Human Anatomy Domain Ontology

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

flow "HumanAnatomyDomainOntology" v1.0 {
  ontology:
    id: "human-anatomy-domain-ontology"
    parent: "medical-domains"
    purpose: "Represent human anatomical structures, spatial relations, part-whole hierarchies, anatomical variants and evidence-backed observations."

  types:
    AnatomicalStructure: {id: string, preferred_name: string, class: enum[organ, tissue, bone, muscle, vessel, nerve, joint, cavity, region, cell, other], laterality: enum[left, right, bilateral, midline, not_applicable]?, terminology_id: string?}
    BodySystem: {id: string, name: string}
    AnatomicalRegion: {id: string, name: string, reference_frame: string?}
    AnatomicalObservation: {id: string, subject_id: string, modality: string, observed_at: datetime?, source: string, uncertainty: number?}
    AnatomicalVariant: {id: string, structure_id: string, description: string, population_context: string?}
    Relationship: {id: string, subject: string, predicate: string, object: string, context: string?, confidence: number, evidence: string[]}

  predicates:
    part_of(part: AnatomicalStructure, whole: AnatomicalStructure)
    located_in(structure: AnatomicalStructure, region: AnatomicalRegion)
    belongs_to_system(structure: AnatomicalStructure, system: BodySystem)
    adjacent_to(a: AnatomicalStructure, b: AnatomicalStructure)
    articulates_with(a: AnatomicalStructure, b: AnatomicalStructure)
    innervates(nerve: AnatomicalStructure, target: AnatomicalStructure)
    supplies(vessel: AnatomicalStructure, target: AnatomicalStructure)
    drains_into(vessel: AnatomicalStructure, recipient: AnatomicalStructure)
    has_variant(structure: AnatomicalStructure, variant: AnatomicalVariant)
    observed_in(structure: AnatomicalStructure, observation: AnatomicalObservation)

  constraints:
    - "All relationship endpoints must resolve to appropriately typed entities."
    - "Confidence values must be within [0, 1]."
    - "Do not equate anatomical adjacency with connection, innervation or blood supply."
    - "Distinguish structural part-of from regional location and system membership."
    - "Preserve laterality, anatomical position, scale and population context."
    - "Do not infer a patient-specific anatomical fact from a population-level norm."
    - "Part-of must be acyclic for strict structural containment; not all relations are transitive."
    - "Observations and variants must retain provenance and uncertainty."

  inference:
    rule part_whole_transitivity:
      if part_of(a,b) and part_of(b,c) and compatible_anatomical_granularity(a,b,c)
      then part_of(a,c)
      confidence: "retain evidence and hierarchical context"
    rule adjacency_symmetry:
      if adjacent_to(a,b) and same_anatomical_context(a,b)
      then adjacent_to(b,a)
      confidence: "preserve source confidence"
    rule articulation_symmetry:
      if articulates_with(a,b)
      then articulates_with(b,a)
      confidence: "preserve evidence and context"
    rule observation_support:
      if observed_in(s,o) and valid(o)
      then evidence_for(s,o)
      confidence: "modality and observation quality dependent"

  SEMANTIC_EQUIVALENCE:
    - "Map synonyms to versioned anatomical terminology identifiers when verified."
    - "Differentiate exact identity, synonymy, broader anatomy and related structures."
    - "Preserve laterality and variant qualifiers when normalising names."

  CONFIDENCE:
    range: [0,1]
    factors: [source_quality, imaging_resolution, interobserver_agreement, anatomical_variability, evidence_independence]
    policy: "Do not increase confidence merely by chaining inferences."

  VALIDATION:
    - "Check entity types, relationship domain and range, and anatomical terminology."
    - "Check laterality, part-whole cycles and conflicting spatial assertions."
    - "Retain contradictory observations for review rather than silently merging them."
    - "Flag patient-specific interpretations unsupported by observations."

  FLOW_HASH:
    algorithm: "SHA-256"
    input: "canonicalised ontology version, typed assertions, inference 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 anatomical knowledge graph with evidence-backed relationships"
    outputs: [anatomical_entities, part_whole_links, spatial_relations, terminology_mappings, uncertainty_annotations, provenance_records]
    safeguards: [no_unverified_patient_specific_claims, preserve_laterality, distinguish_normal_variation, no_unsupported_clinical_inference]
}

END FLOW ALGEBRA