Ecology Ontology

Overview

The Ecology ontology captures where and how a protist organism occurs in its environment, and how it interacts with abiotic and biotic ecological contexts.

This domain is concerned with environmental association, not intrinsic biological mechanisms. It complements, but does not overlap with, morphology, physiology, nutrition, behavior, or life-history ontologies.

All ecological information is expressed as assertions, each linked to: - a taxon - a source - a defined feature–trait–value structure

Scope and Design Principles

What this ontology covers

The ecology ontology models:

Habitat occupancy (e.g. marine, freshwater, terrestrial)
Abiotic tolerance ranges (e.g. temperature, salinity, light)
Trophic ecological roles (not mechanisms)
Substrate association
Symbiotic ecological context
Dispersal ecology

What this ontology does not cover

Morphological adaptations (→ morphology)
Physiological performance (→ physiology)
Feeding mechanisms or nutrition sources (→ nutrition)
Life cycle timing or stages (→ life_history)
Genetic or genomic traits (→ genome, sequence)

This separation ensures conceptual clarity and avoids trait duplication across domains.

Conceptual Model

Ecological assertions follow the shared framework:

Features

Features represent ecological dimensions of an organism’s existence.

Defined Features

Feature ID	Description
`habitat`	Broad environmental setting in which the organism occurs
`abiotic_tolerance`	Environmental limits or preferences
`substrate`	Physical or biological surface associated with the organism
`trophic`	Ecological trophic role or strategy
`symbiosis`	Ecological association with other organisms
`dispersal`	Mode of ecological dispersal

Features are not taxa-specific and may apply to many organisms.

Traits

Traits describe properties of ecological features.

Habitat traits

Trait ID	Description	Value type
`type`	Habitat classification	categorical

Vocabulary: - ontology/ecology/vocabularies/habitat_types.yaml

Abiotic tolerance traits

Trait ID	Description	Value type
`temperature_tolerance`	Temperature range tolerated	measurement
`salinity_tolerance`	Salinity range tolerated	measurement
`light_preference`	Light regime preference	categorical

Vocabularies: - light_preferences.yaml

Measurements use fixed units and represent observed or inferred tolerances.

Substrate traits

Trait ID	Description	Value type
`type`	Substrate association	categorical

Vocabulary: - substrate_types.yaml

Trophic ecology traits

Trait ID	Description	Value type
`mode`	Ecological trophic mode	categorical
`feeding_strategy`	Ecological feeding strategy	categorical

Vocabularies: - trophic_modes.yaml - feeding_strategies.yaml

Note: These traits describe ecological roles, not cellular mechanisms.

Symbiosis traits

Trait ID	Description	Value type
`type`	Type of symbiotic association	categorical

Vocabulary: - symbiotic_types.yaml

Dispersal traits

Trait ID	Description	Value type
`mode`	Ecological dispersal mode	categorical

Vocabulary: - dispersal_modes.yaml

Qualifiers

Ecological assertions may be qualified using shared qualifier ontologies, including:

evidence — how the ecological information was determined
condition — environmental or experimental context
context — ecological or geographic constraints

Life stage qualifiers are generally not required, as ecological traits are often species-level summaries.

Example Assertions

Habitat example

- feature: habitat
  trait: type
  value: marine
  qualifiers:
    evidence: literature