Protozoa Ontology

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

flow "ProtozoaOntology" v1.0

ENTITY ProtozoaOntology {
 TYPE: BiologicalOntology
 DOMAIN: Microbiology
 SUBJECT: Protozoa
 PURPOSE: FormalSemanticRepresentation
}

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

ENTITY Protozoan {
 IS_A: MicrobialEukaryote
 TYPICALLY: Unicellular
 MAY_BE: [FreeLiving, Symbiotic, Parasitic]
}

RULE TaxonomicConstraint {
 "protozoa" IS_A historical_or_functional_grouping
 AND NOT_NECESSARILY: SingleMonophyleticTaxon
}

ENTITY ProtozoanCell {
 IS_A: EukaryoticCell
 HAS: [Nucleus, CellMembrane, Cytoplasm, Ribosome, MitochondrialOrDerivedOrganelle]
 MAY_HAVE: [Cilium, Flagellum, Pseudopodium, ContractileVacuole, FoodVacuole]
}

ENTITY Nucleus {
 STORES: NuclearGenome
}

ENTITY ProtozoanGenome {
 STORES: HeritableGeneticInformation
 MAY_HAVE: LineageSpecificGenomeOrganization
}

ENTITY ProtozoanGene {
 PART_OF: ProtozoanGenome
 MAY_ENCODE: [Protein, FunctionalRNA]
}

PROCESS ProtozoanGeneExpression {
 INCLUDES: [Transcription, RNAProcessing, Translation]
}

PROCESS ProtozoanGeneRegulation {
 MODULATES: GeneExpression
 ACROSS: [LifeCycleStage, Environment, HostContext]
}

ENTITY ProtozoanMotility {
 MAY_USE: [Cilium, Flagellum, Pseudopodium, GlidingMechanism]
}

ENTITY Cilium {
 MAY_SUPPORT: [Motility, Feeding, SensoryFunction]
}

ENTITY Flagellum {
 MAY_SUPPORT: Motility
}

ENTITY Pseudopodium {
 IS_A: DynamicCellProjection
 MAY_SUPPORT: [Motility, Phagocytosis]
}

PROCESS AmoeboidMovement {
 USES: CytoskeletalRemodelling
 MAY_FORM: Pseudopodia
}

PROCESS CiliaryMovement {
 USES: CoordinatedCiliaryBeating
}

PROCESS FlagellarMovement {
 USES: FlagellarMotion
}

ENTITY ProtozoanNutrition {
 MAY_INCLUDE: [Phagotrophy, Osmotrophy, Mixotrophy]
}

PROCESS Phagocytosis {
 INTERNALIZES: ParticulateMaterial
 INTO: Cell
}

ENTITY FoodVacuole {
 MAY_CONTAIN: IngestedMaterial
 SUPPORTS: IntracellularDigestion
}

PROCESS IntracellularDigestion {
 BREAKS_DOWN: InternalizedNutrients
}

PROCESS NutrientUptake {
 MOVES: SolubleNutrients
 INTO: ProtozoanCell
}

ENTITY ContractileVacuole {
 CONTRIBUTES_TO: Osmoregulation
 IN: ApplicableProtozoa
}

PROCESS Osmoregulation {
 MAINTAINS: CellularWaterAndSoluteBalance
}

ENTITY ProtozoanMetabolism {
 MAY_INCLUDE: [AerobicRespiration, AnaerobicMetabolism, FermentationLikeProcesses]
 DEPENDS_ON: LineageAndEnvironment
}

ENTITY Mitochondrion {
 SUPPORTS: EnergyMetabolism
 IN: ManyProtozoa
}

ENTITY MitochondrionRelatedOrganelle {
 MAY_INCLUDE: [Hydrogenosome, Mitosome]
 OCCURS_IN: SomeAnaerobicOrMicroaerophilicLineages
}

RULE OrganelleConstraint {
 absence_of_canonical_mitochondrion != absence_of_mitochondrial_evolutionary_derivatives
}

PROCESS ProtozoanGrowth {
 INCREASES: CellBiomassOrPopulationSize
}

PROCESS ProtozoanCellDivision {
 PRODUCES: DaughterCells
 MAY_INCLUDE: [BinaryFission, MultipleFission, BuddingLikeDivision]
}

PROCESS BinaryFission {
 DIVIDES: ProtozoanCell
 INTO: DaughterCells
}

PROCESS MultipleFission {
 PRODUCES: MultipleDaughterCells
 FROM: ParentCellOrStage
}

ENTITY ProtozoanLifeCycle {
 MAY_INCLUDE: [Trophozoite, Cyst, Oocyst, Gamete, SporeLikeStage, HostSpecificStage]
 DEPENDS_ON: Lineage
}

ENTITY Trophozoite {
 IS_A: ActiveFeedingOrGrowingStage
 IN: ApplicableProtozoa
}

ENTITY Cyst {
 IS_A: ResistantOrDormantStage
 MAY_SUPPORT: SurvivalOrTransmission
}

PROCESS Encystment {
 TRANSITIONS: ActiveCell
 TO: Cyst
}

PROCESS Excystment {
 TRANSITIONS: Cyst
 TO: ActiveStage
 UNDER: SuitableConditions
}

RULE CystConstraint {
 protozoan_cyst != bacterial_endospore
}

PROCESS ProtozoanSexualReproduction {
 MAY_INCLUDE: [GameteFormation, CellFusion, Meiosis]
 DEPENDS_ON: Lineage
}

PROCESS ProtozoanAsexualReproduction {
 MAY_INCLUDE: [BinaryFission, MultipleFission, Budding]
}

ENTITY ProtozoanPopulation {
 COMPOSED_OF: ProtozoanCellsOrLifeCycleStages
}

ENTITY ProtozoanCommunity {
 MAY_INCLUDE: MultipleProtozoanTaxa
 OCCURS_IN: DefinedEnvironment
}

ENTITY ProtozoanHabitat {
 MAY_INCLUDE: [Freshwater, MarineWater, Soil, Sediment, Host, Biofilm, Wastewater]
}

ENTITY EnvironmentalFactor {
 MAY_INCLUDE: [Temperature, pH, Salinity, Oxygen, Nutrients, Moisture]
 MAY_MODULATE: ProtozoanPhysiology
}

PROCESS ProtozoanEcologicalResponse {
 MAY_CHANGE: [Growth, Motility, Feeding, Encystment, CommunityComposition]
 IN_RESPONSE_TO: EnvironmentalFactor
}

ENTITY BacterivorousProtozoan {
 FEEDS_ON: Bacteria
 MAY_INFLUENCE: MicrobialCommunityStructure
}

PROCESS Grazing {
 CONSUMES: MicrobialPrey
 MAY_MODULATE: MicrobialPopulation
}

ENTITY ProtozoanPredator {
 CONSUMES: OtherMicroorganisms
}

PROCESS NutrientCycling {
 MAY_BE_INFLUENCED_BY: ProtozoanFeedingAndExcretion
}

ENTITY SymbioticProtozoan {
 PARTICIPATES_IN: Symbiosis
 WITH: HostOrMicrobialPartner
}

ENTITY ParasiticProtozoan {
 LIVES_IN_OR_ON: Host
 MAY_CAUSE: HostDamageOrDisease
}

ENTITY ProtozoanPathogen {
 SUBCLASS_OF: ParasiticProtozoan
 MAY_CAUSE: Disease
 IN: SusceptibleHostContext
}

PROCESS ProtozoanColonization {
 ESTABLISHES: ProtozoanPopulation
 IN_OR_ON: Host
}

PROCESS ProtozoanInfection {
 INVOLVES: EntryPersistenceReplicationOrTissueInteraction
 IN: Host
}

RULE ColonizationInfectionDistinction {
 ProtozoanColonization != ProtozoanInfection
}

ENTITY HostCellInvasion {
 MAY_BE_USED_BY: IntracellularProtozoan
 TO_ENTER: HostCell
}

PROCESS Adhesion {
 ATTACHES: Protozoan
 TO: HostCellOrSurface
}

PROCESS Invasion {
 MOVES: ProtozoanOrStage
 INTO: HostTissueOrCell
}

ENTITY VirulenceFactor {
 MAY_CONTRIBUTE_TO: [Adhesion, Invasion, TissueDamage, ImmuneEvasion, NutrientAcquisition]
}

PROCESS ImmuneEvasion {
 REDUCES_OR_MODIFIES: HostImmuneResponse
}

ENTITY Vector {
 MAY_TRANSMIT: ProtozoanParasite
 BETWEEN: Hosts
}

PROCESS VectorBorneTransmission {
 USES: BiologicalVector
 TO_TRANSFER: ProtozoanParasite
}

ENTITY DefinitiveHost {
 SUPPORTS: DefinedSexualOrMatureLifeCycleStage
 IN: ApplicableParasiticLifeCycle
}

ENTITY IntermediateHost {
 SUPPORTS: DefinedDevelopmentalOrAsexualStage
 IN: ApplicableParasiticLifeCycle
}

RULE HostRoleConstraint {
 definitive_host != universally_primary_disease_host
 host_role MUST_BE_DEFINED_BY parasite_life_cycle
}

ENTITY ProtozoanDrug {
 ACTS_AGAINST: Protozoan
}

ENTITY AntiprotozoalResistance {
 DESCRIBES: ReducedSusceptibility
 TO: AntiprotozoalDrug
}

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

RULE ResistanceConstraint {
 resistance_variant_detection != phenotypic_drug_resistance
 WITHOUT functional_or_susceptibility_context
}

PROCESS ProtozoanCulture {
 GROWS: Protozoa
 UNDER: ControlledConditions
}

ENTITY CultureCondition {
 MAY_INCLUDE: [Medium, Temperature, pH, Oxygen, HostCells, Nutrients]
}

PROCESS ProtozoanIsolation {
 SEPARATES: ProtozoanPopulationOrClone
 FROM: MixedSample
}

PROCESS ProtozoanMicroscopy {
 VISUALIZES: [CellMorphology, MotilityStructures, Cysts, Trophozoites, IntracellularStages]
}

PROCESS ProtozoanStaining {
 ENHANCES: VisualizationOrDifferentiation
 OF: ProtozoanStructures
}

PROCESS MolecularIdentification {
 USES: NucleicAcidOrMolecularFeatures
 TO_SUPPORT: ProtozoanIdentification
}

PROCESS ProtozoanSequencing {
 DETERMINES: ProtozoanNucleicAcidSequence
 MAY_SUPPORT: [Identification, Genomics, Phylogeny]
}

PROCESS ProtozoanMetagenomics {
 ANALYSES: ProtozoanGeneticMaterial
 WITHIN: MixedCommunity
}

ENTITY ProtozoanTaxonomy {
 CLASSIFIES: ProtozoanLineages
 USING: [Morphology, Ultrastructure, LifeCycle, Phylogeny, Genomics, Nomenclature]
}

ENTITY ProtozoanSpecies {
 IS_A: TaxonomicConcept
 REQUIRES: PhylogeneticGenomicMorphologicalAndNomenclaturalContext
}

ENTITY ProtozoanStrain {
 IS_A: WithinSpeciesOrTaxonVariant
 HAS: DefinedIsolationOrGeneticContext
}

ENTITY ProtozoanPhylogeny {
 REPRESENTS: EvolutionaryRelationships
 AMONG: ProtozoanLineages
}

RULE IdentificationConstraint {
 morphology_or_sequence_similarity != definitive_protozoan_species_or_strain_identity
 WITHOUT resolution_reference_and_threshold_context
}

PROCESS ProtozoaMeasurement {
 MAY_MEASURE: [CellCount, Viability, GrowthRate, Motility, FeedingRate, LifeCycleStage, GeneExpression, DrugSusceptibility]
 MAY_USE: [Culture, Microscopy, Imaging, FlowCytometry, Sequencing, MolecularAssay, FunctionalAssay]
}

ENTITY ProtozoaMeasurementContext {
 HAS: [SpeciesOrStrain, SampleType, LifeCycleStage, EnvironmentOrHost, Temperature, pH, OxygenState, Method, Unit, Timepoint]
}

RULE MeasurementContextRule {
 IF protozoan_measurements ARE_COMPARED
 THEN ProtozoaMeasurementContext MUST_BE preserved
}

ENTITY Evidence {
 TYPES: [CultureEvidence, MicroscopyEvidence, MorphologicalEvidence, MolecularEvidence, GenomicEvidence, PhylogeneticEvidence, EcologicalEvidence, LifeCycleEvidence, PathogenicityEvidence, DrugSusceptibilityEvidence, ExperimentalEvidence, ComputationalEvidence, LiteratureEvidence]
}

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

RULE EvidenceConflict {
 IF EvidenceSources CONFLICT
 THEN {
  PRESERVE competing_protozoan_models
  RECORD species_or_strain
  RECORD sample_type
  RECORD life_cycle_stage
  RECORD environment_or_host
  RECORD temperature_pH_and_oxygen_state
  RECORD measurement_method
  RECORD timepoint
  RECORD provenance
  REDUCE confidence
 }
}

RELATION Protozoan HAS ProtozoanCell
RELATION ProtozoanCell HAS ProtozoanGenome
RELATION ProtozoanGenome CONTAINS ProtozoanGene
RELATION ProtozoanMotility MAY_USE Cilium
RELATION ProtozoanMotility MAY_USE Flagellum
RELATION ProtozoanMotility MAY_USE Pseudopodium
RELATION ProtozoanLifeCycle MAY_INCLUDE Trophozoite
RELATION ProtozoanLifeCycle MAY_INCLUDE Cyst
RELATION ParasiticProtozoan INTERACTS_WITH Host
RELATION ProtozoanSequencing SUPPORTS ProtozoanIdentification

SEMANTIC_EQUIVALENCE {
 "protozoa" ~= "diverse unicellular or microbial eukaryotes historically grouped as protozoans"
 "protozoan" ~= "single protozoan microbial eukaryote"
 "trophozoite" ~= "active feeding or growing protozoan stage" WHEN applicable
 "cyst" ~= "resistant or dormant protozoan stage" WHEN applicable
 "amoeboid movement" ~= "pseudopodia-associated cellular locomotion"
}

CONFIDENCE ProtozoaAssertion {
 INPUTS: [culture_support, microscopy_support, morphological_support, molecular_support, genomic_support, phylogenetic_support, ecological_support, life_cycle_support, functional_support, drug_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 ProtozoanGrowthInference {
 IF cell_number_or_biomass increases_over_time
 UNDER defined_conditions
 THEN ProtozoanGrowth MAY_BE_SUPPORTED
}

RULE LifeCycleInference {
 IF morphologically_or_molecularly_distinct_stages transition_reproducibly
 THEN ProtozoanLifeCycleRelationship MAY_BE_SUPPORTED
}

RULE ProtozoanIdentityInference {
 IF morphological_molecular_genomic_and_phylogenetic_evidence converge
 THEN protozoan_taxonomic_identity confidence MAY_INCREASE
}

RULE HostInteractionInference {
 IF protozoan_presence_and_replication coincide_with host_cell_or_tissue_effect
 AND mechanistic_evidence_supports_interaction
 THEN host_protozoan_relationship MAY_BE_SUPPORTED
}

RULE CausalityConstraint {
 IF protozoan_feature correlates_with host_or_environmental_state
 THEN DO_NOT_INFER causal_relationship
 WITHOUT mechanistic_or_interventional_evidence
}

QUERY ProtozoaLookup(protozoan_identifier) {
 RETURN [taxonomy, species_or_strain, morphology, motility, genome, metabolism, nutrition, life_cycle, habitat, host_interactions, drug_susceptibility, evidence, confidence]
}

QUERY ProtozoanLifeCycleLookup(context_identifier) {
 RETURN [stages, transitions, reproductive_mode, hosts, vectors, environmental_stages, transmission, developmental_conditions, evidence, confidence]
}

QUERY ProtozoanCommunityLookup(sample_identifier) {
 RETURN [protozoan_taxa, abundance, diversity, feeding_modes, ecological_functions, environmental_context, interactions, methods, evidence, confidence]
}

UPDATE_MODEL {
 ON new_protozoan_evidence:
  validate_provenance()
  identify_sample_species_strain_life_cycle_and_environmental_context()
  normalize_taxonomic_gene_metabolite_host_and_drug_identifiers()
  capture_morphology_motility_and_organelle_features()
  capture_environment_host_temperature_pH_oxygen_and_nutrient_state()
  capture_measurement_method_units_and_timepoint()
  map_growth_metabolism_nutrition_and_gene_expression()
  map_life_cycle_reproduction_encystment_and_excystment()
  map_population_grazing_symbiosis_and_ecological_relationships()
  map_host_interactions_transmission_virulence_and_drug_response()
  compare_existing_protozoan_models()
  preserve_conflicting_evidence()
  recalculate_confidence()
  regenerate_protozoan_relationships()
  update_flow_hash()
}

AI_CONSUMPTION {
 MODE: FormalSemanticReasoning
 PARSE_AS: ExecutableFlowAlgebra
 PRIORITIES: [protozoan_identity, species_or_strain, life_cycle_stage, morphology, motility, nutrition, metabolism, habitat, host_interaction, drug_response, evidence_provenance, confidence]
 REQUIREMENTS: [preserve_species_strain_and_sample_context, preserve_life_cycle_stage, preserve_environment_or_host_context, preserve_taxonomic_resolution, recognize_protozoa_as_diverse_nonmonophyletic_grouping_when_required, distinguish_protozoan_cyst_from_bacterial_endospore, distinguish_colonization_from_infection, distinguish_host_role_from_disease_severity, distinguish_resistance_variant_from_phenotypic_resistance, distinguish_morphology_or_sequence_similarity_from_definitive_identity, distinguish_correlation_from_causation, preserve_uncertainty]
}

VALIDATE {
 REQUIRE Protozoan
 REQUIRE ProtozoanCell
 REQUIRE ProtozoanGenome
 REQUIRE ProtozoanMotility
 REQUIRE ProtozoanNutrition
 REQUIRE ProtozoanMetabolism
 REQUIRE ProtozoanGrowth
 REQUIRE ProtozoanLifeCycle
 REQUIRE Trophozoite
 REQUIRE Cyst
 REQUIRE ProtozoanPopulation
 REQUIRE ProtozoanCommunity
 REQUIRE ParasiticProtozoan
 REQUIRE ProtozoanTaxonomy
 REQUIRE ProtozoaMeasurement
 REQUIRE Evidence
 REQUIRE CONFIDENCE
 REQUIRE SEMANTIC_EQUIVALENCE
 REQUIRE UPDATE_MODEL
 REQUIRE AI_CONSUMPTION

 ASSERT Protozoan != Bacterium
 ASSERT ProtozoanCell != ProkaryoticCell
 ASSERT protozoan_cyst != bacterial_endospore
 ASSERT ProtozoanColonization != ProtozoanInfection
 ASSERT definitive_host != universally_primary_disease_host
 ASSERT resistance_variant_detection != phenotypic_drug_resistance
 ASSERT morphology_or_sequence_similarity != definitive_protozoan_species_or_strain_identity
 ASSERT correlation != causal_relationship
}

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 "ProtozoaOntology"