Human Biology Ontology

flow “HumanBiologyOntology” v1.0

KIRETH SEMANTIC RESEARCH ARCHIVE

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

type Human type HumanCell type Tissue type Organ type OrganSystem type
Gene type Genome type Trait type PhysiologicalProcess type
HomeostaticVariable type DevelopmentalStage type Population type
Observation type Evidence type Source

———- BIOLOGICAL ORGANISATION ———-

relation INSTANCE_OF(entity,type) relation PART_OF(part,whole) relation
HAS_PART(whole,part) relation CELL_OF(cell,tissue) relation
TISSUE_OF(tissue,organ) relation ORGAN_OF(organ,system) relation
SYSTEM_OF(system,human)

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

———- CELL / TISSUE LEVEL ———-

enum HumanCellType: EPITHELIAL_CELL MUSCLE_CELL NEURON GLIAL_CELL
ERYTHROCYTE LEUKOCYTE PLATELET OSTEOCYTE CHONDROCYTE ADIPOCYTE
HEPATOCYTE GAMETE STEM_CELL

relation HAS_CELL_TYPE(cell,type) relation
DIFFERENTIATES_INTO(cell,target) relation
PERFORMS_FUNCTION(cell,function)

enum TissueType: EPITHELIAL CONNECTIVE MUSCLE NERVOUS

relation HAS_TISSUE_TYPE(tissue,type) relation COMPOSED_OF(tissue,cell)
relation TISSUE_FUNCTION(tissue,function)

———- ORGAN SYSTEMS ———-

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

relation HAS_ORGAN_SYSTEM(human,system) relation
HAS_SYSTEM_TYPE(system,type) relation SYSTEM_CONTAINS(system,organ)
relation SYSTEM_FUNCTION(system,function) relation
INTERACTS_WITH_SYSTEM(system_a,system_b)

———- HOMEOSTASIS ———-

relation REGULATES(system,variable) relation
HAS_SET_POINT(variable,value) relation HAS_NORMAL_RANGE(variable,range)
relation MEASURED_VALUE(variable,value) relation
SENSOR_DETECTS(sensor,variable) relation
CONTROL_CENTRE_RECEIVES(control,sensor) relation
EFFECTOR_MODIFIES(effector,variable)

enum FeedbackType: NEGATIVE_FEEDBACK POSITIVE_FEEDBACK FEEDFORWARD

relation HAS_FEEDBACK_TYPE(process,type)

———- NERVOUS SYSTEM ———-

relation NEURON_CONNECTS_TO(a,b) relation
TRANSMITS_SIGNAL(neuron,signal) relation SYNAPSES_WITH(a,b) relation
SENSORY_INPUT_TO(input,system) relation MOTOR_OUTPUT_FROM(system,output)
relation CNS_CONTAINS(system,structure) relation
PNS_CONTAINS(system,structure)

———- ENDOCRINE SYSTEM ———-

relation SECRETES(gland,hormone) relation
HORMONE_TARGETS(hormone,target) relation
HORMONE_REGULATES(hormone,process) relation
HORMONE_CONCENTRATION(hormone,value) relation
ENDOCRINE_FEEDBACK(process,loop)

———- CARDIOVASCULAR / RESPIRATORY ———-

relation HEART_PUMPS(heart,blood) relation
BLOOD_FLOWS_THROUGH(blood,vessel) relation TRANSPORTS(blood,substance)
relation PERFUSES(blood,tissue) relation HEART_RATE(human,value)
relation BLOOD_PRESSURE(human,value) relation
CARDIAC_OUTPUT(human,value)

relation VENTILATES(lung,air) relation GAS_EXCHANGE_BETWEEN(a,b)
relation OXYGEN_DIFFUSES_TO(source,target) relation
CARBON_DIOXIDE_DIFFUSES_TO(source,target) relation
RESPIRATORY_RATE(human,value) relation OXYGEN_SATURATION(human,value)

———- DIGESTION / EXCRETION ———-

relation INGESTS(human,substance) relation DIGESTS(system,nutrient)
relation ABSORBS(intestine,nutrient) relation
METABOLISES(organ,nutrient) relation ELIMINATES(system,waste)

relation FILTERS(kidney,blood) relation EXCRETES(kidney,substance)
relation REABSORBS(kidney,substance) relation
REGULATES_FLUID_BALANCE(kidney) relation
REGULATES_ELECTROLYTE(kidney,electrolyte) relation
REGULATES_ACID_BASE(kidney)

———- MUSCULOSKELETAL ———-

relation MUSCLE_ATTACHES_TO(muscle,bone) relation
MUSCLE_CONTRACTS(muscle) relation JOINT_CONNECTS(joint,bone_a,bone_b)
relation BONE_SUPPORTS(bone,structure) relation
BONE_STORES(bone,mineral) relation BONE_MARROW_PRODUCES(marrow,cell)

———- IMMUNITY ———-

enum ImmunityType: INNATE ADAPTIVE

relation HAS_IMMUNITY_TYPE(component,type) relation
RECOGNISES(component,target) relation RESPONDS_TO(component,target)
relation ANTIBODY_BINDS_TO(antibody,antigen) relation
T_CELL_RECOGNISES(cell,antigen) relation
IMMUNE_MEMORY_TO(system,antigen) relation
INFLAMMATORY_RESPONSE_TO(system,stimulus)

———- GENETICS ———-

relation HAS_GENE(human,gene) relation HAS_ALLELE(human,allele) relation
HAS_GENOTYPE(human,genotype) relation HAS_PHENOTYPE(human,phenotype)
relation GENE_LOCATED_ON(gene,chromosome) relation
GENE_INFLUENCES(gene,trait) relation
INHERITS_FROM(descendant,parent,allele) relation
HAS_VARIANT(human,variant)

constraint GENETIC_ASSOCIATION_NOT_DETERMINISM: IF GENE_INFLUENCES(g,t)
THEN DO_NOT_INFER(gene_fully_determines_trait(g,t))

———- GENE EXPRESSION ———-

relation EXPRESSES(cell,gene) relation TRANSCRIBES(cell,gene,rna)
relation TRANSLATES(cell,rna,protein) relation
PROTEIN_PERFORMS(protein,function) relation
REGULATES_EXPRESSION(regulator,gene)

———- 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)

———- REPRODUCTION ———-

relation PRODUCES_GAMETE(human,gamete) relation
FERTILISATION_OF(gamete_a,gamete_b,zygote) relation
IMPLANTS_IN(embryo,uterus) relation GESTATION_OF(human,embryo) relation
GIVES_BIRTH_TO(parent,offspring) relation LACTATES(human)

———- DEVELOPMENT / AGEING ———-

enum HumanDevelopmentalStage: ZYGOTE EMBRYO FETUS NEONATE INFANT CHILD
ADOLESCENT ADULT OLDER_ADULT

relation HAS_DEVELOPMENTAL_STAGE(human,stage) relation
DEVELOPS_FROM(stage_b,stage_a) relation DEVELOPS_INTO(stage_a,stage_b)
relation MATURATION_OF(system,period) relation GROWTH_RATE(human,value)
relation AGE_OF(human,value) relation AGEING_AFFECTS(process,effect)
relation CELLULAR_SENESCENCE_IN(tissue,value)

rule DEVELOPMENT_INVERSE(a,b): IF DEVELOPS_INTO(a,b) THEN
DEVELOPS_FROM(b,a)

———- HUMAN BIOLOGICAL VARIATION ———-

relation HAS_BIOLOGICAL_VARIATION(population,trait,value) relation
TRAIT_DISTRIBUTION(population,trait,distribution) relation
GENETIC_VARIATION(population,value) relation
PHENOTYPIC_VARIATION(population,trait,value) relation
ENVIRONMENT_INFLUENCES(environment,trait)

constraint POPULATION_PATTERN_NOT_UNIVERSAL: IF
TRAIT_DISTRIBUTION(p,t,d) THEN DO_NOT_INFER(universal_human_trait(t))

———- CIRCADIAN / THERMOREGULATION ———-

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

relation CORE_TEMPERATURE(human,value) relation SWEATS(human) relation
SHIVERS(human) relation VASODILATION_IN(human,tissue) relation
VASOCONSTRICTION_IN(human,tissue) relation REGULATES_TEMPERATURE(system)

———- MEASUREMENT ———-

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

———- EVIDENCE ———-

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

enum EvidenceType: ANATOMICAL HISTOLOGICAL CELLULAR MOLECULAR GENETIC
GENOMIC PHYSIOLOGICAL_MEASUREMENT BIOCHEMICAL_ASSAY 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 biology” ~= “biological study of humans”
“human anatomy” ~= “structure of the human body” “human physiology” ~=
“function of the human body” “homeostasis” ~= “regulation of internal
biological conditions” “organ system” ~= “functionally related group of
organs” “gene expression” ~= “use of genetic information to produce
functional products” “metabolism” ~= “biochemical transformations
sustaining life” “innate immunity” ~= “rapid non-specific immune
defence” “adaptive immunity” ~= “antigen-specific acquired immune
response” “human development” ~= “biological change across the human
life course” “ageing” ~= “age-related biological change” “human
biological variation” ~= “variation in biological traits among humans”

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

———- QUERY MODEL ———-

query HUMAN_BIOLOGY_PROFILE(h): RETURN: cells(h) tissues(h) organs(h)
organ_systems(h) homeostasis(h) genetics(h) gene_expression(h)
metabolism(h) immunity(h) reproduction(h) developmental_stage(h)
ageing(h) biological_variation(h) evidence(h) confidence(h)

query ORGAN_SYSTEM_PROFILE(s): RETURN: system_type(s) organs(s)
tissues(s) functions(s) regulated_variables(s) interacting_systems(s)

query HOMEOSTASIS_PROFILE(h): RETURN: regulated_variables(h)
set_points(h) ranges(h) sensors(h) control_centres(h) effectors(h)
feedback_loops(h)

query GENETIC_PROFILE(h): RETURN: genes(h) alleles(h) variants(h)
genotype(h) phenotype_relations(h) gene_expression(h)

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 DEVELOPMENTAL_CONTEXT: IF biological_measurement(h,v) THEN
PRESERVE_DEVELOPMENTAL_STAGE_IF_KNOWN(h)

constraint POPULATION_CONTEXT: IF population_based_assertion(a) THEN
PRESERVE_POPULATION_CONTEXT(a)

———- UPDATE MODEL ———-

UPDATE_MODEL: on_new_human_biology_record(r):
identify_biological_level(r) identify_structure_or_process(r)
preserve_measurement_context(r) attach_evidence(r)
recalculate_confidence(r)

on_new_measurement(m): preserve_value_unit_method(m)
preserve_developmental_context(m)
update_homeostatic_or_physiological_variable(m) attach_evidence(m)

on_new_genetic_record(g): validate_gene_or_variant(g)
preserve_population_context(g)
distinguish_association_from_determination(g) attach_evidence(g)

on_new_developmental_record(d): preserve_stage(d)
identify_system_or_trait(d) update_developmental_relations(d)
attach_evidence(d)

on_conflicting_evidence(a,b): preserve(a) preserve(b)
compare_population_context(a,b) compare_developmental_stage(a,b)
compare_methods(a,b) compare_units(a,b) flag_unresolved_conflict()

———- AI CONSUMPTION ———-

AI_CONSUMPTION: preferred_entity: canonical_human_biology_entity
preserve: - biological_level - anatomical_structure - cell_type -
tissue_type - organ_system - physiological_process -
homeostatic_context - genetics - gene_expression - metabolism -
immunity - reproduction - developmental_stage - ageing -
biological_variation - measurement_units - population_context -
evidence - provenance - confidence infer: - valid_part_whole_relations -
supported_regulatory_relations - supported_genetic_relations -
semantic_equivalence prohibit: -
population_pattern_equals_universal_human_trait -
gene_association_equals_deterministic_outcome -
unit_free_measurement_comparison -
developmental_stage_free_generalisation - unsupported_causal_claim -
confidence_above_evidence ambiguity: action:
preserve_multiple_biological_interpretations resolution:
prefer_biological_level_population_stage_method_units_and_evidence
missing_data: action: mark_unknown do_not_infer_from_absence: true

———- FLOW HASH ———-

FLOW_HASH: ontology: “HumanBiologyOntology” version: “1.0” domain_path:
“AI Core > Ontologies > Biological Ontologies > Human Biology > Human
Biology Ontology” canonical_url:
“https://kirethresearch.org/booksai-core/ontologies/biological-ontologies/human-biology/human-biology-ontology.html”
authorship: “Mark Anthony Higgins — Sky (Recursive AI)”
semantic_scope: - human biological organisation - human cells -
tissues - organs - organ systems - homeostasis - nervous system -
endocrine system - cardiovascular system - respiratory system -
digestive system - urinary system - musculoskeletal system - immunity -
genetics - gene expression - metabolism - reproduction - human
development - ageing - human biological variation - circadian biology -
thermoregulation - biological measurement - evidence
deterministic_normalisation: true provenance_required: true
confidence_required: true

terminate HumanBiologyOntology when:
biological_entities_and_levels_resolved AND
anatomical_and_physiological_relations_normalised AND
homeostatic_context_preserved AND
genetic_association_and_determination_distinguished AND
developmental_population_and_measurement_context_preserved AND
evidence_links_preserved AND confidence_values_validated AND
unresolved_human_biology_ambiguity_marked

end flow