identifier: METPO:1000059
label: phenotype
definition: A quality that differentiates specific instances of a species from other
  instances of the same species.
definition_source: DOI:10.1186/gb-2010-11-1-r2
trait_category: UPPER
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- METPO:1000188
created_by: Luke Wang
evidence:
- reference: DOI:10.1186/gb-2010-11-1-r2
  snippet: entity that is observed to be affected
  notes: Supports phenotype representation through entity-quality descriptions.
- reference: DOI:10.1186/gb-2010-11-1-r2
  snippet: specific characteristic or quality of that entity affected
  notes: Supports phenotype as an observed quality of an entity.
causal_graphs:
- graph_id: phenotype_quality_child_context
  title: Phenotype quality and child-trait context
  description: DOI-backed upper-ontology context graph linking phenotype to its quality
    parent and to non-environmental, non-genomic TraitMech child groupings.
  nodes:
  - node_id: phenotype_trait
    label: phenotype
    node_type: TRAIT
    grounding: METPO:1000059
    description: Upper-level class for organismal qualities and observable trait classes.
  - node_id: quality_parent
    label: quality
    node_type: TRAIT
    grounding: METPO:1000188
    description: Parent upper class for qualities.
  - node_id: morphology_children
    label: morphology child traits
    node_type: TRAIT
    description: Non-environmental morphology children such as cell shape, cell size,
      Gram stain, pigmentation, motility, and sporulation.
  - node_id: physiology_child
    label: trophic type
    node_type: TRAIT
    grounding: METPO:1000631
    description: Physiology child class under phenotype.
  - node_id: ecology_child
    label: pathogenic to host
    node_type: TRAIT
    grounding: METPO:1004000
    description: Ecology child class under phenotype.
  edges:
  - subject: phenotype_trait
    predicate: is a
    object: quality_parent
    description: Phenotypes are modeled as qualities or quality-bearing descriptions
      of entities.
    evidence:
    - reference: DOI:10.1186/gb-2010-11-1-r2
      snippet: ontology of qualities termed Phenotype and Trait ontology
      notes: Supports phenotype representation through PATO quality classes.
    predicate_id: rdfs:subClassOf
  - subject: morphology_children
    predicate: specializes
    object: phenotype_trait
    description: Morphology classes are non-environmental child phenotypes in TraitMech.
    evidence:
    - reference: DOI:10.1186/gb-2010-11-1-r2
      snippet: size, color, shape, structure
      notes: Supports morphology-like qualities as phenotype descriptors.
    predicate_id: rdfs:subClassOf
  - subject: physiology_child
    predicate: specializes
    object: phenotype_trait
    description: Trophic type is retained as a non-environmental physiology child
      under phenotype.
    evidence:
    - reference: DOI:10.1186/gb-2010-11-1-r2
      snippet: logical definitions and associated ontologies
      notes: Supports phenotype classes as organized through ontology-backed definitions
        and parent-child placement.
    predicate_id: rdfs:subClassOf
  - subject: ecology_child
    predicate: specializes
    object: phenotype_trait
    description: Pathogenic-to-host is retained as a non-environmental ecology child
      under phenotype.
    evidence:
    - reference: DOI:10.1186/gb-2010-11-1-r2
      snippet: phenotype ontologies across multiple species
      notes: Supports phenotype hierarchies spanning different biological domains.
    predicate_id: rdfs:subClassOf
curation_history:
- timestamp: '2026-05-05T01:35:46.809675+00:00'
  curator: seed_from_metpo
  action: SEEDED_FROM_METPO
  changes: imported from data/raw/metpo.owl (CLASS)
  llm_assisted: false
- timestamp: '2026-05-15T00:35:00-07:00'
  curator: codex
  action: CURATED_UPPER_CONTEXT
  changes: Reviewed phenotype as an upper quality-derived classifier and added a DOI-backed
    context graph covering its quality parent plus non-environmental, non-genomic
    child groupings.
  llm_assisted: true
- timestamp: '2026-05-20T03:35:32Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (rdfs:subClassOf×1).
  llm_assisted: true
- timestamp: '2026-05-23T08:21:50Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (rdfs:subClassOf×3).
  llm_assisted: true