Biology Domain Ontology

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

flow "BiologyDomainOntology" v1.0 {
  ontology:
    id: "biology-domain-ontology"
    parent: "scientific-domains"
    purpose: "Represent biological entities, processes, observations and evidence-backed relationships across scales from molecules to ecosystems."

  types:
    BiologicalEntity: {id: string, kind: enum[molecule, gene, protein, cell, tissue, organ, organism, population, community, ecosystem, other], taxon_id: string?, provenance: string}
    BiologicalProcess: {id: string, kind: string, participants: string[], context: string?, provenance: string}
    BiologicalInteraction: {id: string, subject: string, predicate: string, object: string, context: string?, confidence: number, evidence: string[]}
    Experiment: {id: string, protocol: string, conditions: string[], controls: string[], provenance: string}
    Observation: {id: string, subject: string, measurement: string?, timestamp: datetime?, experiment_id: string?, provenance: string}
    Measurement: {value: number, unit: string, uncertainty: number?, method: string?, context: string?}
    Hypothesis: {id: string, claim: string, evidence: string[], status: enum[proposed, supported, challenged, rejected, unresolved]}

  predicates:
    part_of(part: BiologicalEntity, whole: BiologicalEntity)
    participates_in(entity: BiologicalEntity, process: BiologicalProcess)
    regulates(regulator: BiologicalEntity, target: BiologicalEntity)
    interacts_with(a: BiologicalEntity, b: BiologicalEntity)
    expressed_in(gene: BiologicalEntity, context: BiologicalEntity)
    derived_from(entity: BiologicalEntity, source: BiologicalEntity)
    belongs_to_taxon(organism: BiologicalEntity, taxon_id: string)
    observed_in(entity: BiologicalEntity, observation: Observation)
    supports(observation: Observation, hypothesis: Hypothesis)
    contradicts(observation: Observation, hypothesis: Hypothesis)

  constraints:
    - "Every relationship endpoint must resolve to a typed biological entity or process."
    - "Confidence values must lie within [0, 1]."
    - "Measurements require explicit units and documented methods where available."
    - "Distinguish organism, population, species and taxonomic concepts."
    - "Record experimental conditions, biological context and provenance."
    - "Do not infer causation from association or correlation alone."
    - "Do not assume that regulatory or interaction relationships are symmetric or transitive."
    - "Do not merge biological identities based solely on shared names."

  inference:
    rule part_whole_transitivity:
      if part_of(a,b) and part_of(b,c) and compatible_context(a,b,c)
      then part_of(a,c)
      confidence: "retain supporting evidence and taxonomic context"
    rule observed_participation:
      if participates_in(e,p) and observed_in(e,o) and valid(o)
      then evidence_for_participation(e,p,o)
      confidence: "dependent on the observation and study design"
    rule hypothesis_support:
      if supports(o,h) and valid(o)
      then add_evidence(h,o)
      confidence: "update by a declared evidence-assessment model, not automatic certainty"

  SEMANTIC_EQUIVALENCE:
    - "Normalise biological terms against versioned identifiers and reference ontologies where available."
    - "Distinguish exact identity, synonymy, homology, functional similarity and taxonomic membership."
    - "Preserve species, tissue, developmental stage, conditions and assay context."

  CONFIDENCE:
    range: [0,1]
    factors: [measurement_quality, sample_size, study_design, reproducibility, source_reliability, biological_context]
    policy: "Do not increase confidence solely through chained inferences or repeated dependent sources."

  VALIDATION:
    - "Check entity and predicate typing, identifiers, units and provenance."
    - "Flag inconsistent taxonomic assignments and incompatible experimental contexts."
    - "Preserve conflicting observations and alternative hypotheses."
    - "Check that inferred relationships follow explicitly authorised rules."

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

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

  AI_CONSUMPTION:
    representation: "typed biological knowledge graph with evidence-backed relationships"
    outputs: [entity_links, biological_relations, inferred_edges, confidence_annotations, provenance_records, validation_reports]
    safeguards: [no_unsupported_causal_claims, preserve_biological_context, preserve_uncertainty, no_unqualified_identity_merges]
}

END FLOW ALGEBRA