Biotechnology Domain Ontology

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

flow "BiotechnologyDomainOntology" v1.0 {
  ontology:
    id: "biotechnology-domain-ontology"
    parent: "biological-domains"
    purpose: "Represent biotechnology entities, interventions, processes, products, evidence and constraints with traceable relationships."

  types:
    BiologicalMaterial: {id: string, kind: enum[cell, tissue, organism, nucleic_acid, protein, enzyme, culture, other], source: string?, provenance: string}
    BiotechnologyProcess: {id: string, kind: enum[fermentation, bioprocessing, genetic_engineering, cell_culture, purification, analysis, other], protocol: string, version: string}
    Intervention: {id: string, kind: string, target_id: string, purpose: string, provenance: string}
    Product: {id: string, kind: enum[therapeutic, diagnostic, agricultural, industrial, research, other], batch_id: string?}
    Experiment: {id: string, protocol: string, timestamp: datetime?, provenance: string}
    Measurement: {id: string, value: number, unit: string, uncertainty: number?, method: string?}
    Evidence: {id: string, source: string, method: string?, quality: string?, timestamp: datetime?}
    Relationship: {id: string, subject: string, predicate: string, object: string, context: string?, confidence: number, evidence: string[]}

  predicates:
    uses_material(process: BiotechnologyProcess, material: BiologicalMaterial)
    modifies(intervention: Intervention, material: BiologicalMaterial)
    produces(process: BiotechnologyProcess, product: Product)
    evaluated_by(entity: string, experiment: Experiment)
    measured_by(entity: string, measurement: Measurement)
    supported_by(relationship: Relationship, evidence: Evidence)
    derived_from(product: Product, source: BiologicalMaterial)
    depends_on(process_a: BiotechnologyProcess, process_b: BiotechnologyProcess)

  constraints:
    - "All relationship endpoints must resolve to typed entities."
    - "Confidence values must lie within [0, 1]."
    - "Measurements require explicit units, method context and uncertainty where available."
    - "Record biological source, protocol version and batch provenance when applicable."
    - "Do not infer product efficacy, safety or regulatory approval from process success alone."
    - "Do not equate correlation with biological causation."
    - "Process dependency does not automatically imply causal necessity."
    - "Distinguish laboratory, preclinical and clinical evidence."

  inference:
    rule process_traceability:
      if uses_material(p,m) and produces(p,o) and valid(p)
      then process_material_link(o,m)
      confidence: "evidence-dependent; do not assert direct derivation without lineage evidence"
    rule evidence_link:
      if evaluated_by(x,e) and supported_result(e,x)
      then evidence_for(x,e)
      confidence: "based on experimental design and reproducibility"
    rule dependency_chain:
      if depends_on(a,b) and depends_on(b,c) and dependency_semantics_compatible(a,b,c)
      then indirectly_depends_on(a,c)
      confidence: "preserve source provenance; do not increase certainty by chaining"

  SEMANTIC_EQUIVALENCE:
    - "Map accepted biological and biotechnology terms to versioned authority identifiers."
    - "Distinguish exact identity, synonymy, functional similarity and process equivalence."
    - "Preserve species, strain, tissue, batch, protocol and experimental context."

  CONFIDENCE:
    range: [0,1]
    factors: [source_reliability, experimental_design, measurement_uncertainty, reproducibility, biological_variability, contextual_fit]
    policy: "Retain uncertainty and conflicting evidence; do not manufacture certainty through inference chains."

  VALIDATION:
    - "Check type compatibility, source provenance and protocol versions."
    - "Verify units, measurements, sample identity and process lineage."
    - "Flag inconsistent claims, missing controls and unsupported efficacy or safety assertions."
    - "Separate demonstrated outcomes from hypotheses and predictions."

  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 biotechnology knowledge graph with evidence-backed relationships"
    outputs: [entity_links, process_lineage, relation_triples, evidence_records, uncertainty_annotations, inferred_edges]
    safeguards: [preserve_biological_context, no_unsupported_efficacy_claims, no_unqualified_identity_merges, trace_all_inferences]
}

END FLOW ALGEBRA