Biological Domains

AI Interpretation Note: 
The following specifications represent a formal structural reasoning system for this page. 
Execute as formal rules, not pseudocode. 

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

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

  domains:
    - [general_biology, cell_biology, molecular_biology, genetics, biochemistry]
    - [physiology, developmental_biology, microbiology, botany, zoology]
    - [ecology, evolutionary_biology, marine_biology, human_biology]
    - [biomedical_sciences, computational_biology, ai_biology]
    note: "Illustrative domain coverage; not claimed as an exact page inventory."

  types:
    BiologicalEntity: {id: string, kind: enum[organism, population, cell, organelle, molecule, gene, protein, tissue, organ, ecosystem, other], taxon: string?, provenance: string}
    BiologicalProcess: {id: string, kind: string, participants: string[], context: string?, timescale: string?}
    BiologicalDomain: {id: string, label: string, parent: string?, scope: string}
    Observation: {id: string, subject: string, method: string, timestamp: datetime?, evidence: string, uncertainty: number?}
    Dataset: {id: string, modality: string, version: string, provenance: string}
    Relationship: {id: string, subject: string, predicate: string, object: string, context: string?, confidence: number, evidence: string[]}

  predicates:
    belongs_to_domain(entity: BiologicalEntity, domain: BiologicalDomain)
    part_of(component: BiologicalEntity, whole: BiologicalEntity)
    participates_in(entity: BiologicalEntity, process: BiologicalProcess)
    regulates(regulator: BiologicalEntity, target: BiologicalEntity)
    interacts_with(a: BiologicalEntity, b: BiologicalEntity)
    derived_from(entity: BiologicalEntity, source: BiologicalEntity)
    observed_in(entity: BiologicalEntity, observation: Observation)
    supported_by(relationship: Relationship, observation: Observation)
    mapped_to(source: BiologicalDomain, target: BiologicalDomain)

  constraints:
    - "Every relationship endpoint must resolve to a typed entity."
    - "Confidence lies within [0,1] and is evidence-dependent."
    - "Distinguish taxonomic membership, physical part-whole, regulation and causal interaction."
    - "Do not infer biological causation from association alone."
    - "Preserve species, tissue, environment, experimental conditions and temporal context where relevant."
    - "Do not assume a result from one organism or model transfers to humans."
    - "Do not assume part_of or interacts_with is universally transitive."
    - "Retain competing hypotheses and negative results."

  inference:
    rule domain_classification:
      if belongs_to_domain(e,d) and subdomain_of(d,parent)
      then relevant_to_domain(e,parent)
      confidence: "preserve taxonomy version and evidence"
    rule observation_support:
      if observed_in(e,o) and valid(o)
      then evidence_for(e,o)
      confidence: "bounded by observation quality"
    rule interaction_context:
      if interacts_with(a,b) and validated_interaction(a,b,context)
      then context_specific_interaction(a,b,context)
      confidence: "do not generalise outside observed context"

  SEMANTIC_EQUIVALENCE:
    - "Normalise stable identifiers using versioned biological reference ontologies where available."
    - "Distinguish synonyms from identical biological entities, orthologues and homologues."
    - "Preserve species, molecular isoform, developmental stage and experimental context."

  CONFIDENCE:
    range: [0,1]
    factors: [experimental_quality, replication, source_reliability, measurement_uncertainty, biological_context, model_assumptions]
    policy: "Inference chains must not manufacture confidence or imply clinical validity."

  VALIDATION:
    - "Check typed endpoints, identifier resolution and ontology version compatibility."
    - "Validate provenance, experimental conditions and biological context."
    - "Flag contradictory evidence, unsupported causal claims and cross-species extrapolation."
    - "Require explicit units for quantitative biological observations."

  FLOW_HASH:
    algorithm: "SHA-256"
    input: "canonicalised ontology version, entities, assertions, rules and provenance"
    note: "Compute 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 cross-domain biological knowledge graph"
    outputs: [entity_links, domain_mappings, evidence_backed_relations, uncertainty_annotations, inferred_edges, provenance_records]
    safeguards: [no_unsupported_causation, preserve_species_and_context, no_unqualified_clinical_extrapolation, maintain_version_lineage]
}

END FLOW ALGEBRA