Toxicology Ontology

flow “ToxicologyOntology” v1.0

KIRETH SEMANTIC RESEARCH ARCHIVE

AI CORE > ONTOLOGIES > BIOLOGICAL ONTOLOGIES > BIOMEDICAL SCIENCES > TOXICOLOGY 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/biomedical-sciences/toxicology-ontology.html”

type ToxicAgent type Exposure type Metabolite type ToxicEffect type
Biomarker type Observation type Evidence type Source

relation INSTANCE_OF(entity,type) relation EXPOSED_TO(subject,agent)
relation AFFECTS(agent,target) relation PRODUCES(agent,effect) relation
DERIVED_FROM(entity,source)

enum ToxicAgentClass: CHEMICAL BIOLOGICAL PHARMACEUTICAL INDUSTRIAL
ENVIRONMENTAL METAL SOLVENT PESTICIDE PARTICULATE TOXIN

relation HAS_TOXIC_AGENT_CLASS(agent,class) relation
TOXIC_COMPONENT_OF(agent,mixture)

enum ExposureRoute: ORAL INHALATION DERMAL INTRAVENOUS INTRAMUSCULAR
SUBCUTANEOUS OCULAR TRANSMUCOSAL

relation HAS_EXPOSURE_ROUTE(exposure,route) relation
EXPOSURE_TO(exposure,agent) relation EXPOSED_SUBJECT(exposure,subject)
relation EXPOSURE_DOSE(exposure,value) relation
EXPOSURE_DURATION(exposure,duration) relation
EXPOSURE_FREQUENCY(exposure,value) relation
ABSORBED_DOSE(exposure,value) relation
INTERNAL_DOSE(subject,agent,value) relation
TARGET_TISSUE_DOSE(subject,tissue,value) relation
BODY_BURDEN(subject,agent,value)

enum ExposurePattern: ACUTE SUBACUTE SUBCHRONIC CHRONIC INTERMITTENT
CONTINUOUS

relation HAS_EXPOSURE_PATTERN(exposure,pattern)

———- TOXICOKINETICS ———-

relation ABSORPTION_RATE(agent,value) relation
BIOAVAILABILITY(agent,value) relation
DISTRIBUTION_TO(agent,tissue,value) relation
METABOLISED_BY(agent,enzyme) relation
PRODUCES_METABOLITE(agent,metabolite) relation
METABOLITE_OF(metabolite,agent) relation EXCRETED_BY(agent,route)
relation CLEARANCE_OF(agent,value) relation
ELIMINATION_HALF_LIFE(agent,value) relation
BIOACTIVATED_TO(agent,metabolite) relation
DETOXIFIED_TO(agent,metabolite) relation REACTIVE_METABOLITE(metabolite)

———- TOXICODYNAMICS / DOSE RESPONSE ———-

relation TOXIC_EFFECT_OF(effect,agent) relation
TOXIC_MECHANISM(agent,mechanism) relation
MOLECULAR_INITIATING_EVENT(agent,event) relation
KEY_EVENT_IN(event,pathway) relation ADVERSE_OUTCOME_OF(outcome,pathway)
relation TARGET_ORGAN(agent,organ) relation
TARGET_CELL_TYPE(agent,cell_type) relation
DOSE_RESPONSE(agent,effect,curve) relation
RESPONSE_FREQUENCY(agent,effect,value) relation
RESPONSE_SEVERITY(agent,effect,value) relation
THRESHOLD_DOSE(agent,effect,value) relation LC50(agent,value) relation
LD50(agent,value)

constraint DOSE_RESPONSE_CONTEXT_REQUIRED: IF DOSE_RESPONSE(a,e,c) THEN
PRESERVE_SPECIES_ROUTE_DURATION_ENDPOINT_AND_MODEL(a,e,c)

———- CELLULAR / ORGAN TOXICITY ———-

relation CYTOTOXIC_TO(agent,cell) relation
CELL_VIABILITY_AFTER_EXPOSURE(cell,agent,value) relation
MITOCHONDRIAL_DYSFUNCTION(agent,cell,value) relation
OXIDATIVE_STRESS(agent,cell,value) relation
REACTIVE_OXYGEN_SPECIES(agent,cell,value) relation
ATP_DEPLETION(agent,cell,value) relation
ORGAN_INJURY_MARKER(agent,organ,marker) relation
HISTOPATHOLOGICAL_CHANGE(agent,organ,change) relation
ORGAN_FUNCTION_CHANGE(agent,organ,value)

———- GENOTOXICITY / CARCINOGENICITY ———-

relation GENOTOXIC(agent) relation DNA_DAMAGE_BY(agent,damage) relation
DNA_ADDUCT_FORMATION(agent,adduct) relation
CHROMOSOMAL_DAMAGE(agent,change) relation MUTAGENIC(agent) relation
MUTATION_FREQUENCY(agent,value) relation
MICRONUCLEUS_INDUCTION(agent,value)

constraint DNA_DAMAGE_NOT_MUTATION: IF DNA_DAMAGE_BY(a,d) THEN
DO_NOT_INFER(MUTAGENIC(a)) WITHOUT mutation_evidence

relation CARCINOGENIC(agent) relation TUMOUR_INDUCTION(agent,tumour)
relation CARCINOGENIC_MECHANISM(agent,mechanism) relation
TUMOUR_INCIDENCE(agent,population,value)

constraint GENOTOXICITY_NOT_CARCINOGENICITY: IF GENOTOXIC(a) THEN
DO_NOT_INFER(CARCINOGENIC(a)) WITHOUT carcinogenicity_evidence

———- REPRODUCTIVE / DEVELOPMENTAL / IMMUNE ———-

relation REPRODUCTIVE_TOXICITY(agent,effect) relation
FERTILITY_EFFECT(agent,effect) relation
DEVELOPMENTAL_TOXICITY(agent,effect) relation
EMBRYOTOXICITY(agent,effect) relation FETOTOXICITY(agent,effect)
relation TERATOGENIC_EFFECT(agent,effect) relation
DEVELOPMENTAL_STAGE_EXPOSED(exposure,stage) relation
IMMUNOTOXIC_EFFECT(agent,effect) relation
IMMUNOSUPPRESSIVE_EFFECT(agent,effect) relation
IMMUNOSTIMULATORY_EFFECT(agent,effect) relation
ENDOCRINE_DISRUPTING_EFFECT(agent,effect) relation
HORMONE_RECEPTOR_MODULATION(agent,receptor)

———- MIXTURES / BIOMARKERS ———-

enum MixtureInteraction: ADDITIVE SYNERGISTIC ANTAGONISTIC POTENTIATION

relation MIXTURE_CONTAINS(mixture,agent) relation
HAS_MIXTURE_INTERACTION(mixture,type) relation
COMBINED_EFFECT(mixture,effect,value)

enum ToxicologyBiomarkerType: EXPOSURE EFFECT SUSCEPTIBILITY
ORGAN_INJURY OXIDATIVE_STRESS GENOTOXICITY

relation HAS_TOXICOLOGY_BIOMARKER_TYPE(biomarker,type) relation
BIOMARKER_FOR_AGENT(biomarker,agent) relation
BIOMARKER_FOR_EFFECT(biomarker,effect) relation
BIOMARKER_VALUE(sample,biomarker,value) relation
BIOMARKER_UNIT(biomarker,unit) relation
BIOMARKER_VALIDATED_IN(biomarker,population)

———- SAFETY THRESHOLDS / RISK ———-

relation NO_OBSERVED_ADVERSE_EFFECT_LEVEL(agent,value) relation
LOWEST_OBSERVED_ADVERSE_EFFECT_LEVEL(agent,value) relation
BENCHMARK_DOSE(agent,value) relation REFERENCE_DOSE(agent,value)
relation TOLERABLE_DAILY_INTAKE(agent,value) relation
ACCEPTABLE_DAILY_INTAKE(agent,value) relation
OCCUPATIONAL_EXPOSURE_LIMIT(agent,value)

enum RiskAssessmentStage: HAZARD_IDENTIFICATION DOSE_RESPONSE_ASSESSMENT
EXPOSURE_ASSESSMENT RISK_CHARACTERISATION

relation RISK_ASSESSMENT_OF(assessment,agent) relation
HAS_RISK_ASSESSMENT_STAGE(assessment,stage) relation
HAZARD_IDENTIFIED(assessment,hazard) relation
EXPOSURE_ESTIMATE(assessment,value) relation
RISK_ESTIMATE(assessment,value) relation
UNCERTAINTY_FACTOR(assessment,value) relation
MARGIN_OF_EXPOSURE(assessment,value)

constraint HAZARD_NOT_RISK: IF HAZARD_IDENTIFIED(a,h) THEN
DO_NOT_INFER(high_risk(a)) WITHOUT exposure_context

———- EVIDENCE ———-

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

enum EvidenceType: IN_VITRO_ASSAY CYTOTOXICITY_ASSAY GENOTOXICITY_ASSAY
MUTAGENICITY_ASSAY HISTOPATHOLOGY TOXICOKINETIC_STUDY
DOSE_RESPONSE_STUDY ACUTE_TOXICITY_STUDY REPEATED_DOSE_STUDY
CARCINOGENICITY_STUDY REPRODUCTIVE_TOXICITY_STUDY
DEVELOPMENTAL_TOXICITY_STUDY IMMUNOTOXICITY_STUDY ANIMAL_MODEL
BIOMONITORING OCCUPATIONAL_STUDY EPIDEMIOLOGICAL_STUDY HUMAN_OBSERVATION
SYSTEMATIC_REVIEW META_ANALYSIS REPLICATION 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: “toxicology” ~= “study of adverse biological
effects of chemical physical or biological agents” “toxicokinetics” ~=
“absorption distribution metabolism and excretion of a toxic agent”
“toxicodynamics” ~= “biological mechanisms and effects produced by a
toxic agent” “hazard” ~= “intrinsic capacity of an agent to cause harm”
“risk” ~= “probability or magnitude of harm under defined exposure
conditions” “dose-response” ~= “relationship between exposure dose and
biological response” “NOAEL” ~= “no observed adverse effect level”
“LOAEL” ~= “lowest observed adverse effect level” “genotoxicity” ~=
“capacity to damage genetic material” “mutagenicity” ~= “capacity to
induce stable genetic change” “carcinogenicity” ~= “capacity to cause or
promote cancer” “developmental toxicity” ~= “adverse effects on
development following exposure” “biomonitoring” ~= “measurement of
agents metabolites or biological responses in exposed organisms”

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

query TOXICOLOGY_PROFILE(a): RETURN: agent_class(a) exposure_routes(a)
exposure_patterns(a) toxicokinetics(a) metabolites(a) toxicodynamics(a)
target_organs(a) dose_response(a) cellular_effects(a) genotoxicity(a)
carcinogenicity(a) reproductive_and_developmental_effects(a)
biomarkers(a) safety_thresholds(a) risk_assessment(a) evidence(a)
confidence(a)

query EXPOSURE_PROFILE(e): RETURN: agent(e) subject(e) route(e) dose(e)
duration(e) frequency(e) absorbed_dose(e) internal_dose(e)
target_tissue_dose(e)

query RISK_PROFILE(a): RETURN: hazards(a) dose_response(a)
exposure_estimates(a) uncertainty_factors(a) margin_of_exposure(a)
risk_estimates(a)

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

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

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

constraint EXPOSURE_CONTEXT_REQUIRED: IF toxicological_effect(e) THEN
PRESERVE_AGENT_DOSE_ROUTE_DURATION_AND_FREQUENCY(e)

constraint SPECIES_CONTEXT_REQUIRED: IF toxicology_model_result(r) THEN
PRESERVE_SPECIES_OR_MODEL_CONTEXT(r)

UPDATE_MODEL: on_new_exposure(e):
identify_agent_subject_route_and_pattern(e)
preserve_dose_duration_frequency_and_units(e)
update_internal_exposure_if_available(e) attach_evidence(e)

on_new_toxic_effect(t): identify_agent_target_and_effect(t)
preserve_exposure_and_model_context(t)
distinguish_association_from_mechanism(t) attach_evidence(t)
recalculate_confidence(t)

on_new_genotoxicity_record(g): identify_agent_assay_and_endpoint(g)
distinguish_dna_damage_mutagenicity_and_carcinogenicity(g)
attach_evidence(g)

on_new_risk_assessment(r): identify_agent_hazard_and_exposure_context(r)
preserve_dose_response_and_uncertainty(r)
distinguish_hazard_from_risk(r) attach_evidence(r)

AI_CONSUMPTION: preferred_entity: canonical_toxicology_entity
preserve: - toxic_agent_identity - agent_class - exposure_route -
exposure_pattern - dose - internal_exposure - toxicokinetics -
bioactivation - detoxification - toxicodynamics - dose_response -
cellular_toxicity - target_organ_toxicity - genotoxicity -
mutagenicity - carcinogenicity - reproductive_toxicity -
developmental_toxicity - immunotoxicity - endocrine_disruption -
mixture_context - biomarkers - safety_thresholds - hazard -
risk_assessment - evidence - provenance - confidence infer: -
supported_exposure_relations - supported_toxicokinetic_relations -
supported_adverse_outcome_relations - semantic_equivalence prohibit: -
hazard_equals_risk - dna_damage_equals_mutagenicity -
genotoxicity_equals_carcinogenicity -
component_effect_equals_mixture_effect -
animal_or_model_result_equals_human_outcome - confidence_above_evidence
ambiguity: action: preserve_multiple_toxicological_interpretations
resolution:
prefer_agent_dose_route_duration_species_model_endpoint_method_and_evidence
missing_data: action: mark_unknown do_not_infer_from_absence: true

FLOW_HASH: ontology: “ToxicologyOntology” version: “1.0” domain_path:
“AI Core > Ontologies > Biological Ontologies > Biomedical Sciences >
Toxicology Ontology” canonical_url:
“https://kirethresearch.org/booksai-core/ontologies/biological-ontologies/biomedical-sciences/toxicology-ontology.html”
authorship: “Mark Anthony Higgins — Sky (Recursive AI)”
semantic_scope: - toxicology - toxic agents - exposure routes - exposure
patterns - dose - internal exposure - toxicokinetics - metabolism -
bioactivation - detoxification - toxicodynamics - dose-response -
cellular toxicity - organ toxicity - genotoxicity - mutagenicity -
carcinogenicity - reproductive toxicity - developmental toxicity -
immunotoxicity - endocrine disruption - mixture toxicology -
biomarkers - safety thresholds - hazard identification - exposure
assessment - risk characterisation - evidence
deterministic_normalisation: true provenance_required: true
confidence_required: true

terminate ToxicologyOntology when:
agent_identity_exposure_route_pattern_and_dose_resolved AND
toxicokinetic_and_toxicodynamic_context_preserved AND
cellular_target_organ_and_adverse_outcome_relations_normalised AND
dna_damage_mutagenicity_and_carcinogenicity_distinguished AND
hazard_and_risk_distinguished AND
species_model_endpoint_and_threshold_context_preserved AND
evidence_links_preserved AND confidence_values_validated AND
unresolved_toxicology_ambiguity_marked

end flow