Expand `EnvironmentTerm` to allow for additional environment types.

[caufieldjh]

Currently, EnvironmentTerm is restricted to the following range of ENVO terms:

  EnvironmentTerm:
    description: A term representing an environmental context, material, or feature (from ENVO)
    comments:
      - ENVO (Environment Ontology) describes habitats, biomes, environmental features, and materials
    reachable_from:
      source_nodes:
        - ENVO:01000254  ## environmental system (ecosystems, biomes)
        - ENVO:00010483  ## environmental material (water, soil, air, etc.)
        - ENVO:01001886  ## landform (mountains, valleys, etc.)
      is_direct: false
      relationship_types:
        - rdfs:subClassOf

This does not support healthcare environments or other built environments (e.g., public transport hub, ENVO:03501118).

[github-actions]

Analysis of EnvironmentTerm Expansion

Current State

The EnvironmentTerm enum in the schema (lines 225-236) is currently restricted to three ENVO source nodes:

• ENVO:01000254 - environmental system (ecosystems, biomes)
• ENVO:00010483 - environmental material (water, soil, air, etc.)
• ENVO:01001886 - landform (mountains, valleys, etc.)

This covers natural environments well, as evidenced by current usage:

• Pulmonary_hypertension.yaml: ENVO:00000081 (mountain) - natural landform
• Cholera.yaml: ENVO:00002186 (contaminated water) - environmental material
• Whipple_Disease.yaml: ENVO:00002018 and ENVO:00001998 - environmental materials

The Gap

The current restrictions exclude built environments, which are critical for disease pathophysiology, particularly:

1. Healthcare-associated infections (HAIs) - nosocomial infections acquired in hospitals, clinics, nursing homes
2. Occupational diseases - workplace exposures in factories, laboratories, offices
3. Transportation-related exposures - public transport hubs (as mentioned: ENVO:03501118), airports, train stations
4. Urban health factors - indoor environments, housing conditions, schools

ENVO Hierarchy for Built Environments

Based on ENVO structure, built environments typically fall under:

• ENVO:00000073 - built environment (root for human-constructed environments)
• ENVO:01000744 - anthropogenic terrestrial biome (broader category)
• ENVO:01001405 - human construction (buildings, infrastructure)

Recommended Solution

Add the following source node to EnvironmentTerm:

EnvironmentTerm:
  description: A term representing an environmental context, material, or feature (from ENVO)
  comments:
    - ENVO (Environment Ontology) describes habitats, biomes, environmental features, materials, and built environments
  reachable_from:
    source_nodes:
      - ENVO:01000254  ## environmental system (ecosystems, biomes)
      - ENVO:00010483  ## environmental material (water, soil, air, etc.)
      - ENVO:01001886  ## landform (mountains, valleys, etc.)
      - ENVO:00000073  ## built environment (hospitals, workplaces, transport hubs)
    is_direct: false
    relationship_types:
      - rdfs:subClassOf

Relevant Built Environment Terms

This expansion would enable annotation of disease-relevant contexts such as:

• ENVO:03501118 - public transport hub
• ENVO:00002173 - hospital
• ENVO:01000425 - clinic
• ENVO:01000422 - laboratory environment
• ENVO:01000536 - factory
• ENVO:01000744 - anthropogenic terrestrial biome
• ENVO:00002268 - healthcare facility
• ENVO:01001405 - human construction

Use Cases in dismech

This would be particularly valuable for:

• Healthcare-associated infections (MRSA, C. difficile, etc.)
• Occupational lung diseases (asbestosis, silicosis)
• Legionnaire's disease (building water systems)
• Tuberculosis transmission (crowded indoor spaces, healthcare settings)
• Nosocomial outbreaks of various infectious diseases

Implementation

The change is straightforward - just adding one line to the schema's EnvironmentTerm enum. The ENVO ontology adapter is already configured in conf/oak_config.yaml (line 52), so term validation will work immediately.