Add `environmental_context` field
- **This repo #24**: SPRUCE Peatland Community (trigger issue)

## References

- **Full Proposal**: `culturebotai-claw/workspace/reports/Cross_Repo_Environment_Linking_Proposal.md`
- **ENVO Ontology**: http://www.obofoundry.org/ontology/envo.html
- **SPARQL Cross-Repo Examples**: See proposal document

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Enhance cross-repository environmental linking with CultureMech and MediaIngredientMech #30

Summary

Background

Related Schema Enhancements

Proposed CommunityMech Enhancements

Option 1: Enhance `growth_media` Field (Recommended)

Option 2: Add `related_media` Field

Option 3: Add `related_ingredients` Field

Use Cases

Use Case 1: Adding a New Peatland Community

Use Case 2: Environmental Coverage Dashboard

Use Case 3: Cross-Repository SPARQL Query

Use Case 4: `add_community` Skill Enhancement

Implementation Plan

Phase 1: Schema Review (Weeks 1-2)

Phase 2: Schema Enhancement (Weeks 3-4)

Phase 3: Tooling Enhancement (Weeks 5-6)

Phase 4: Documentation (Week 7)

Phase 5: Backfill (Ongoing)

Example: SPRUCE Community Enhancement

Current State (Issue #24)

Enhanced State (After Implementation)

Benefits

Success Metrics

Related Issues

References

Metadata

Assignees

Labels

Type

Projects

Milestone

Relationships

Development

Enhance cross-repository environmental linking with CultureMech and MediaIngredientMech #30

Description

Summary

Background

Related Schema Enhancements

Proposed CommunityMech Enhancements

Option 1: Enhance growth_media Field (Recommended)

Option 2: Add related_media Field

Option 3: Add related_ingredients Field

Use Cases

Use Case 1: Adding a New Peatland Community

Use Case 2: Environmental Coverage Dashboard

Use Case 3: Cross-Repository SPARQL Query

Use Case 4: add_community Skill Enhancement

Implementation Plan

Phase 1: Schema Review (Weeks 1-2)

Phase 2: Schema Enhancement (Weeks 3-4)

Phase 3: Tooling Enhancement (Weeks 5-6)

Phase 4: Documentation (Week 7)

Phase 5: Backfill (Ongoing)

Example: SPRUCE Community Enhancement

Current State (Issue #24)

Enhanced State (After Implementation)

Benefits

Success Metrics

Related Issues

References

Metadata

Metadata

Assignees

Labels

Type

Projects

Milestone

Relationships

Development

Issue actions

Option 1: Enhance `growth_media` Field (Recommended)

Option 2: Add `related_media` Field

Option 3: Add `related_ingredients` Field

Use Case 4: `add_community` Skill Enhancement