Botany Domain Ontology

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

flow "BotanyDomainOntology" v1.0 {
  ontology:
    id: "botany-domain-ontology"
    parent: "biological-domains"
    purpose: "Represent plant taxa, structures, physiological processes, environments, observations and evidence-backed botanical relationships."

  types:
    PlantTaxon: {id: string, scientific_name: string, rank: string, authority: string?, taxonomic_source: string?}
    PlantOrganism: {id: string, taxon_id: string, life_stage: string?, provenance: string}
    PlantStructure: {id: string, kind: enum[root, stem, leaf, flower, fruit, seed, tissue, cell, other], organism_id: string?}
    BotanicalProcess: {id: string, kind: enum[photosynthesis, respiration, transpiration, germination, growth, pollination, reproduction, nutrient_uptake, other]}
    Habitat: {id: string, description: string, geographic_reference: string?}
    EnvironmentalFactor: {id: string, kind: enum[light, water, temperature, soil, nutrient, salinity, other], value: number?, unit: string?}
    Observation: {id: string, subject_id: string, timestamp: datetime?, method: string, provenance: string, uncertainty: number?}
    Relationship: {id: string, subject: string, predicate: string, object: string, context: string?, confidence: number, evidence: string[]}

  predicates:
    classified_as(organism: PlantOrganism, taxon: PlantTaxon)
    part_of(structure: PlantStructure, organism: PlantOrganism)
    participates_in(structure: PlantStructure, process: BotanicalProcess)
    occurs_in(organism: PlantOrganism, habitat: Habitat)
    influenced_by(process: BotanicalProcess, factor: EnvironmentalFactor)
    interacts_with(a: PlantOrganism, b: PlantOrganism)
    observed_in(entity_id: string, observation: Observation)
    descendant_taxon_of(child: PlantTaxon, ancestor: PlantTaxon)

  constraints:
    - "All relationship endpoints must resolve to correctly typed entities."
    - "Confidence values must be within [0, 1]."
    - "Taxonomic identities require a stated authority and version where available."
    - "Quantitative observations must specify units and relevant conditions."
    - "Do not infer causation solely from co-occurrence or correlation."
    - "Do not infer individual identity from shared taxonomic classification."
    - "Taxon ancestry and organism-level parentage are distinct relationships."
    - "Preserve geographic, seasonal and experimental context."

  inference:
    rule taxonomic_ancestry:
      if descendant_taxon_of(a,b) and descendant_taxon_of(b,c)
      then descendant_taxon_of(a,c)
      confidence: "preserve taxonomy version and source lineage"
    rule observation_support:
      if observed_in(x,o) and valid(o)
      then evidence_for(x,o)
      confidence: "conditioned on observation quality and provenance"
    rule environmental_association:
      if influenced_by(p,f) and observed_in(p,o)
      then candidate_environmental_context(p,f,o)
      confidence: "hypothesis only; no automatic causal confirmation"

  SEMANTIC_EQUIVALENCE:
    - "Resolve botanical synonyms using versioned taxonomic authorities."
    - "Distinguish taxonomic synonymy from organism identity and trait similarity."
    - "Preserve nomenclatural, geographic and temporal context."

  CONFIDENCE:
    range: [0,1]
    factors: [source_reliability, observation_quality, identification_certainty, measurement_uncertainty, replication, context_fit]
    policy: "Never increase certainty solely through repeated or chained inference."

  VALIDATION:
    - "Validate type compatibility and referential integrity."
    - "Check accepted taxon names and synonym mappings against cited catalogue versions."
    - "Validate units, timestamps, methods and observation provenance."
    - "Flag conflicting taxonomic assignments and unsupported causal assertions."
    - "Retain competing classifications or interpretations where evidence is unresolved."

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

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

  AI_CONSUMPTION:
    representation: "typed botanical knowledge graph with evidence-backed edges"
    outputs: [taxon_links, organism_structure_links, process_relations, environmental_context, inferred_edges, uncertainty_annotations, provenance_records]
    safeguards: [no_unsupported_causal_claims, no_unqualified_taxonomic_merges, preserve_units_and_context, preserve_alternative_hypotheses]
}

END FLOW ALGEBRA