Add source_environment field to media schema for cross-repo environmental linking

[realmarcin]

Summary

Add source_environment field to CultureMech media records to enable environmental linking with CommunityMech and improve cross-repository queries.

Background

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

Currently, CommunityMech has robust environmental metadata using ENVO terms:

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

However, CultureMech has no corresponding field to link media to environments, creating a gap in cross-repository environmental linking.

Proposed Schema Addition

Add a source_environment field to media records:

# In culturemech.yaml schema
SourceEnvironmentDescriptor:
  is_a: Descriptor
  description: Environment from which target organisms originate
  attributes:
    preferred_term:
      description: Human-readable environment name
      required: true
      range: string
    term:
      description: ENVO term for the environment
      range: EnvironmentTerm
      recommended: true
      inlined: true
    notes:
      description: Additional environmental context
      range: string

# Add to CultureMedia class:
source_environment:
  description: Environment(s) from which target organisms originate
  range: SourceEnvironmentDescriptor
  multivalued: true
  inlined_as_list: true

Example Usage

id: CultureMech:010001
name: Acidic Peatland Medium
category: bacterial
medium_type: COMPLEX

source_environment:
  - preferred_term: peatland
    term:
      id: ENVO:00000044
      label: peatland
    notes: "Designed for acidophilic bacteria from northern boreal peatlands"
  
  - preferred_term: peat bog
    term:
      id: ENVO:00005773
      label: peat bog

ingredients:
  - preferred_term: Humic acid
    concentration:
      value: '0.5'
      unit: G_PER_L

Benefits

1. Cross-repository queries: Find all media for specific environments (e.g., "all peatland media")
2. Community curation: Auto-suggest relevant media when adding communities
3. Environmental coverage: Track which environments have cultivation media
4. FAIR data: Standardized environmental metadata across repos
5. Discovery: Enable environment-based browsing and search

Use Cases

Use Case 1: Adding a Peatland Community

When curating a peatland community (like SPRUCE), automatically find and suggest:

• Media tagged with source_environment: ENVO:00000044 (peatland)
• Media for acidophilic organisms
• Media for methanogenic archaea

Use Case 2: Environmental Coverage Analysis

Environment: Peatland (ENVO:00000044)
- Communities: 3 (CommunityMech)
- Media: 15 (CultureMech) ✅
- Coverage: HIGH

Environment: Deep-sea hydrothermal vent (ENVO:01000030)  
- Communities: 5 (CommunityMech)
- Media: 2 (CultureMech) ⚠️ LOW
- Action needed: Create more media for this environment

Use Case 3: Cross-Repository SPARQL Query

SELECT ?community ?media ?ingredient
WHERE {
  ?community communitymech:environment_term ENVO:00000044 .
  ?media culturemech:source_environment ENVO:00000044 .
  ?ingredient mediaingredientmech:environmental_context ENVO:00000044 .
}

Implementation Plan

Phase 1: Schema Design

• Review and refine SourceEnvironmentDescriptor class
• Decide on required vs. recommended fields
• Define validation rules for ENVO terms

Phase 2: Schema Migration

• Update culturemech.yaml schema
• Regenerate Python dataclasses
• Update validation pipelines
• Create migration documentation

Phase 3: Data Curation (Optional)

• Automated: Infer environments from organism metadata in existing media
• LLM-assisted: Suggest ENVO terms based on media names, ingredients, notes
• Manual: Curate high-priority environments (peatland, marine, soil, gut)

Notes

• ENVO prefix already exists in CultureMech schema: ENVO: http://purl.obolibrary.org/obo/ENVO_
• Field should be optional to avoid breaking existing records
• Field is multivalued (media can be relevant to multiple environments)
• Coordinated with MediaIngredientMech issue for environmental_context field

Related Issues

• MediaIngredientMech: [Issue for environmental_context field]
• CommunityMech: [Issue for cross-repo coordination]

References

• Full Proposal: culturebotai-claw/workspace/reports/Cross_Repo_Environment_Linking_Proposal.md
• ENVO Ontology: http://www.obofoundry.org/ontology/envo.html
• Triggering Community: CommunityMech issue #24 (SPRUCE Peatland)