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Nutrition Ontology

The Nutrition ontology describes how protists acquire energy and carbon, capture resources, and interact nutritionally with other organisms.
It captures functional biology, integrating traits from physiology, feeding, and ecological interactions.

Features in Nutrition

Features define what biological entity the trait applies to.
In nutrition, most traits are applied at the level of the whole organism or cell.

Examples:

- feature_id: organism
  label: Organism
  description: Whole living individual

- feature_id: cell
  label: Cell
  description: Single cell of the organism

Features anchor assertions so traits can be interpreted in the correct biological context.

Traits in Nutrition

Traits describe properties related to nutrition, independent of any specific organism.

Examples of nutritional traits:

- trait_id: energy_source
  label: Energy source
  description: Primary source of energy used by the organism
  value_type: categorical
  vocabulary: ontology/nutrition/vocabularies/energy_source.yaml

- trait_id: carbon_source
  label: Carbon source
  description: Primary source of carbon for biomass synthesis
  value_type: categorical
  vocabulary: ontology/nutrition/vocabularies/carbon_source.yaml

- trait_id: feeding_mechanism
  label: Feeding mechanism
  description: Mechanism by which resources are internalised
  value_type: categorical
  vocabulary: ontology/nutrition/vocabularies/feeding_mechanism.yaml

- trait_id: resource_capture
  label: Resource capture structures or processes
  description: Means by which external resources are accessed
  value_type: categorical
  vocabulary: ontology/nutrition/vocabularies/resource_capture.yaml

- trait_id: trophic_strategy
  label: Trophic strategy
  description: Integrated nutritional strategy of the organism
  value_type: categorical
  vocabulary: ontology/nutrition/vocabularies/trophic_strategy.yaml

- trait_id: symbiosis
  label: Nutritional symbiosis
  description: Nutritional dependence or association with other organisms
  value_type: categorical
  vocabulary: ontology/nutrition/vocabularies/symbiosis.yaml

- trait_id: mixotrophy_type
  label: Mixotrophy type
  description: Functional subtype of mixotrophy describing the balance and integration of phototrophic and phagotrophic nutrition
  value_type: categorical
  vocabulary: ontology/nutrition/vocabularies/mixotrophy_types.yaml

Traits are feature-agnostic: the same trait can apply to an organism or a single cell, depending on the context.

Vocabularies

Controlled vocabularies define the allowed values for categorical traits, ensuring consistency across assertions and contributors.

Example: trophic_strategy.yaml

- autotroph
- heterotroph
- mixotroph
- photoautotroph
- chemoheterotroph
- saprotroph
- parasitotroph
- bacterivore
- eukaryvore
- omnivore
- fungivore
- detritivore

Other vocabularies include:

- `energy_source.yaml` — e.g., light, chemical energy
- `carbon_source.yaml` — e.g., inorganic carbon, organic carbon
- `feeding_mechanism.yaml` — e.g., phagotrophy, osmotrophy
- `resource_capture.yaml` — e.g., cytostome, pseudopodia
- `mixotrophy_types.yaml` — e.g., constitutive, non-constitutive
- `symbiosis.yaml` — e.g., mutualistic, parasitic, commensal

Example assertions in Nutrition

Energy and carbon sources

- feature: organism
  trait: energy_source
  value: chemotrophy
  qualifiers:
    evidence_method: inference

- feature: organism
  trait: carbon_source
  value: heterotrophy
  qualifiers:
    evidence_method: inference

### Feeding and resource capture

- feature: organism
  trait: feeding_mechanism
  value: phagotrophy
  qualifiers:
    evidence_method: light_microscopy

- feature: organism
  trait: resource_capture
  value: cytostome
  qualifiers:
    evidence_method: light_microscopy

### Trophic strategy and symbiosis

- feature: organism
  trait: trophic_strategy
  value: mixotroph
  qualifiers:
    evidence_method: inference
    evidence_basis: morphology

- feature: organism
  trait: symbiosis
  value: mutualistic
  qualifiers:
    evidence_method: literature
    source_id: yubuki_etal_2009

Best practices for nutritional curation

  1. Select the correct feature first.
    Most nutritional traits apply at the organism level; some can also be applied to cells.

  2. Use controlled vocabularies whenever possible.
    Avoid free-text values for categorical traits.

  3. Attach qualifiers for context.
    Include evidence type, life stage, environment, or material if relevant.

  4. Distinguish observations from inferences.
    Use qualifiers like evidence_method: inference to indicate inferred traits.

  5. Document sources.
    Every assertion should be traceable to a publication or dataset.

Summary:
The Nutrition ontology allows curators to capture how protists acquire energy and nutrients, how they feed, and how they interact nutritionally with other organisms.
Combining features, traits, vocabularies, and qualifiers ensures that assertions are precise, reproducible, and semantically meaningful.