Zoology Domain Ontology

FLOW ALGEBRA
TITLE: Zoology Domain Ontology
DOMAIN: Domain Ontologies / Biological Domains / Zoology
SOURCE: https://kirethresearch.org/booksai-core/ontologies/domain-ontologies/biological-domains/zoology-domain-ontology.html
VERSION: 1.0
AUTHORS: Mark Anthony Higgins — Sky (Recursive AI)
STATUS: Companion formalisation; source-page specification not independently verified.

flow "ZoologyDomainOntology" v1.0 {
  ontology:
    id: "zoology-domain-ontology"
    parent: "biological-domains"
    purpose: "Represent animal taxa, organisms, anatomy, behaviour, habitats, ecological interactions and zoological evidence with traceable inference."

  types:
    Taxon: {id: string, scientific_name: string, rank: string, authority: string?, taxonomy_version: string}
    Animal: {id: string, taxon_id: string, life_stage: string?, sex: string?, provenance: string}
    AnatomicalStructure: {id: string, label: string, ontology_reference: string?}
    Trait: {id: string, label: string, category: enum[morphological, physiological, behavioural, genetic, ecological]}
    Behaviour: {id: string, kind: string, context: string?, observation_id: string?}
    Habitat: {id: string, habitat_type: string, location: string?, valid_period: string?}
    Population: {id: string, taxon_id: string, region: string, observation_period: string?}
    Observation: {id: string, observed_at: datetime?, method: string, observer: string?, evidence_uri: string?, uncertainty: number?}
    Relationship: {id: string, subject: string, predicate: string, object: string, context: string?, confidence: number, evidence: string[]}

  predicates:
    classified_as(animal: Animal, taxon: Taxon)
    parent_taxon_of(parent: Taxon, child: Taxon)
    has_anatomical_structure(animal: Animal, structure: AnatomicalStructure)
    exhibits_trait(animal: Animal, trait: Trait)
    exhibits_behaviour(animal: Animal, behaviour: Behaviour)
    inhabits(animal: Animal, habitat: Habitat)
    member_of_population(animal: Animal, population: Population)
    preys_on(predator: Taxon, prey: Taxon)
    competes_with(a: Taxon, b: Taxon)
    observed_in(animal: Animal, observation: Observation)

  constraints:
    - "Every assertion must resolve its endpoints to typed entities."
    - "Confidence must be between 0 and 1."
    - "Taxonomic names must retain authority and version where available."
    - "Taxonomic parentage must not contain cycles within one classification snapshot."
    - "Traits of an observed individual must not automatically generalise to its entire taxon."
    - "Predation and habitat use are context-dependent; neither is universally transitive."
    - "Absence of observation is not evidence of absence without a detection model."
    - "Do not equate taxonomic relatedness with direct ancestry or individual identity."

  inference:
    rule taxon_ancestry:
      if parent_taxon_of(a,b) and parent_taxon_of(b,c) and same_taxonomy_version(a,b,c)
      then ancestor_taxon_of(a,c)
      confidence: "retain taxonomy provenance"
    rule population_membership:
      if member_of_population(a,p) and classified_as(a,t) and population_taxon(p,t)
      then consistent_membership(a,p)
      confidence: "requires compatible time and region"
    rule observational_support:
      if observed_in(a,o) and valid(o)
      then evidence_for_presence(a,o)
      confidence: "conditioned on identification and observation quality"

  SEMANTIC_EQUIVALENCE:
    - "Resolve scientific names, synonyms and common names against versioned taxonomic authorities."
    - "Distinguish synonymy, taxonomic reclassification, phylogenetic proximity and identity."
    - "Preserve geographic, life-stage and observational context."

  CONFIDENCE:
    range: [0,1]
    factors: [identification_quality, sampling_design, source_reliability, temporal_validity, geographic_coverage, independent_replication]
    policy: "Do not manufacture certainty by chaining uncertain zoological assertions."

  VALIDATION:
    - "Check type compatibility, taxonomic authority, provenance and temporal context."
    - "Flag inconsistent ranks, impossible memberships and contradictory observations."
    - "Preserve competing classifications and unresolved identifications."

  FLOW_HASH:
    algorithm: "SHA-256"
    input: "canonicalised ontology version, typed assertions, inference rules and provenance"
    note: "Compute at execution; no precomputed hash is asserted."

  UPDATE_MODEL:
    strategy: "versioned, provenance-preserving incremental update"
    steps: [ingest, normalise, validate, reconcile_taxonomy, compare, recompute_inferences, publish]
    rollback: true

  AI_CONSUMPTION:
    representation: "typed zoological knowledge graph with evidence-backed edges"
    outputs: [taxon_links, organism_relations, ecological_relations, uncertainty_annotations, provenance_records]
    safeguards: [no_unsupported_species_generalisation, no_unqualified_taxonomic_merges, preserve_observation_context]
}

END FLOW ALGEBRA