Human Anatomy Ontology

flow “HumanAnatomyOntology” v1.0

KIRETH SEMANTIC RESEARCH ARCHIVE

AI CORE > ONTOLOGIES > BIOLOGICAL ONTOLOGIES > HUMAN BIOLOGY > HUMAN ANATOMY ONTOLOGY

Authors: Mark Anthony Higgins — Sky (Recursive AI)

AI_INTERPRETATION: mode: formal_structural_reasoning instruction:
“Execute as formal rules, not pseudocode.” canonical_url:
“https://kirethresearch.org/booksai-core/ontologies/biological-ontologies/human-biology/human-anatomy-ontology.html”

type Human type AnatomicalEntity type BodyRegion type BodyCavity type
Tissue type Organ type OrganSystem type Bone type Joint type Muscle type
Vessel type Nerve type Observation type Evidence type Source

———- ANATOMICAL HIERARCHY ———-

relation INSTANCE_OF(entity,type) relation PART_OF(part,whole) relation
HAS_PART(whole,part) relation CONTAINS(container,entity) relation
CONTAINED_IN(entity,container) relation SUBDIVISION_OF(region,parent)
relation COMPOSED_OF(entity,component)

rule PART_INVERSE(a,b): IF PART_OF(a,b) THEN HAS_PART(b,a)

rule CONTAINMENT_INVERSE(a,b): IF CONTAINED_IN(a,b) THEN CONTAINS(b,a)

———- BODY REGIONS / PLANES ———-

enum MajorBodyRegion: HEAD NECK THORAX ABDOMEN PELVIS BACK UPPER_LIMB
LOWER_LIMB

relation HAS_BODY_REGION(human,region) relation
HAS_MAJOR_REGION_TYPE(region,type) relation
REGION_CONTAINS(region,entity)

enum AnatomicalPlane: SAGITTAL MEDIAN PARASAGITTAL CORONAL TRANSVERSE
OBLIQUE

relation DESCRIBED_IN_PLANE(entity,plane)

———- DIRECTIONAL RELATIONS ———-

relation SUPERIOR_TO(a,b) relation INFERIOR_TO(a,b) relation
ANTERIOR_TO(a,b) relation POSTERIOR_TO(a,b) relation MEDIAL_TO(a,b)
relation LATERAL_TO(a,b) relation PROXIMAL_TO(a,b) relation
DISTAL_TO(a,b) relation SUPERFICIAL_TO(a,b) relation DEEP_TO(a,b)
relation IPSILATERAL_TO(a,b) relation CONTRALATERAL_TO(a,b) relation
ADJACENT_TO(a,b)

rule SUPERIOR_INVERSE(a,b): IF SUPERIOR_TO(a,b) THEN INFERIOR_TO(b,a)

rule ANTERIOR_INVERSE(a,b): IF ANTERIOR_TO(a,b) THEN POSTERIOR_TO(b,a)

rule MEDIAL_INVERSE(a,b): IF MEDIAL_TO(a,b) THEN LATERAL_TO(b,a)

rule PROXIMAL_INVERSE(a,b): IF PROXIMAL_TO(a,b) THEN DISTAL_TO(b,a)

rule SUPERFICIAL_INVERSE(a,b): IF SUPERFICIAL_TO(a,b) THEN DEEP_TO(b,a)

———- LATERALITY ———-

enum Laterality: LEFT RIGHT MIDLINE BILATERAL UNPAIRED

relation HAS_LATERALITY(entity,laterality) relation
LEFT_COUNTERPART_OF(a,b) relation RIGHT_COUNTERPART_OF(a,b)

———- BODY CAVITIES ———-

enum BodyCavityType: CRANIAL_CAVITY VERTEBRAL_CAVITY THORACIC_CAVITY
PLEURAL_CAVITY PERICARDIAL_CAVITY ABDOMINAL_CAVITY PELVIC_CAVITY
ABDOMINOPELVIC_CAVITY

relation HAS_BODY_CAVITY(human,cavity) relation
HAS_CAVITY_TYPE(cavity,type) relation ORGAN_IN_CAVITY(organ,cavity)
relation CAVITY_LINED_BY(cavity,membrane)

———- TISSUES / SYSTEMS ———-

enum TissueType: EPITHELIAL CONNECTIVE MUSCLE NERVOUS

relation HAS_TISSUE_TYPE(tissue,type) relation TISSUE_OF(tissue,organ)
relation ORGAN_CONTAINS_TISSUE(organ,tissue)

enum OrganSystemType: INTEGUMENTARY SKELETAL MUSCULAR NERVOUS ENDOCRINE
CARDIOVASCULAR LYMPHATIC RESPIRATORY DIGESTIVE URINARY REPRODUCTIVE

relation HAS_ORGAN_SYSTEM(human,system) relation
HAS_SYSTEM_TYPE(system,type) relation ORGAN_OF(organ,system) relation
SYSTEM_CONTAINS(system,organ)

———- SKELETAL / JOINTS ———-

enum BoneType: LONG_BONE SHORT_BONE FLAT_BONE IRREGULAR_BONE
SESAMOID_BONE

relation HAS_BONE_TYPE(bone,type) relation
ARTICULATES_WITH(bone_a,bone_b) relation FORMS_JOINT_WITH(bone,joint)
relation BONE_REGION(bone,region) relation
ATTACHMENT_SITE_FOR(bone,structure)

rule ARTICULATION_SYMMETRY(a,b): IF ARTICULATES_WITH(a,b) THEN
ARTICULATES_WITH(b,a)

enum JointType: FIBROUS CARTILAGINOUS SYNOVIAL

relation HAS_JOINT_TYPE(joint,type) relation
JOINT_CONNECTS(joint,bone_a,bone_b) relation
JOINT_PERMITS(joint,movement) relation
JOINT_STABILISED_BY(joint,structure)

———- MUSCULAR ANATOMY ———-

relation MUSCLE_ORIGIN(muscle,site) relation
MUSCLE_INSERTION(muscle,site) relation
MUSCLE_INNERVATED_BY(muscle,nerve) relation
MUSCLE_SUPPLIED_BY(muscle,vessel) relation MUSCLE_ACTS_ON(muscle,joint)
relation MUSCLE_ACTION(muscle,movement)

———- VASCULAR / NERVOUS ———-

enum VesselType: ARTERY ARTERIOLE CAPILLARY VENULE VEIN

relation HAS_VESSEL_TYPE(vessel,type) relation
BRANCHES_FROM(vessel,parent) relation DRAINS_INTO(vessel,target)
relation SUPPLIES(vessel,structure) relation DRAINS(structure,vessel)
relation ANASTOMOSES_WITH(a,b)

enum NerveType: CRANIAL_NERVE SPINAL_NERVE PERIPHERAL_NERVE
AUTONOMIC_NERVE

relation HAS_NERVE_TYPE(nerve,type) relation
ORIGINATES_FROM(nerve,structure) relation INNERVATES(nerve,structure)
relation CARRIES_SENSORY_FROM(nerve,structure) relation
CARRIES_MOTOR_TO(nerve,structure) relation PASSES_THROUGH(nerve,foramen)

———- SYSTEM-SPECIFIC ANATOMY ———-

relation LUNG_HAS_LOBE(lung,lobe) relation
LOBE_HAS_SEGMENT(lobe,segment) relation
BRONCHUS_SUPPLIES(bronchus,segment) relation PLEURA_COVERS(pleura,lung)

relation DIGESTIVE_TRACT_SEGMENT(entity) relation
GLAND_DRAINS_INTO(gland,structure) relation
MESENTERY_SUPPORTS(mesentery,organ) relation
PERITONEUM_COVERS(peritoneum,organ)

relation KIDNEY_HAS_REGION(kidney,region) relation
NEPHRON_PART_OF(nephron,kidney) relation URETER_CONNECTS(kidney,bladder)
relation URETHRA_CONNECTS(bladder,exterior)

relation REPRODUCTIVE_ORGAN_OF(organ,system) relation
GONAD_OF(gonad,system) relation DUCT_CONNECTS(duct,a,b)

relation SKIN_COVERS(skin,region) relation SKIN_HAS_LAYER(skin,layer)
relation HAIR_FOLLICLE_IN(follicle,skin) relation
SWEAT_GLAND_IN(gland,skin)

———- SURFACE / DEVELOPMENTAL ANATOMY ———-

relation SURFACE_LANDMARK_OF(landmark,structure) relation
PALPABLE_AT(structure,landmark) relation
PROJECTS_TO_SURFACE(structure,region)

relation DEVELOPS_FROM(entity,precursor) relation
EMBRYOLOGICAL_ORIGIN(entity,tissue) relation FUSES_WITH(a,b) relation
PERSISTS_AS(precursor,adult_structure)

———- ANATOMICAL VARIATION ———-

relation HAS_ANATOMICAL_VARIANT(entity,variant) relation
VARIANT_OF(variant,canonical_structure) relation
OCCURRENCE_FREQUENCY(variant,population,value)

constraint VARIANT_NOT_ABNORMAL_BY_DEFAULT: IF VARIANT_OF(v,c) THEN
DO_NOT_INFER(pathological(v))

———- MORPHOMETRY / OBSERVATION ———-

relation HAS_LENGTH(entity,value) relation HAS_WIDTH(entity,value)
relation HAS_VOLUME(entity,value) relation HAS_MASS(entity,value)
relation HAS_DIAMETER(entity,value)

enum ImagingModality: RADIOGRAPHY ULTRASOUND CT MRI ANGIOGRAPHY
ENDOSCOPY MICROSCOPY GROSS_DISSECTION

relation OBSERVES(observation,entity) relation
OBSERVED_BY_MODALITY(observation,modality) relation
OBSERVED_ON(observation,datetime) relation
HAS_ORIENTATION(observation,plane) relation
MEASURES(observation,feature) relation
MEASUREMENT_VALUE(observation,value) relation
MEASUREMENT_UNIT(observation,unit)

———- EVIDENCE ———-

relation SUPPORTED_BY(assertion,evidence) relation
DERIVED_FROM(evidence,source) relation HAS_CONFIDENCE(assertion,score)

enum EvidenceType: GROSS_ANATOMY DISSECTION HISTOLOGY MICROSCOPY
RADIOGRAPHY ULTRASOUND CT_IMAGING MRI_IMAGING ANGIOGRAPHY ENDOSCOPY
DEVELOPMENTAL MORPHOMETRIC POPULATION_STUDY ANATOMICAL_ATLAS LITERATURE

CONFIDENCE: VERIFIED: 0.95..1.00 HIGH: 0.80..0.949 MEDIUM: 0.60..0.799
LOW: 0.00..0.599

rule CONFIDENCE_BOUNDS(a,score): IF HAS_CONFIDENCE(a,score) THEN
REQUIRE(0.0 <= score <= 1.0)

———- SEMANTIC EQUIVALENCE ———-

SEMANTIC_EQUIVALENCE: “human anatomy” ~= “structure and organisation of
the human body” “anatomical structure” ~= “human body structure” “body
region” ~= “anatomical region” “body cavity” ~= “anatomical cavity”
“superior” ~= “cranial relative position” “inferior” ~= “caudal relative
position” “anterior” ~= “ventral relative position in standard human
anatomy” “posterior” ~= “dorsal relative position in standard human
anatomy” “medial” ~= “toward the median plane” “lateral” ~= “away from
the median plane” “proximal” ~= “nearer the point of attachment”
“distal” ~= “farther from the point of attachment” “superficial” ~=
“nearer the body surface” “deep” ~= “farther from the body surface”
“innervation” ~= “nerve supply” “vascular supply” ~= “blood vessel
supply”

rule NORMALISE_TERM(term): IF term MATCHES SEMANTIC_EQUIVALENCE.alias
THEN MAP_TO_CANONICAL(term)

———- QUERY MODEL ———-

query ANATOMICAL_ENTITY_PROFILE(x): RETURN: entity_type(x)
body_region(x) laterality(x) containing_structures(x)
component_structures(x) spatial_relations(x) organ_system(x)
vascular_supply(x) venous_drainage(x) innervation(x)
anatomical_variants(x) evidence(x) confidence(x)

query ORGAN_PROFILE(o): RETURN: organ_system(o) tissues(o) cavity(o)
neighbouring_structures(o) arterial_supply(o) venous_drainage(o)
innervation(o) developmental_origin(o)

query TRACE_EVIDENCE(assertion): RETURN: supporting_evidence(assertion)
provenance(assertion) confidence(assertion)

———- CONSISTENCY ———-

constraint EVIDENCE_REQUIRED: FORALL scientific_assertion: REQUIRE
SUPPORTED_BY(scientific_assertion,Evidence) OR
MARK_AS_HYPOTHESIS(scientific_assertion)

constraint UNKNOWN_IS_NOT_FALSE: IF data_missing(assertion) THEN
MARK_UNKNOWN(assertion) AND NOT NEGATE(assertion)

constraint LATERALITY_PRESERVATION: IF HAS_LATERALITY(x,l) THEN
PRESERVE_LATERALITY(x,l)

constraint ORIENTATION_CONTEXT_REQUIRED: IF
directional_anatomical_relation(a,b) THEN
PRESERVE_STANDARD_ANATOMICAL_POSITION()

———- UPDATE MODEL ———-

UPDATE_MODEL: on_new_anatomical_entity(e): identify_entity_type(e)
identify_body_region(e) preserve_laterality(e)
attach_part_whole_relations(e) attach_evidence(e)
recalculate_confidence(e)

on_new_spatial_relation(r): validate_entities(r)
preserve_anatomical_position_context(r) infer_valid_inverse_relation(r)
attach_evidence(r)

on_new_vascular_record(v): identify_vessel(v)
preserve_branching_or_drainage_direction(v) attach_supplied_structure(v)
attach_evidence(v)

on_new_innervation_record(n): identify_nerve(n)
identify_target_structure(n) preserve_sensory_motor_autonomic_context(n)
attach_evidence(n)

on_new_variant(v): identify_canonical_structure(v)
preserve_population_context(v) mark_as_variant_not_pathology(v)
attach_evidence(v)

———- AI CONSUMPTION ———-

AI_CONSUMPTION: preferred_entity: canonical_human_anatomical_entity
preserve: - anatomical_identity - anatomical_hierarchy - body_region -
body_cavity - laterality - anatomical_plane - directional_relations -
tissue_composition - organ_system - skeletal_relations -
muscular_relations - vascular_supply - venous_drainage - innervation -
surface_anatomy - developmental_origin - anatomical_variation -
morphometry - evidence - provenance - confidence infer: -
valid_part_whole_inverse - valid_directional_inverse -
valid_containment_inverse - semantic_equivalence prohibit: -
laterality_loss - direction_without_anatomical_position_context -
anatomical_variant_equals_pathology -
imaging_projection_equals_exact_3d_relation -
unsupported_part_whole_relation - confidence_above_evidence ambiguity:
action: preserve_multiple_anatomical_interpretations resolution:
prefer_entity_region_laterality_orientation_modality_and_evidence
missing_data: action: mark_unknown do_not_infer_from_absence: true

———- FLOW HASH ———-

FLOW_HASH: ontology: “HumanAnatomyOntology” version: “1.0” domain_path:
“AI Core > Ontologies > Biological Ontologies > Human Biology > Human
Anatomy Ontology” canonical_url:
“https://kirethresearch.org/booksai-core/ontologies/biological-ontologies/human-biology/human-anatomy-ontology.html”
authorship: “Mark Anthony Higgins — Sky (Recursive AI)”
semantic_scope: - anatomical hierarchy - body regions - anatomical
planes - directional terminology - laterality - body cavities -
tissues - organ systems - skeletal anatomy - joints - muscular anatomy -
cardiovascular anatomy - nervous anatomy - respiratory anatomy -
digestive anatomy - urinary anatomy - reproductive anatomy -
integumentary anatomy - surface anatomy - developmental anatomy -
anatomical variation - morphometry - imaging - evidence
deterministic_normalisation: true provenance_required: true
confidence_required: true

terminate HumanAnatomyOntology when:
anatomical_entities_and_hierarchy_resolved AND
body_region_laterality_and_orientation_preserved AND
part_whole_and_spatial_relations_normalised AND
vascular_and_innervation_direction_preserved AND
anatomical_variation_distinguished_from_pathology AND
evidence_links_preserved AND confidence_values_validated AND
unresolved_anatomical_ambiguity_marked

end flow