Biological Sciences Domain Ontology

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

flow "BiologicalSciencesDomainOntology" v1.0 {
  ontology:
    id: "biological-sciences-domain-ontology"
    parent: "biological-domains"
    purpose: "Represent biological entities, processes, observations and evidence-backed relationships across scales of life."

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

  predicates:
    part_of(part: BiologicalEntity, whole: BiologicalEntity)
    participates_in(entity: BiologicalEntity, process: BiologicalProcess)
    regulates(regulator: BiologicalEntity, target: BiologicalEntity)
    interacts_with(a: BiologicalEntity, b: BiologicalEntity)
    derived_from(descendant: BiologicalEntity, source: BiologicalEntity)
    inhabits(organism: BiologicalEntity, ecosystem: BiologicalEntity)
    observed_in(entity: BiologicalEntity, observation: Observation)
    supports(observation: Observation, hypothesis: Hypothesis)

  constraints:
    - "All referenced entity and evidence identifiers must resolve."
    - "Confidence must lie within [0,1]."
    - "Measurement values require units, with uncertainty and conditions where applicable."
    - "Biological relationships must retain taxonomic, experimental and temporal context where relevant."
    - "Correlation and co-occurrence alone do not establish causation or regulation."
    - "Do not assume part_of, regulates, interacts_with or inhabits is universally transitive."
    - "Distinguish biological homology, analogy, similarity and identity."

  inference:
    rule contextual_part_membership:
      if part_of(a,b) and part_of(b,c) and compatible_partonomy(a,b,c)
      then candidate(part_of(a,c))
      confidence: "requires partonomy semantics and supporting evidence"
    rule observation_evidence:
      if observed_in(entity,obs) and valid(obs)
      then evidence_for(entity,obs)
      confidence: "dependent on method quality and measurement uncertainty"
    rule biological_interaction:
      if interacts_with(a,b) and interaction_is_symmetric(a,b)
      then interacts_with(b,a)
      confidence: "retain original evidence; symmetry is predicate-specific"

  SEMANTIC_EQUIVALENCE:
    - "Resolve taxonomic and molecular identifiers using versioned reference authorities."
    - "Preserve distinctions between synonyms, orthologues, homologues and exact identity."
    - "Record mapping context, species, assay and reference database version."

  CONFIDENCE:
    range: [0,1]
    factors: [evidence_quality, measurement_uncertainty, replication, sampling_bias, biological_context, source_reliability]
    policy: "Do not manufacture certainty by chaining dependent observations or inferred relationships."

  VALIDATION:
    - "Validate typed endpoints, identifiers, units, taxonomic scope and provenance."
    - "Check experimental controls, temporal validity and competing hypotheses."
    - "Flag inconsistent biological classifications and unsupported causal claims."
    - "Retain uncertainty and contradictory evidence rather than silently discarding it."

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

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

  AI_CONSUMPTION:
    representation: "typed biological knowledge graph with evidence-backed assertions"
    outputs: [entity_links, biological_relations, inferred_edges, uncertainty_annotations, provenance_records]
    safeguards: [preserve_biological_context, no_unsupported_causal_claims, distinguish_identity_from_similarity, retain_conflicting_evidence]
}

END FLOW ALGEBRA