Human Development Ontology

flow “HumanDevelopmentOntology” v1.0

KIRETH SEMANTIC RESEARCH ARCHIVE

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

type Human type Gamete type Zygote type Embryo type Fetus type
DevelopmentalStage type DevelopmentalEvent type Tissue type Organ type
OrganSystem type CellLineage type Trait type Population type Observation
type Evidence type Source

———- DEVELOPMENTAL IDENTITY ———-

relation INSTANCE_OF(entity,type) relation
HAS_DEVELOPMENTAL_STAGE(human,stage) relation
DEVELOPS_FROM(stage_b,stage_a) relation DEVELOPS_INTO(stage_a,stage_b)
relation PRECEDES(stage_a,stage_b) relation FOLLOWS(stage_b,stage_a)
relation OCCURS_DURING(event,stage)

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

rule TEMPORAL_INVERSE(a,b): IF PRECEDES(a,b) THEN FOLLOWS(b,a)

———- LIFE COURSE ———-

enum HumanDevelopmentalStage: GAMETE ZYGOTE CLEAVAGE MORULA BLASTOCYST
EMBRYO FETUS NEONATE INFANT EARLY_CHILDHOOD MIDDLE_CHILDHOOD ADOLESCENT
YOUNG_ADULT ADULT OLDER_ADULT

relation HAS_STAGE_TYPE(stage,type) relation STAGE_STARTS_AT(stage,time)
relation STAGE_ENDS_AT(stage,time) relation
STAGE_DURATION(stage,duration)

———- FERTILISATION ———-

relation PRODUCES_GAMETE(human,gamete) relation
FERTILISATION_OF(gamete_a,gamete_b,zygote) relation
FERTILISATION_OCCURS_AT(event,location) relation
FORMS_ZYGOTE(event,zygote) relation ACTIVATES_DEVELOPMENT(event,zygote)

———- CLEAVAGE / BLASTOCYST ———-

relation CLEAVES_INTO(entity,descendants) relation
FORMS_MORULA(entity,morula) relation FORMS_BLASTOCYST(entity,blastocyst)
relation HAS_INNER_CELL_MASS(blastocyst,mass) relation
HAS_TROPHOBLAST(blastocyst,trophoblast)

———- IMPLANTATION ———-

relation IMPLANTS_IN(blastocyst,endometrium) relation
IMPLANTATION_EVENT(blastocyst,event) relation
TROPHOBLAST_INVADES(trophoblast,tissue) relation
PLACENTATION_BEGINS(event,time)

———- GASTRULATION ———-

enum GermLayer: ECTODERM MESODERM ENDODERM

relation GASTRULATION_EVENT(embryo,event) relation
FORMS_GERM_LAYER(embryo,layer) relation
DERIVED_FROM_GERM_LAYER(structure,layer) relation
ESTABLISHES_BODY_AXIS(event,axis)

———- NEURULATION ———-

relation NEURULATION_EVENT(embryo,event) relation
NEURAL_PLATE_FORMS(embryo,structure) relation
NEURAL_TUBE_FORMS(embryo,structure) relation
NEURAL_CREST_FORMS(embryo,structure) relation
NEURAL_CREST_DERIVATIVE(structure,derivative)

———- CELL DIFFERENTIATION ———-

relation CELL_LINEAGE_OF(lineage,organism) relation
DIFFERENTIATES_INTO(cell,target) relation PROGENITOR_OF(cell,target)
relation STEM_CELL_GIVES_RISE_TO(cell,lineage) relation
CELL_FATE(cell,fate) relation MATURATION_OF(cell,process)

———- MORPHOGENESIS ———-

relation MORPHOGENESIS_OF(structure,process) relation
PATTERNING_OF(structure,process) relation
INDUCTIVE_SIGNAL(signal,target) relation MIGRATES_TO(cell,location)
relation FOLDS_INTO(structure,target) relation FUSES_WITH(a,b)

———- ORGANOGENESIS ———-

relation ORGANOGENESIS_OF(organ,event) relation
ORGAN_DEVELOPS_FROM(organ,precursor) relation
SYSTEM_DEVELOPS_FROM(system,precursors) relation
ORGAN_MATURATION(organ,period) relation FUNCTION_BEGINS_AT(organ,time)

———- PLACENTA / FETAL SUPPORT ———-

relation PLACENTA_SUPPORTS(placenta,fetus) relation
EXCHANGES_BETWEEN(placenta,maternal,fetal,substance) relation
UMBILICAL_CORD_CONNECTS(fetus,placenta) relation
FETAL_CIRCULATION_HAS(fetus,structure)

———- FETAL DEVELOPMENT ———-

relation FETAL_GROWTH(fetus,rate) relation FETAL_LENGTH(fetus,value)
relation FETAL_MASS(fetus,value) relation FETAL_MOVEMENT(fetus,event)
relation ORGAN_SYSTEM_MATURATION(fetus,system,stage) relation
VIABILITY_CONTEXT(fetus,context)

———- BIRTH / NEONATAL TRANSITION ———-

relation PARTURITION_EVENT(human,event) relation
GIVES_BIRTH_TO(parent,offspring) relation
NEONATAL_TRANSITION(offspring,event) relation
RESPIRATORY_TRANSITION(offspring,event) relation
CIRCULATORY_TRANSITION(offspring,event) relation
FEEDING_TRANSITION(offspring,event)

———- POSTNATAL GROWTH ———-

relation BODY_LENGTH(human,value) relation BODY_MASS(human,value)
relation GROWTH_RATE(human,value) relation
HEAD_CIRCUMFERENCE(human,value) relation BONE_GROWTH(human,value)
relation DENTAL_DEVELOPMENT(human,stage)

———- MOTOR DEVELOPMENT ———-

relation MOTOR_MILESTONE(human,milestone) relation
POSTURAL_CONTROL(human,stage) relation
LOCOMOTOR_DEVELOPMENT(human,stage) relation
FINE_MOTOR_DEVELOPMENT(human,stage)

———- NEURAL / SENSORY DEVELOPMENT ———-

relation BRAIN_MATURATION(human,process) relation
MYELINATION_OF(structure,period) relation
SYNAPTIC_DEVELOPMENT(structure,period) relation
SENSORY_SYSTEM_MATURATION(human,system) relation
NEURAL_PLASTICITY(human,value)

———- PUBERTY / ADOLESCENCE ———-

relation PUBERTY_BEGINS(human,time) relation PUBERTAL_STAGE(human,stage)
relation GONADAL_MATURATION(human,process) relation
SECONDARY_SEX_CHARACTER_DEVELOPMENT(human,trait) relation
GROWTH_SPURT(human,period) relation REPRODUCTIVE_MATURITY(human,time)

———- ADULT MATURATION ———-

relation PHYSIOLOGICAL_MATURITY(system,time) relation
PEAK_FUNCTION(system,time) relation ADULT_HOMEOSTATIC_STATE(human,state)
relation BODY_COMPOSITION_CHANGE(human,period)

———- AGEING ———-

relation AGE_OF(human,value) relation AGEING_AFFECTS(process,effect)
relation CELLULAR_SENESCENCE_IN(tissue,value) relation
REPAIR_CAPACITY(tissue,value) relation FUNCTIONAL_RESERVE(system,value)
relation AGE_RELATED_CHANGE(variable,value)

———- DEVELOPMENTAL TIMING ———-

relation EVENT_STARTS_AT(event,time) relation EVENT_ENDS_AT(event,time)
relation DEVELOPMENTAL_RATE(entity,value) relation
DEVELOPMENTAL_SEQUENCE(entity,sequence) relation
TEMPORAL_OVERLAP(event_a,event_b)

———- DEVELOPMENTAL REGULATION ———-

relation GENE_REGULATES_DEVELOPMENT(gene,process) relation
SIGNAL_REGULATES_DEVELOPMENT(signal,process) relation
HORMONE_REGULATES_DEVELOPMENT(hormone,process) relation
ENVIRONMENT_INFLUENCES_DEVELOPMENT(environment,process) relation
NUTRITION_INFLUENCES_DEVELOPMENT(nutrient,process)

constraint INFLUENCE_NOT_DETERMINISM: IF
ENVIRONMENT_INFLUENCES_DEVELOPMENT(e,p) THEN
DO_NOT_INFER(deterministically_determines(e,p))

———- DEVELOPMENTAL VARIATION ———-

relation DEVELOPMENTAL_VARIATION(population,trait,distribution) relation
MILESTONE_DISTRIBUTION(population,milestone,distribution) relation
GROWTH_DISTRIBUTION(population,measure,distribution) relation
TIMING_VARIATION(population,event,distribution)

constraint POPULATION_DISTRIBUTION_NOT_EXACT_INDIVIDUAL: IF
MILESTONE_DISTRIBUTION(p,m,d) THEN
DO_NOT_INFER(exact_individual_timing(m))

———- SEXUAL DIMORPHISM CONTEXT ———-

relation DEVELOPMENTAL_TRAJECTORY(population,trait,trajectory) relation
HORMONAL_CONTEXT(human,state) relation PUBERTAL_TIMING(human,value)

———- 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
DEVELOPMENTAL_AGE(observation,value)

———- EVIDENCE ———-

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

enum EvidenceType: EMBRYOLOGICAL HISTOLOGICAL MOLECULAR GENETIC GENOMIC
ULTRASOUND FETAL_IMAGING ANATOMICAL PHYSIOLOGICAL GROWTH_MEASUREMENT
LONGITUDINAL CROSS_SECTIONAL COHORT_STUDY POPULATION_STUDY EXPERIMENTAL
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 development” ~= “biological development
across the human life course” “embryonic development” ~= “development
during the embryonic period” “fetal development” ~= “development during
the fetal period” “gastrulation” ~= “formation and organisation of
embryonic germ layers” “neurulation” ~= “formation of the neural tube”
“organogenesis” ~= “development of organs” “morphogenesis” ~=
“development of biological form” “cell differentiation” ~= “acquisition
of specialised cell identity” “implantation” ~= “attachment and
embedding of the blastocyst in the uterine lining” “puberty” ~=
“developmental transition toward reproductive maturity” “maturation” ~=
“progression toward functional adult state” “ageing” ~= “age-related
biological change” “developmental milestone” ~= “observable
developmental achievement”

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

———- QUERY MODEL ———-

query HUMAN_DEVELOPMENT_PROFILE(h): RETURN: developmental_stage(h)
developmental_age(h) growth(h) organ_maturation(h) neural_development(h)
motor_development(h) pubertal_development(h) ageing(h)
developmental_variation(h) evidence(h) confidence(h)

query PRENATAL_DEVELOPMENT_PROFILE(x): RETURN: fertilisation(x)
cleavage(x) blastocyst(x) implantation(x) gastrulation(x) neurulation(x)
organogenesis(x) fetal_growth(x) placental_support(x)

query DEVELOPMENTAL_EVENT_PROFILE(e): RETURN: stage(e) start_time(e)
end_time(e) precursor_state(e) resulting_state(e) regulatory_factors(e)
evidence(e)

query GROWTH_PROFILE(h): RETURN: body_length(h) body_mass(h)
growth_rate(h) skeletal_growth(h) developmental_stage(h)
population_reference(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 DEVELOPMENTAL_STAGE_REQUIRED: IF developmental_measurement(o)
THEN REQUIRE(DEVELOPMENTAL_AGE(o,a)) OR preserve_stage_if_known(o)

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

constraint SEQUENCE_NOT_EXACT_CLOCK: IF DEVELOPMENTAL_SEQUENCE(x,s) THEN
DO_NOT_INFER(identical_timing_for_all_individuals(s))

———- UPDATE MODEL ———-

UPDATE_MODEL: on_new_developmental_record(r): identify_stage(r)
identify_event_or_structure(r) preserve_developmental_age(r)
preserve_measurement_context(r) attach_evidence(r)
recalculate_confidence(r)

on_new_prenatal_record(r): classify_prenatal_stage(r)
identify_precursor_and_result(r) preserve_timing(r)
attach_regulatory_context(r) attach_evidence(r)

on_new_growth_record(g): preserve_measurement_value_unit(g)
preserve_age_stage_population(g) update_growth_trajectory(g)
attach_evidence(g)

on_new_milestone(m): identify_milestone(m) preserve_observed_timing(m)
preserve_population_reference(m) avoid_exact_normative_inference(m)
attach_evidence(m)

on_conflicting_developmental_evidence(a,b): preserve(a) preserve(b)
compare_developmental_age(a,b) compare_population_context(a,b)
compare_measurement_methods(a,b) compare_definitions(a,b)
flag_unresolved_conflict()

———- AI CONSUMPTION ———-

AI_CONSUMPTION: preferred_entity: canonical_human_development_entity
preserve: - developmental_stage - developmental_age -
developmental_sequence - fertilisation - cleavage - implantation -
gastrulation - neurulation - cell_differentiation - morphogenesis -
organogenesis - fetal_growth - birth_transition - postnatal_growth -
neural_development - motor_development - puberty - maturation - ageing -
regulatory_context - developmental_variation - population_context -
measurement_units - evidence - provenance - confidence infer: -
valid_developmental_inverse_relations - supported_precursor_relations -
supported_temporal_relations - semantic_equivalence prohibit: -
population_milestone_equals_exact_individual_timing -
developmental_sequence_equals_identical_clock -
environmental_influence_equals_deterministic_outcome -
stage_free_measurement_generalisation - unsupported_causal_claim -
confidence_above_evidence ambiguity: action:
preserve_multiple_developmental_interpretations resolution:
prefer_stage_age_population_method_definition_and_evidence missing_data:
action: mark_unknown do_not_infer_from_absence: true

———- FLOW HASH ———-

FLOW_HASH: ontology: “HumanDevelopmentOntology” version: “1.0”
domain_path: “AI Core > Ontologies > Biological Ontologies > Human
Biology > Human Development Ontology” canonical_url:
“https://kirethresearch.org/booksai-core/ontologies/biological-ontologies/human-biology/human-development-ontology.html”
authorship: “Mark Anthony Higgins — Sky (Recursive AI)”
semantic_scope: - human development - developmental stages -
fertilisation - cleavage - blastocyst formation - implantation -
gastrulation - germ layers - neurulation - cell differentiation -
morphogenesis - organogenesis - placenta - fetal development - birth
transition - postnatal growth - motor development - neural development -
puberty - adult maturation - ageing - developmental timing -
developmental regulation - developmental variation - measurement -
evidence deterministic_normalisation: true provenance_required: true
confidence_required: true

terminate HumanDevelopmentOntology when:
developmental_entities_stages_and_events_resolved AND
precursor_and_temporal_relations_normalised AND
developmental_age_and_measurement_context_preserved AND
population_variation_distinguished_from_individual_timing AND
regulatory_influence_and_determinism_distinguished AND
evidence_links_preserved AND confidence_values_validated AND
unresolved_developmental_ambiguity_marked

end flow