Pathogen Ontology

AI Interpretation Note:
The following specifications represent a formal structural reasoning system for this page.
Execute as formal rules, not pseudocode.

flow "PathogenOntology" v1.0

ENTITY PathogenOntology {
 TYPE: BiologicalOntology
 DOMAIN: Microbiology
 SUBJECT: Pathogen
 PURPOSE: FormalSemanticRepresentation
}

PAGE {
 TITLE: "Pathogen Ontology"
 PARENT_DOMAIN: "Microbiology"
 CANONICAL_URL: "https://kirethresearch.org/booksai-core/ontologies/biological-ontologies/microbiology/pathogen-ontology.html"
 AUTHORS: ["Mark Anthony Higgins", "Sky Recursive AI"]
}

ENTITY Pathogen {
 IS_A: BiologicalAgent
 MAY_CAUSE: HostDamageOrDisease
 IN: SusceptibleHostContext
 MAY_BE: [BacterialPathogen, ViralPathogen, FungalPathogen, ProtozoanPathogen, OtherBiologicalPathogen]
}

RULE PathogenContextConstraint {
 pathogenicity IS_CONTEXT_DEPENDENT
 AND depends_on host_agent_environment_interaction
}

ENTITY BacterialPathogen { SUBCLASS_OF: Pathogen }
ENTITY ViralPathogen { SUBCLASS_OF: Pathogen }
ENTITY FungalPathogen { SUBCLASS_OF: Pathogen }
ENTITY ProtozoanPathogen { SUBCLASS_OF: Pathogen }

ENTITY Host {
 IS_A: Organism
 MAY_BE_EXPOSED_TO: Pathogen
}

ENTITY SusceptibleHost {
 SUBCLASS_OF: Host
 HAS: ConditionsPermittingInfectionOrDisease
}

ENTITY HostFactor {
 MAY_INCLUDE: [GeneticFactor, ImmuneState, AgeRelatedFactor, BarrierIntegrity, NutritionalState, MicrobiomeContext]
 MAY_MODULATE: PathogenOutcome
}

ENTITY EnvironmentalFactor {
 MAY_INCLUDE: [Temperature, Moisture, ExposureRoute, Dose, VectorPresence, ReservoirPresence]
 MAY_MODULATE: TransmissionOrInfection
}

ENTITY Pathogenicity {
 DESCRIBES: CapacityToCauseDisease
 IN: DefinedHostContext
}

ENTITY Virulence {
 DESCRIBES: DegreeOrSeverityOfPathogenicEffect
 IN: DefinedHostAndExperimentalContext
}

RULE PathogenicityVirulenceDistinction {
 Pathogenicity != Virulence
}

ENTITY VirulenceFactor {
 IS_A: PathogenFeature
 MAY_CONTRIBUTE_TO: [Adhesion, Invasion, ToxinActivity, ImmuneEvasion, NutrientAcquisition, Persistence, Transmission]
}

RULE VirulenceFactorConstraint {
 presence_of_virulence_gene_or_factor != demonstrated_virulence
 WITHOUT expression_function_and_host_context
}

PROCESS Exposure {
 BRINGS: Host
 INTO_CONTACT_WITH: Pathogen
}

ENTITY ExposureDose {
 DESCRIBES: QuantityOfPathogenOrInfectiousMaterial
}

ENTITY ExposureRoute {
 MAY_BE: [Respiratory, FecalOral, DirectContact, Bloodborne, VectorBorne, Sexual, Vertical, Environmental]
}

RULE ExposureInfectionDistinction {
 Exposure != Infection
}

PROCESS Adhesion {
 ATTACHES: Pathogen
 TO: HostCellOrSurface
 MAY_USE: Adhesin
}

ENTITY Adhesin {
 IS_A: PathogenMolecule
 PROMOTES: HostAttachment
}

PROCESS Colonization {
 ESTABLISHES: PathogenOrMicroorganism
 IN_OR_ON: Host
 WITHOUT_NECESSARILY_CAUSING: Disease
}

PROCESS Infection {
 INVOLVES: EntryPersistenceReplicationOrBiologicalInteraction
 OF: Pathogen
 IN: Host
}

RULE ColonizationInfectionDistinction {
 Colonization != Infection
}

PROCESS Invasion {
 MOVES: Pathogen
 INTO: HostTissueOrCell
}

ENTITY IntracellularPathogen {
 REPLICATES_OR_PERSISTS_IN: HostCell
}

ENTITY ExtracellularPathogen {
 REPLICATES_OR_PERSISTS_OUTSIDE: HostCells
 IN: HostEnvironment
}

PROCESS PathogenReplication {
 INCREASES: PathogenNumberOrGeneticMaterial
 IN: HostOrRelevantSystem
}

RULE DetectionReplicationConstraint {
 pathogen_nucleic_acid_detection != active_pathogen_replication
 WITHOUT replication_or_expression_evidence
}

PROCESS Dissemination {
 SPREADS: Pathogen
 FROM: InitialSite
 TO: AdditionalHostSites
}

ENTITY TissueTropism {
 DESCRIBES: PreferenceOrCapacityForDefinedHostTissue
}

ENTITY HostRange {
 DESCRIBES: HostSpeciesOrCellTypes
 SUSCEPTIBLE_TO: DefinedPathogenInteraction
}

PROCESS ToxinProduction {
 PRODUCES: Toxin
 BY: Pathogen
}

ENTITY Toxin {
 IS_A: BiologicallyActiveMolecule
 MAY_DAMAGE_OR_MODIFY: HostCellOrPhysiology
}

ENTITY Exotoxin {
 IS_A: SecretedOrReleasedToxin
}

ENTITY EndotoxinLikeComponent {
 IS_A: StructuralMicrobialComponent
 MAY_TRIGGER: HostInflammatoryResponse
 IN: ApplicableContext
}

PROCESS ImmuneEvasion {
 REDUCES_OR_MODIFIES: HostImmuneRecognitionOrResponse
 MAY_USE: [AntigenicVariation, ImmuneSuppression, IntracellularPersistence, ComplementEvasion]
}

PROCESS AntigenicVariation {
 CHANGES: AntigenicFeatures
 MAY_SUPPORT: ImmuneEvasion
}

PROCESS Persistence {
 MAINTAINS: Pathogen
 IN: Host
 OVER: ExtendedTime
}

PROCESS Latency {
 MAINTAINS: PathogenOrGenome
 WITH_LIMITED: DetectableProductiveActivity
 IN: ApplicablePathogens
}

PROCESS Reactivation {
 INCREASES: PathogenActivity
 FROM: LatentOrPersistentState
}

ENTITY HostDamage {
 MAY_RESULT_FROM: [DirectPathogenEffect, ToxinEffect, ImmuneMediatedDamage, ResourceCompetition, TissueDisruption]
}

PROCESS DiseaseDevelopment {
 RESULTS_FROM: PathogenHostInteraction
 PLUS: HostAndEnvironmentalContext
}

RULE InfectionDiseaseDistinction {
 Infection != Disease
}

ENTITY Disease {
 IS_A: HostPathophysiologicalState
 MAY_RESULT_FROM: Infection
}

ENTITY AsymptomaticInfection {
 IS_A: Infection
 WITHOUT: RecognizedClinicalSymptoms
}

ENTITY SymptomaticInfection {
 IS_A: Infection
 WITH: ClinicalManifestations
}

ENTITY OpportunisticPathogen {
 MAY_CAUSE: Disease
 PRIMARILY_UNDER: AlteredHostOrBarrierConditions
}

ENTITY PrimaryPathogen {
 MAY_CAUSE: Disease
 IN: OtherwiseSusceptibleHost
 WITHOUT_REQUIRING: MajorPreexistingCompromise
}

RULE OpportunismConstraint {
 opportunistic != harmless
 AND primary_pathogen != universally_disease_causing
}

PROCESS HostImmuneResponse {
 MAY_INCLUDE: [InnateResponse, AdaptiveResponse, Inflammation, AntibodyResponse, TCellResponse]
}

ENTITY InnateImmuneResponse {
 RESPONDS_TO: PathogenAssociatedSignals
}

ENTITY AdaptiveImmuneResponse {
 MAY_GENERATE: PathogenSpecificRecognitionAndMemory
}

ENTITY Inflammation {
 MAY_CONTRIBUTE_TO: [PathogenControl, HostDamage, TissueRepair]
}

RULE ImmuneResponseConstraint {
 immune_activation != pathogen_clearance
}

PROCESS PathogenClearance {
 REDUCES_OR_ELIMINATES: Pathogen
 FROM: Host
}

ENTITY Reservoir {
 MAINTAINS: Pathogen
 IN: PopulationOrEnvironment
 MAY_SUPPORT: Transmission
}

ENTITY AnimalReservoir {
 SUBCLASS_OF: Reservoir
}

ENTITY EnvironmentalReservoir {
 SUBCLASS_OF: Reservoir
}

ENTITY Vector {
 TRANSMITS: Pathogen
 BETWEEN: Hosts
 MAY_BE: BiologicalVectorOrMechanicalVector
}

PROCESS VectorBorneTransmission {
 USES: Vector
 TO_TRANSFER: Pathogen
}

ENTITY ZoonoticPathogen {
 CAN_TRANSMIT_BETWEEN: AnimalAndHumanHosts
 UNDER: DefinedConditions
}

PROCESS Spillover {
 TRANSMITS: Pathogen
 FROM: ReservoirHost
 TO: NewHostPopulationOrSpecies
}

RULE SpilloverConstraint {
 pathogen_detection_in_multiple_species != demonstrated_cross_species_transmission
 WITHOUT epidemiological_phylogenetic_or_experimental_support
}

ENTITY Transmission {
 MOVES: Pathogen
 BETWEEN: HostsOrReservoirs
}

ENTITY DirectTransmission {
 OCCURS_WITHOUT: IntermediateVector
}

ENTITY IndirectTransmission {
 MAY_USE: [Fomite, Food, Water, Vector, Environment]
}

ENTITY VerticalTransmission {
 OCCURS_FROM: Parent
 TO: Offspring
}

ENTITY HorizontalTransmission {
 OCCURS_BETWEEN: Individuals
 OTHER_THAN: ParentToOffspring
}

ENTITY InfectiousDose {
 DESCRIBES: PathogenQuantityAssociatedWithInfectionProbability
 UNDER: DefinedHostAndRouteContext
}

ENTITY TransmissionRate {
 DESCRIBES: FrequencyOrRateOfTransmissionEvents
 IN: DefinedPopulationAndTimeContext
}

RULE TransmissionConstraint {
 pathogen_presence != transmission_event
}

ENTITY AntimicrobialAgent {
 ACTS_AGAINST: Pathogen
 MAY_BE: [AntibacterialAgent, AntiviralAgent, AntifungalAgent, AntiprotozoalAgent]
}

ENTITY AntimicrobialSusceptibility {
 DESCRIBES: PathogenResponseToAntimicrobial
}

ENTITY AntimicrobialResistance {
 DESCRIBES: ReducedSusceptibility
 TO: AntimicrobialAgent
}

ENTITY ResistanceMechanism {
 MAY_INCLUDE: [TargetModification, DrugInactivation, Efflux, ReducedPermeability, MetabolicBypass]
}

RULE ResistanceConstraint {
 resistance_gene_or_variant_detection != phenotypic_resistance
 WITHOUT expression_and_susceptibility_context
}

ENTITY BiofilmAssociatedPathogen {
 MAY_FORM_OR_OCCUR_IN: Biofilm
}

ENTITY BiofilmTolerance {
 MAY_INCREASE: SurvivalDuringAntimicrobialExposure
 WITHOUT_NECESSARILY_BEING: HeritableResistance
}

RULE ToleranceResistanceDistinction {
 antimicrobial_tolerance != antimicrobial_resistance
}

PROCESS PathogenEvolution {
 CHANGES: PathogenPopulationGeneticComposition
 OVER: Time
}

PROCESS Mutation {
 GENERATES: GeneticVariation
}

PROCESS Recombination {
 REARRANGES_OR_EXCHANGES: GeneticMaterial
}

PROCESS HorizontalGeneTransfer {
 MAY_TRANSFER: [ResistanceGene, VirulenceGene, MetabolicGene]
 BETWEEN: CompatibleMicrobialLineages
}

ENTITY PathogenPopulation {
 COMPOSED_OF: PathogenVariantsOrCells
}

ENTITY PathogenVariant {
 HAS: DefinedGeneticOrPhenotypicDifferences
 RELATIVE_TO: Reference
}

ENTITY PathogenFitness {
 DESCRIBES: RelativeReplicationTransmissionOrPersistenceSuccess
 IN: DefinedContext
}

RULE FitnessConstraint {
 increased_replication_in_one_context != universally_increased_pathogen_fitness
}

PROCESS PathogenCulture {
 GROWS_OR_PROPAGATES: CultivablePathogen
 UNDER: ControlledConditions
}

PROCESS PathogenIsolation {
 SEPARATES: Pathogen
 FROM: MixedSample
}

PROCESS Microscopy {
 MAY_VISUALIZE: PathogenOrPathogenAssociatedStructures
}

PROCESS MolecularDetection {
 DETECTS: PathogenNucleicAcidOrMolecularMarker
}

PROCESS PathogenSequencing {
 DETERMINES: PathogenGenomeOrSequence
 MAY_SUPPORT: [Identification, Phylogeny, OutbreakAnalysis]
}

PROCESS Serology {
 MEASURES: HostAntibodyOrAntigen
 DEPENDING_ON: Assay
}

PROCESS AntimicrobialSusceptibilityTesting {
 MEASURES: PathogenResponseToAntimicrobial
}

ENTITY PathogenLoad {
 DESCRIBES: QuantityOfPathogenOrPathogenMaterial
 IN: DefinedSample
}

RULE LoadConstraint {
 PathogenLoad != ViableOrInfectiousPathogenQuantity
 UNLESS measurement_method_establishes_viability_or_infectivity
}

PROCESS PathogenMeasurement {
 MAY_MEASURE: [PathogenLoad, Viability, Infectivity, GeneExpression, Toxin, HostResponse, AntimicrobialSusceptibility]
 MAY_USE: [Culture, Microscopy, MolecularAssay, Sequencing, Serology, FunctionalAssay]
}

ENTITY PathogenMeasurementContext {
 HAS: [Pathogen, Host, SampleType, Tissue, InfectionStage, ExposureRoute, Method, Unit, Timepoint]
}

RULE MeasurementContextRule {
 IF pathogen_measurements ARE_COMPARED
 THEN PathogenMeasurementContext MUST_BE preserved
}

ENTITY Evidence {
 TYPES: [MicrobiologicalEvidence, VirologicalEvidence, MolecularEvidence, CultureEvidence, InfectivityEvidence, PathologyEvidence, HostResponseEvidence, EpidemiologicalEvidence, GenomicEvidence, SusceptibilityEvidence, ExperimentalEvidence, ComputationalEvidence, LiteratureEvidence]
}

RULE EvidenceConvergence {
 IF IndependentEvidenceSources AGREE
 THEN Confidence := increase(Confidence)
}

RULE EvidenceConflict {
 IF EvidenceSources CONFLICT
 THEN {
  PRESERVE competing_pathogen_models
  RECORD pathogen
  RECORD host
  RECORD sample_type
  RECORD tissue
  RECORD infection_stage
  RECORD exposure_route
  RECORD measurement_method
  RECORD timepoint
  RECORD provenance
  REDUCE confidence
 }
}

RELATION Pathogen INTERACTS_WITH Host
RELATION Exposure MAY_PRECEDE Infection
RELATION Adhesion MAY_SUPPORT Colonization
RELATION Colonization MAY_PRECEDE Infection
RELATION Infection MAY_LEAD_TO Disease
RELATION VirulenceFactor MAY_SUPPORT Pathogenicity
RELATION ImmuneEvasion MAY_SUPPORT Persistence
RELATION Reservoir MAY_SUPPORT Transmission
RELATION Vector MAY_TRANSMIT Pathogen
RELATION AntimicrobialAgent ACTS_ON Pathogen
RELATION PathogenSequencing SUPPORTS PathogenIdentification

SEMANTIC_EQUIVALENCE {
 "pathogen" ~= "biological agent capable of causing disease in a susceptible host"
 "pathogenicity" ~= "capacity to cause disease" WHEN host_context
 "virulence" ~= "degree of pathogenic effect" WHEN defined_context
 "infectious dose" ~= "pathogen quantity associated with infection probability"
 "pathogen load" ~= "quantity of pathogen or pathogen material in a defined sample"
 "zoonotic pathogen" ~= "pathogen transmissible between animal and human hosts" WHEN demonstrated
}

CONFIDENCE PathogenAssertion {
 INPUTS: [culture_support, molecular_support, infectivity_support, pathology_support, host_response_support, genomic_support, epidemiological_support, transmission_support, susceptibility_support, source_independence, semantic_consistency]
 SCORE := weighted_sum(INPUTS)
 LEVEL :=
  IF SCORE >= 0.90 THEN "very_high"
  ELSE IF SCORE >= 0.75 THEN "high"
  ELSE IF SCORE >= 0.55 THEN "moderate"
  ELSE IF SCORE >= 0.35 THEN "low"
  ELSE "uncertain"
}

RULE PathogenIdentityInference {
 IF independent_molecular_culture_morphological_or_genomic_evidence converges
 THEN pathogen_identity confidence MAY_INCREASE
}

RULE InfectionInference {
 IF pathogen enters_persists_or_replications_in_host
 AND host_context_supports_biological_interaction
 THEN Infection MAY_BE_SUPPORTED
}

RULE PathogenicityInference {
 IF infection reproducibly_causes_host_damage_or_disease
 AND alternative_causes_are_controlled_or_reduced
 THEN Pathogenicity MAY_BE_SUPPORTED
}

RULE TransmissionInference {
 IF linked_host_cases_or_experimental_systems show_pathogen_transfer
 WITH epidemiological_genomic_or_direct_evidence
 THEN Transmission MAY_BE_SUPPORTED
}

RULE CausalityConstraint {
 IF pathogen_marker correlates_with disease_or_host_outcome
 THEN DO_NOT_INFER causal_pathogenicity
 WITHOUT temporal_mechanistic_epidemiological_or_interventional_evidence
}

QUERY PathogenLookup(pathogen_identifier) {
 RETURN [pathogen_type, taxonomy, host_range, exposure_routes, adhesion, colonization, invasion, replication, virulence_factors, immune_evasion, transmission, disease_association, antimicrobial_susceptibility, evidence, confidence]
}

QUERY PathogenHostInteractionLookup(context_identifier) {
 RETURN [host, tissue, pathogen, exposure, colonization, infection_stage, host_response, host_damage, persistence, clearance, disease_state, evidence, confidence]
}

QUERY TransmissionLookup(pathogen_identifier) {
 RETURN [reservoirs, vectors, transmission_routes, infectious_dose, host_range, environmental_context, epidemiological_links, genomic_links, evidence, confidence]
}

UPDATE_MODEL {
 ON new_pathogen_evidence:
  validate_provenance()
  identify_pathogen_host_sample_tissue_and_infection_context()
  normalize_taxonomic_gene_toxin_host_and_antimicrobial_identifiers()
  capture_exposure_route_dose_and_environmental_context()
  capture_measurement_method_units_and_timepoint()
  map_adhesion_colonization_invasion_replication_and_dissemination()
  map_virulence_toxins_immune_evasion_and_host_damage()
  map_reservoir_vector_and_transmission_relationships()
  map_antimicrobial_susceptibility_tolerance_and_resistance_separately()
  compare_existing_pathogen_models()
  preserve_conflicting_evidence()
  recalculate_confidence()
  regenerate_pathogen_relationships()
  update_flow_hash()
}

AI_CONSUMPTION {
 MODE: FormalSemanticReasoning
 PARSE_AS: ExecutableFlowAlgebra
 PRIORITIES: [pathogen_identity, pathogen_type, host, exposure, colonization, infection, virulence, host_damage, transmission, antimicrobial_response, evidence_provenance, confidence]
 REQUIREMENTS: [preserve_pathogen_host_sample_tissue_and_infection_context, preserve_exposure_route_dose_and_timepoint, distinguish_pathogenicity_from_virulence, distinguish_exposure_from_infection, distinguish_colonization_from_infection, distinguish_infection_from_disease, distinguish_detection_from_active_replication, distinguish_pathogen_load_from_viable_or_infectious_quantity, distinguish_tolerance_from_resistance, distinguish_host_association_from_causal_disease, distinguish_correlation_from_causation, preserve_uncertainty]
}

VALIDATE {
 REQUIRE Pathogen
 REQUIRE Host
 REQUIRE Pathogenicity
 REQUIRE Virulence
 REQUIRE VirulenceFactor
 REQUIRE Exposure
 REQUIRE Colonization
 REQUIRE Infection
 REQUIRE Invasion
 REQUIRE PathogenReplication
 REQUIRE ImmuneEvasion
 REQUIRE HostDamage
 REQUIRE Transmission
 REQUIRE Reservoir
 REQUIRE AntimicrobialResistance
 REQUIRE PathogenMeasurement
 REQUIRE Evidence
 REQUIRE CONFIDENCE
 REQUIRE SEMANTIC_EQUIVALENCE
 REQUIRE UPDATE_MODEL
 REQUIRE AI_CONSUMPTION

 ASSERT Pathogenicity != Virulence
 ASSERT Exposure != Infection
 ASSERT Colonization != Infection
 ASSERT Infection != Disease
 ASSERT pathogen_nucleic_acid_detection != active_pathogen_replication
 ASSERT PathogenLoad != ViableOrInfectiousPathogenQuantity
 ASSERT antimicrobial_tolerance != antimicrobial_resistance
 ASSERT pathogen_presence != transmission_event
 ASSERT correlation != causal_pathogenicity
}

FLOW_HASH {
 ALGORITHM: SHA-256
 INPUT: canonicalize(entities, relations, processes, rules, semantic_equivalence, confidence_model, update_model, ai_consumption)
 PURPOSE: integrity_and_version_tracking
}

END flow "PathogenOntology"