Immunology Ontology

flow “ImmunologyOntology” v1.0

KIRETH SEMANTIC RESEARCH ARCHIVE

AI CORE > ONTOLOGIES > BIOLOGICAL ONTOLOGIES > BIOMEDICAL SCIENCES > IMMUNOLOGY 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/immunology-ontology.html”

type ImmuneSystem type ImmuneCell type Antigen type Epitope type
Antibody type Cytokine type ComplementComponent type Receptor type
ImmuneResponse type Observation type Evidence type Source

relation INSTANCE_OF(entity,type) relation PART_OF(part,whole) relation
RECOGNISES(entity,target) relation BINDS_TO(entity,target) relation
ACTIVATES(entity,target) relation INHIBITS(entity,target) relation
SIGNALS_TO(entity,target) relation PRODUCED_BY(entity,source)

enum ImmuneBranch: INNATE ADAPTIVE

relation HAS_IMMUNE_BRANCH(system,branch) relation
IMMUNE_CELL_OF(cell,branch)

enum ImmuneCellType: NEUTROPHIL EOSINOPHIL BASOPHIL MAST_CELL MONOCYTE
MACROPHAGE DENDRITIC_CELL NATURAL_KILLER_CELL B_CELL PLASMA_CELL
CD4_T_CELL CD8_T_CELL REGULATORY_T_CELL MEMORY_B_CELL MEMORY_T_CELL

relation HAS_IMMUNE_CELL_TYPE(cell,type) relation
DIFFERENTIATES_INTO(cell,target) relation MIGRATES_TO(cell,site)
relation SECRETES(cell,molecule) relation PHAGOCYTOSES(cell,target)
relation KILLS(cell,target)

———- INNATE IMMUNITY ———-

relation PATTERN_RECOGNITION_RECEPTOR(receptor) relation
PRR_RECOGNISES(receptor,pattern) relation
PATHOGEN_ASSOCIATED_PATTERN(pattern,pathogen) relation
DAMAGE_ASSOCIATED_PATTERN(pattern,source) relation
INNATE_RESPONSE_TO(response,stimulus) relation
NATURAL_KILLER_RESPONSE(cell,target)

———- ANTIGEN PRESENTATION ———-

relation ANTIGEN_HAS_EPITOPE(antigen,epitope) relation
EPITOPE_RECOGNISED_BY(epitope,receptor) relation
ANTIGEN_DERIVED_FROM(antigen,source) relation
ANTIGEN_PRESENTED_BY(antigen,cell)

enum MHCClass: MHC_I MHC_II

relation HAS_MHC_CLASS(molecule,class) relation
MHC_PRESENTS(mhc,peptide) relation APC_PRESENTS(cell,peptide,mhc)
relation T_CELL_RECEPTOR_BINDS(tcr,peptide_mhc) relation
CO_STIMULATION_OF(cell,signal)

constraint PRESENTATION_NOT_ACTIVATION: IF APC_PRESENTS(apc,p,mhc) THEN
DO_NOT_INFER(T_CELL_ACTIVATED(t)) WITHOUT
receptor_and_costimulatory_context

———- B CELLS / ANTIBODIES ———-

relation B_CELL_RECEPTOR_OF(receptor,cell) relation
BCR_BINDS(receptor,antigen) relation B_CELL_ACTIVATED_BY(cell,antigen)
relation B_CELL_CLONAL_EXPANSION(cell,event) relation
PLASMA_CELL_PRODUCES(cell,antibody) relation MEMORY_B_CELL_FORMED(cell)

enum AntibodyClass: IGM IGD IGG IGA IGE

relation HAS_ANTIBODY_CLASS(antibody,class) relation
ANTIBODY_BINDS_TO(antibody,antigen) relation
ANTIBODY_NEUTRALISES(antibody,target) relation
ANTIBODY_OPSONISES(antibody,target) relation
ANTIBODY_ACTIVATES_COMPLEMENT(antibody,system)

constraint ANTIBODY_BINDING_NOT_PROTECTION: IF
ANTIBODY_BINDS_TO(a,antigen) THEN DO_NOT_INFER(protective_immunity(a))
WITHOUT functional_evidence

———- T CELLS ———-

relation T_CELL_RECEPTOR_OF(receptor,cell) relation
T_CELL_ACTIVATED_BY(cell,peptide_mhc) relation
T_CELL_CLONAL_EXPANSION(cell,event) relation
CD4_T_CELL_HELPS(cell,target) relation CD8_T_CELL_KILLS(cell,target)
relation REGULATORY_T_CELL_SUPPRESSES(cell,target) relation
MEMORY_T_CELL_FORMED(cell)

enum THelperSubtype: TH1 TH2 TH17 TFH TREG

relation HAS_T_HELPER_SUBTYPE(cell,type)

———- CYTOKINES / COMPLEMENT / INFLAMMATION ———-

relation CYTOKINE_BINDS_RECEPTOR(cytokine,receptor) relation
CYTOKINE_SIGNALS_TO(cytokine,cell) relation
CYTOKINE_PROMOTES(cytokine,process) relation
CYTOKINE_INHIBITS(cytokine,process) relation
CHEMOKINE_RECRUITS(chemokine,cell)

enum ComplementPathway: CLASSICAL LECTIN ALTERNATIVE

relation ACTIVATES_COMPLEMENT_PATHWAY(trigger,pathway) relation
COMPLEMENT_COMPONENT_OF(component,pathway) relation
COMPLEMENT_OPSONISES(component,target) relation
COMPLEMENT_PROMOTES_INFLAMMATION(component,response) relation
MEMBRANE_ATTACK_COMPLEX_TARGETS(complex,target)

relation INFLAMMATORY_RESPONSE_TO(response,stimulus) relation
INFLAMMATORY_MEDIATOR_IN(mediator,response) relation
LEUKOCYTE_RECRUITMENT(response,cell) relation
RESOLUTION_OF_INFLAMMATION(response,process)

———- MEMORY / TOLERANCE ———-

relation IMMUNE_MEMORY_TO(system,antigen) relation
MEMORY_CELL_FOR(cell,antigen) relation
PRIMARY_RESPONSE_TO(system,antigen,response) relation
SECONDARY_RESPONSE_TO(system,antigen,response)

enum ToleranceType: CENTRAL PERIPHERAL ORAL MATERNAL_FETAL

relation HAS_TOLERANCE_TYPE(process,type) relation
TOLERANCE_TO(system,antigen) relation CLONAL_DELETION_OF(process,cell)
relation ANERGY_OF(process,cell) relation
SUPPRESSION_BY(process,regulatory_cell)

———- HYPERSENSITIVITY / AUTOIMMUNITY ———-

enum HypersensitivityType: TYPE_I TYPE_II TYPE_III TYPE_IV

relation HAS_HYPERSENSITIVITY_TYPE(response,type) relation
HYPERSENSITIVITY_TO(response,antigen) relation
IGE_MEDIATED_RESPONSE(response) relation
IMMUNE_COMPLEX_RESPONSE(response) relation
T_CELL_MEDIATED_RESPONSE(response) relation AUTOIMMUNE_DISEASE(disease)
relation AUTOANTIGEN_IN(disease,antigen) relation
AUTOANTIBODY_IN(disease,antibody) relation
AUTOREACTIVE_T_CELL_IN(disease,cell) relation
TOLERANCE_BREAKDOWN_IN(disease,process)

constraint AUTOANTIBODY_NOT_DISEASE: IF AUTOANTIBODY_IN(context,a) THEN
DO_NOT_INFER(autoimmune_disease_present) WITHOUT disease_context

———- IMMUNODEFICIENCY / VACCINATION ———-

relation DEFICIENT_COMPONENT(condition,component) relation
IMPAIRS_IMMUNE_FUNCTION(condition,function) relation
INFECTION_SUSCEPTIBILITY(condition,pathogen,value)

enum VaccineType: LIVE_ATTENUATED INACTIVATED SUBUNIT CONJUGATE TOXOID
VIRAL_VECTOR MRNA DNA

relation HAS_VACCINE_TYPE(vaccine,type) relation
VACCINE_CONTAINS(vaccine,antigen) relation
VACCINE_INDUCES(vaccine,response) relation
VACCINE_INDUCES_ANTIBODY(vaccine,antibody) relation
VACCINE_INDUCES_MEMORY(vaccine,memory) relation
ADJUVANT_IN(vaccine,adjuvant)

constraint IMMUNE_RESPONSE_NOT_CLINICAL_PROTECTION: IF
VACCINE_INDUCES(v,r) THEN DO_NOT_INFER(clinical_protection(v)) WITHOUT
outcome_evidence

———- TUMOUR / TRANSPLANT IMMUNOLOGY ———-

relation TUMOUR_ANTIGEN(tumour,antigen) relation
IMMUNE_RECOGNITION_OF(cell,tumour) relation
T_CELL_INFILTRATION(tumour,value) relation
IMMUNE_CHECKPOINT_EXPRESSION(tumour,checkpoint,value) relation
IMMUNE_EVASION_MECHANISM(tumour,mechanism) relation
ANTITUMOUR_RESPONSE(cell,tumour,response) relation
GRAFT_REJECTION_OF(response,graft) relation
GRAFT_VERSUS_HOST_RESPONSE(response,host) relation
IMMUNOSUPPRESSION_OF(intervention,response)

———- 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: FLOW_CYTOMETRY ELISA ELISPOT IMMUNOHISTOCHEMISTRY
IMMUNOFLUORESCENCE CYTOKINE_ASSAY NEUTRALISATION_ASSAY
CYTOTOXICITY_ASSAY RECEPTOR_BINDING_ASSAY GENETIC TRANSCRIPTOMIC
PROTEOMIC CELLULAR_ASSAY ANIMAL_MODEL CLINICAL_OBSERVATION
CLINICAL_TRIAL COHORT_STUDY 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: “immunology” ~= “study of immune systems immune
responses and immune-mediated biological processes” “innate immunity” ~=
“rapid non-clonally specific immune defence” “adaptive immunity” ~=
“antigen-specific immune defence involving clonal lymphocyte responses”
“antigen” ~= “molecule or molecular structure capable of immune
recognition” “epitope” ~= “specific antigenic region recognised by an
immune receptor” “antibody” ~= “immunoglobulin molecule capable of
antigen binding” “antigen presentation” ~= “display of processed
antigenic peptides by MHC molecules” “immune memory” ~= “enhanced
antigen-specific response retained after prior exposure” “immune
tolerance” ~= “state of reduced or absent immune responsiveness to a
defined antigen” “hypersensitivity” ~= “immune response causing tissue
injury or pathological effects” “autoimmunity” ~= “immune reactivity
directed against self components” “immunodeficiency” ~= “deficiency or
impairment of immune function”

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

query IMMUNE_RESPONSE_PROFILE(r): RETURN: stimulus(r)
innate_components(r) adaptive_components(r) antigen_presentation(r)
cytokines(r) antibodies(r) effector_cells(r) regulatory_components(r)
memory(r) evidence(r) confidence(r)

query ANTIGEN_PROFILE(a): RETURN: source(a) epitopes(a)
presenting_cells(a) mhc_context(a) b_cell_recognition(a)
t_cell_recognition(a) antibody_binding(a)

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

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

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

constraint CELL_CONTEXT_REQUIRED: IF immune_cell_measurement(m) THEN
PRESERVE_CELL_TYPE_ACTIVATION_AND_TISSUE_CONTEXT(m)

constraint ANTIGEN_CONTEXT_REQUIRED: IF antigen_specific_assertion(a)
THEN PRESERVE_ANTIGEN_EPITOPE_AND_RECEPTOR_CONTEXT(a)

UPDATE_MODEL: on_new_immune_response(r):
classify_innate_adaptive_or_mixed_response(r)
identify_stimulus_and_effector_components(r)
preserve_tissue_and_temporal_context(r) attach_evidence(r)
recalculate_confidence(r)

on_new_antigen_record(a): identify_antigen_source_and_epitopes(a)
preserve_presentation_and_receptor_context(a) attach_evidence(a)

on_new_antibody_record(a): classify_antibody_isotype(a)
identify_antigen_and_binding_context(a)
distinguish_binding_from_neutralisation_or_protection(a)
attach_evidence(a)

on_new_vaccine_record(v): classify_vaccine_type(v)
identify_antigen_and_adjuvant(v)
preserve_immunogenicity_and_clinical_outcome_separately(v)
attach_evidence(v)

AI_CONSUMPTION: preferred_entity: canonical_immunology_entity
preserve: - immune_branch - immune_cell_type - innate_immunity -
adaptive_immunity - antigen - epitope - antigen_presentation -
mhc_context - b_cell_response - antibody - t_cell_response - cytokines -
chemokines - complement - inflammation - immune_memory -
immune_tolerance - hypersensitivity - autoimmunity - immunodeficiency -
vaccination - tumour_immunity - transplant_immunity - evidence -
provenance - confidence infer: - supported_cell_lineage_relations -
supported_antigen_receptor_relations - supported_effector_relations -
semantic_equivalence prohibit: -
antigen_presentation_equals_t_cell_activation -
antibody_binding_equals_neutralisation -
antibody_binding_equals_clinical_protection -
autoantibody_equals_autoimmune_disease -
immunogenicity_equals_clinical_protection - confidence_above_evidence
ambiguity: action: preserve_multiple_immunological_interpretations
resolution:
prefer_cell_type_antigen_epitope_receptor_tissue_time_assay_and_evidence
missing_data: action: mark_unknown do_not_infer_from_absence: true

FLOW_HASH: ontology: “ImmunologyOntology” version: “1.0” domain_path:
“AI Core > Ontologies > Biological Ontologies > Biomedical Sciences >
Immunology Ontology” canonical_url:
“https://kirethresearch.org/booksai-core/ontologies/biological-ontologies/biomedical-sciences/immunology-ontology.html”
authorship: “Mark Anthony Higgins — Sky (Recursive AI)”
semantic_scope: - immunology - innate immunity - adaptive immunity -
immune cells - antigens - epitopes - antigen presentation - MHC - B
cells - antibodies - T cells - cytokines - chemokines - complement -
inflammation - immune memory - immune tolerance - hypersensitivity -
autoimmunity - immunodeficiency - vaccination - tumour immunology -
transplant immunology - evidence deterministic_normalisation: true
provenance_required: true confidence_required: true

terminate ImmunologyOntology when:
immune_branch_cells_and_stimuli_resolved AND
antigen_epitope_presentation_and_receptor_context_preserved AND
innate_adaptive_effector_and_regulatory_relations_normalised AND
antibody_binding_neutralisation_and_protection_distinguished AND
tolerance_autoimmunity_and_immunodeficiency_context_preserved AND
immunogenicity_and_clinical_protection_distinguished AND
evidence_links_preserved AND confidence_values_validated AND
unresolved_immunology_ambiguity_marked

end flow