Human Physiology Ontology

flow “HumanPhysiologyOntology” v1.0

KIRETH SEMANTIC RESEARCH ARCHIVE

AI CORE > ONTOLOGIES > BIOLOGICAL ONTOLOGIES > HUMAN BIOLOGY > HUMAN PHYSIOLOGY 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-physiology-ontology.html”

type Human type Cell type Tissue type Organ type OrganSystem type
PhysiologicalProcess type PhysiologicalVariable type Signal type Hormone
type Metabolite type Observation type Evidence type Source

relation INSTANCE_OF(entity,type) relation PART_OF(part,whole) relation
PERFORMS(entity,process) relation REGULATES(regulator,target) relation
INTERACTS_WITH(a,b)

———- HOMEOSTASIS ———-

relation HOMEOSTATIC_VARIABLE(variable) relation
HAS_SET_POINT(variable,value) relation
HAS_REFERENCE_RANGE(variable,range) relation
MEASURED_VALUE(variable,value) relation SENSOR_DETECTS(sensor,variable)
relation CONTROL_CENTRE_INTEGRATES(control,input) relation
EFFECTOR_MODIFIES(effector,variable)

enum FeedbackType: NEGATIVE_FEEDBACK POSITIVE_FEEDBACK FEEDFORWARD

relation HAS_FEEDBACK_TYPE(process,type)

———- MEMBRANE / CELL PHYSIOLOGY ———-

relation MEMBRANE_POTENTIAL(cell,value) relation
ION_CONCENTRATION(compartment,ion,value) relation
ION_CHANNEL_TRANSPORTS(channel,ion) relation
PUMP_TRANSPORTS(pump,substance) relation
DIFFUSES_ACROSS(substance,membrane) relation
OSMOSIS_ACROSS(water,membrane) relation
ACTIVE_TRANSPORT_OF(process,substance)

———- NERVOUS PHYSIOLOGY ———-

relation GENERATES_ACTION_POTENTIAL(neuron,event) relation
CONDUCTS_IMPULSE(neuron,signal) relation
RELEASES_NEUROTRANSMITTER(neuron,transmitter) relation
NEUROTRANSMITTER_BINDS(transmitter,receptor) relation
SYNAPTIC_TRANSMISSION(a,b) relation
SENSORY_TRANSDUCTION(receptor,stimulus) relation
MOTOR_CONTROL(system,movement)

———- ENDOCRINE PHYSIOLOGY ———-

relation SECRETES(gland,hormone) relation
HORMONE_CONCENTRATION(hormone,value) relation
HORMONE_BINDS(hormone,receptor) relation HORMONE_TARGETS(hormone,tissue)
relation HORMONE_REGULATES(hormone,process) relation
ENDOCRINE_AXIS(axis,components)

———- CARDIOVASCULAR PHYSIOLOGY ———-

relation HEART_RATE(human,value) relation STROKE_VOLUME(human,value)
relation CARDIAC_OUTPUT(human,value) relation
BLOOD_PRESSURE(human,value) relation VASCULAR_RESISTANCE(region,value)
relation BLOOD_FLOW(region,value) relation PERFUSION_OF(tissue,value)
relation VASOCONSTRICTION(region) relation VASODILATION(region)

rule CARDIAC_OUTPUT_RULE(h): IF HEART_RATE(h,hr) AND STROKE_VOLUME(h,sv)
THEN CARDIAC_OUTPUT(h,hr*sv)

———- BLOOD PHYSIOLOGY ———-

relation OXYGEN_CONTENT(blood,value) relation
CARBON_DIOXIDE_CONTENT(blood,value) relation
HEMOGLOBIN_CONCENTRATION(blood,value) relation
OXYGEN_SATURATION(human,value) relation
COAGULATION_PROCESS(blood,process) relation TRANSPORTS(blood,substance)

———- RESPIRATORY PHYSIOLOGY ———-

relation RESPIRATORY_RATE(human,value) relation
TIDAL_VOLUME(human,value) relation MINUTE_VENTILATION(human,value)
relation ALVEOLAR_VENTILATION(human,value) relation
GAS_EXCHANGE_BETWEEN(a,b) relation OXYGEN_DIFFUSES_TO(source,target)
relation CARBON_DIOXIDE_DIFFUSES_TO(source,target) relation
VENTILATION_PERFUSION_RATIO(region,value)

rule MINUTE_VENTILATION_RULE(h): IF RESPIRATORY_RATE(h,r) AND
TIDAL_VOLUME(h,v) THEN MINUTE_VENTILATION(h,r*v)

———- RENAL / FLUID PHYSIOLOGY ———-

relation GLOMERULAR_FILTRATION_RATE(human,value) relation
FILTERS(kidney,substance) relation REABSORBS(kidney,substance) relation
SECRETES_TO_TUBULE(kidney,substance) relation EXCRETES(kidney,substance)
relation URINE_FLOW_RATE(human,value) relation
REGULATES_OSMOLALITY(kidney) relation
REGULATES_ELECTROLYTE(kidney,electrolyte) relation
REGULATES_ACID_BASE(kidney)

———- DIGESTIVE PHYSIOLOGY ———-

relation DIGESTS(system,nutrient) relation
SECRETES_DIGESTIVE_FACTOR(organ,factor) relation
ABSORBS(intestine,nutrient) relation MOTILITY_OF(segment,pattern)
relation GASTRIC_EMPTYING_RATE(human,value) relation
NUTRIENT_TRANSPORT_TO(nutrient,tissue) relation
LIVER_METABOLISES(liver,substance)

———- METABOLISM ———-

enum MetabolicProcess: GLYCOLYSIS CITRIC_ACID_CYCLE
OXIDATIVE_PHOSPHORYLATION GLYCOGENESIS GLYCOGENOLYSIS GLUCONEOGENESIS
LIPOGENESIS LIPOLYSIS PROTEIN_SYNTHESIS AMINO_ACID_CATABOLISM

relation PERFORMS_METABOLIC_PROCESS(cell,process) relation
CONSUMES(process,substrate) relation PRODUCES(process,product) relation
ATP_PRODUCTION(process,amount) relation METABOLIC_RATE(human,value)
relation ENERGY_EXPENDITURE(human,value)

———- MUSCLE PHYSIOLOGY ———-

relation MUSCLE_CONTRACTS(muscle) relation
EXCITATION_CONTRACTION_COUPLING(muscle,process) relation
CALCIUM_RELEASE_IN(muscle,value) relation FORCE_PRODUCTION(muscle,value)
relation MUSCLE_LENGTH(muscle,value) relation
MUSCLE_FATIGUE(muscle,value) relation
MOTOR_UNIT_RECRUITMENT(muscle,value)

———- THERMOREGULATION ———-

relation CORE_TEMPERATURE(human,value) relation
SKIN_TEMPERATURE(human,value) relation SWEATS(human) relation
SHIVERS(human) relation CUTANEOUS_VASODILATION(human) relation
CUTANEOUS_VASOCONSTRICTION(human) relation HEAT_PRODUCTION(human,value)
relation HEAT_LOSS(human,value)

———- IMMUNE PHYSIOLOGY ———-

enum ImmunityType: INNATE ADAPTIVE

relation IMMUNE_RESPONSE_TYPE(response,type) relation
RECOGNISES(component,antigen) relation ACTIVATES(component,target)
relation ANTIBODY_BINDS_TO(antibody,antigen) relation
CYTOKINE_SIGNALS_TO(cytokine,cell) relation
INFLAMMATORY_RESPONSE_TO(system,stimulus) relation
IMMUNE_MEMORY_TO(system,antigen)

———- ACID-BASE PHYSIOLOGY ———-

relation BLOOD_PH(human,value) relation
BICARBONATE_CONCENTRATION(human,value) relation
PARTIAL_PRESSURE_CO2(human,value) relation
BUFFER_SYSTEM(buffer,compartment) relation
RESPIRATORY_COMPENSATION(human,response) relation
RENAL_COMPENSATION(human,response)

———- ENDOCRINE-METABOLIC REGULATION ———-

relation BLOOD_GLUCOSE(human,value) relation
INSULIN_CONCENTRATION(human,value) relation
GLUCAGON_CONCENTRATION(human,value) relation INSULIN_PROMOTES(process)
relation GLUCAGON_PROMOTES(process) relation
GLUCOSE_HOMEOSTASIS(human,process)

———- REPRODUCTIVE PHYSIOLOGY ———-

relation GAMETOGENESIS_IN(organ,process) relation
OVULATION_IN(human,event) relation MENSTRUAL_CYCLE(human,cycle) relation
SPERMATOGENESIS_IN(human,process) relation FERTILISATION(event) relation
GESTATION(human,period) relation PARTURITION(human,event) relation
LACTATION(human,process)

———- CIRCADIAN / SLEEP PHYSIOLOGY ———-

relation HAS_CIRCADIAN_RHYTHM(human,rhythm) relation
CIRCADIAN_PHASE(human,value) relation ENTRAINED_BY(rhythm,cue) relation
SLEEP_WAKE_CYCLE(human,pattern) relation SLEEP_STAGE(human,stage)
relation MELATONIN_CONCENTRATION(human,value)

———- EXERCISE PHYSIOLOGY ———-

relation EXERCISE_INTENSITY(human,value) relation
OXYGEN_CONSUMPTION(human,value) relation
CARBON_DIOXIDE_PRODUCTION(human,value) relation
LACTATE_CONCENTRATION(human,value) relation
VENTILATORY_RESPONSE(human,value) relation
CARDIOVASCULAR_RESPONSE(human,value)

———- DEVELOPMENT / AGEING CONTEXT ———-

relation HAS_DEVELOPMENTAL_STAGE(human,stage) relation
AGE_OF(human,value) relation
PHYSIOLOGICAL_CHANGE_WITH_AGE(variable,effect) relation
MATURATION_AFFECTS(process,effect)

———- BIOLOGICAL VARIATION ———-

relation PHYSIOLOGICAL_DISTRIBUTION(population,variable,distribution)
relation ENVIRONMENT_INFLUENCES(environment,variable) relation
ACTIVITY_INFLUENCES(activity,variable) relation
TIME_OF_DAY_INFLUENCES(time,variable)

constraint POPULATION_REFERENCE_NOT_INDIVIDUAL_CERTAINTY: IF
PHYSIOLOGICAL_DISTRIBUTION(p,v,d) THEN
DO_NOT_INFER(exact_individual_value(v))

———- MEASUREMENT ———-

relation OBSERVES(observation,entity) relation
MEASURES(observation,variable) relation
OBSERVED_ON(observation,datetime) relation
MEASUREMENT_VALUE(observation,value) relation
MEASUREMENT_UNIT(observation,unit) relation
MEASUREMENT_METHOD(observation,method) relation
MEASUREMENT_CONDITION(observation,condition)

———- EVIDENCE ———-

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

enum EvidenceType: PHYSIOLOGICAL_MEASUREMENT ELECTROPHYSIOLOGY
BLOOD_ANALYSIS BIOCHEMICAL_ASSAY RESPIRATORY_TEST CARDIOVASCULAR_TEST
RENAL_FUNCTION_TEST ENDOCRINE_ASSAY METABOLIC_TEST EXERCISE_TEST IMAGING
EXPERIMENTAL OBSERVATIONAL LONGITUDINAL POPULATION_STUDY
SYSTEMATIC_REVIEW META_ANALYSIS 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 physiology” ~= “study of human biological
function” “homeostasis” ~= “regulation of internal physiological
conditions” “cardiac output” ~= “volume of blood pumped by the heart per
unit time” “minute ventilation” ~= “volume of air ventilated per minute”
“glomerular filtration rate” ~= “GFR” “metabolic rate” ~= “rate of
energy metabolism” “thermoregulation” ~= “physiological regulation of
body temperature” “acid-base balance” ~= “regulation of hydrogen ion and
buffer systems” “blood glucose regulation” ~= “glucose homeostasis”
“circadian rhythm” ~= “approximately 24-hour biological rhythm”
“physiological variable” ~= “measurable biological functional quantity”

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

———- QUERY MODEL ———-

query HUMAN_PHYSIOLOGY_PROFILE(h): RETURN: homeostasis(h)
nervous_function(h) endocrine_function(h) cardiovascular_function(h)
respiratory_function(h) renal_function(h) digestive_function(h)
metabolism(h) muscle_function(h) thermoregulation(h) immunity(h)
reproductive_function(h) circadian_function(h) evidence(h) confidence(h)

query PHYSIOLOGICAL_VARIABLE_PROFILE(v): RETURN: measured_value(v)
reference_range(v) regulatory_systems(v) influencing_factors(v)
measurement_method(v) units(v) evidence(v)

query HOMEOSTASIS_PROFILE(v): RETURN: set_point(v) reference_range(v)
sensors(v) control_centres(v) effectors(v) feedback_type(v)

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 UNIT_CONTEXT_REQUIRED: IF MEASUREMENT_VALUE(o,v) THEN
REQUIRE(MEASUREMENT_UNIT(o,u)) OR MARK_UNIT_UNKNOWN(o)

constraint CONDITION_CONTEXT_REQUIRED: IF physiological_measurement(o)
THEN PRESERVE_MEASUREMENT_CONDITION_IF_KNOWN(o)

constraint DEVELOPMENTAL_CONTEXT: IF physiological_assertion(h,v) THEN
PRESERVE_DEVELOPMENTAL_STAGE_IF_KNOWN(h)

———- UPDATE MODEL ———-

UPDATE_MODEL: on_new_physiological_record(r):
identify_system_and_process(r) identify_variable(r)
preserve_value_unit_condition(r) attach_evidence(r)
recalculate_confidence(r)

on_new_homeostatic_record(h): identify_regulated_variable(h)
identify_sensor_control_effector(h) preserve_feedback_type(h)
attach_evidence(h)

on_new_measurement(m): preserve_value_unit_method(m)
preserve_time_activity_and_condition(m)
preserve_developmental_context(m) update_variable(m)

on_conflicting_measurements(a,b): preserve(a) preserve(b)
compare_units(a,b) compare_methods(a,b) compare_conditions(a,b)
compare_population_context(a,b) flag_unresolved_conflict()

———- AI CONSUMPTION ———-

AI_CONSUMPTION: preferred_entity: canonical_human_physiology_entity
preserve: - physiological_system - physiological_process -
variable_identity - homeostatic_context - nervous_regulation -
endocrine_regulation - cardiovascular_function - respiratory_function -
renal_function - digestive_function - metabolism - muscle_function -
thermoregulation - immune_function - reproductive_function -
circadian_context - developmental_stage - measurement_condition -
measurement_units - population_context - evidence - provenance -
confidence infer: - supported_regulatory_relations -
valid_derived_physiological_quantities - supported_feedback_relations -
semantic_equivalence prohibit: -
population_reference_equals_individual_certainty -
unit_free_measurement_comparison - condition_free_generalisation -
developmental_stage_free_generalisation - unsupported_causal_claim -
confidence_above_evidence ambiguity: action:
preserve_multiple_physiological_interpretations resolution:
prefer_system_variable_condition_time_method_units_and_evidence
missing_data: action: mark_unknown do_not_infer_from_absence: true

———- FLOW HASH ———-

FLOW_HASH: ontology: “HumanPhysiologyOntology” version: “1.0”
domain_path: “AI Core > Ontologies > Biological Ontologies > Human
Biology > Human Physiology Ontology” canonical_url:
“https://kirethresearch.org/booksai-core/ontologies/biological-ontologies/human-biology/human-physiology-ontology.html”
authorship: “Mark Anthony Higgins — Sky (Recursive AI)”
semantic_scope: - human physiology - homeostasis - cell physiology -
nervous physiology - endocrine physiology - cardiovascular physiology -
blood physiology - respiratory physiology - renal physiology - digestive
physiology - metabolism - muscle physiology - thermoregulation - immune
physiology - acid-base physiology - glucose homeostasis - reproductive
physiology - circadian physiology - exercise physiology - development
and ageing - physiological variation - measurement - evidence
deterministic_normalisation: true provenance_required: true
confidence_required: true

terminate HumanPhysiologyOntology when:
physiological_entities_processes_and_variables_resolved AND
homeostatic_and_regulatory_relations_normalised AND
measurement_units_conditions_and_time_context_preserved AND
population_and_developmental_context_preserved AND
derived_quantities_validated AND evidence_links_preserved AND
confidence_values_validated AND
unresolved_physiological_ambiguity_marked

end flow