Fungi Ontology

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

flow "FungiOntology" v1.0

ENTITY FungiOntology {
 TYPE: BiologicalOntology
 DOMAIN: Microbiology
 SUBJECT: Fungi
 PURPOSE: FormalSemanticRepresentation
}

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

ENTITY Fungus {
 IS_A: EukaryoticOrganism
 KINGDOM: Fungi
 MAY_EXIST_AS: [Yeast, FilamentousFungus, DimorphicFungus]
 OBTAINS_NUTRIENTS_BY: AbsorptiveHeterotrophy
}

ENTITY FungalCell {
 IS_A: EukaryoticCell
 HAS: [Nucleus, CellMembrane, Cytoplasm, Ribosome, Mitochondrion]
 TYPICALLY_HAS: FungalCellWall
}

ENTITY FungalCellWall {
 MAY_CONTAIN: [Chitin, Glucan, Mannoprotein]
 PROVIDES: StructuralSupport
}

ENTITY FungalMembrane {
 MAY_CONTAIN: Ergosterol
}

RULE CellularConstraint {
 Fungus != Bacterium
 FungalCell != ProkaryoticCell
}

ENTITY Yeast {
 IS_A: UnicellularOrPredominantlyUnicellularFungalForm
 MAY_REPRODUCE_BY: [Budding, Fission]
}

ENTITY FilamentousFungus {
 FORMS: Hyphae
 MAY_FORM: Mycelium
}

ENTITY Hypha {
 IS_A: FilamentousFungalStructure
 MAY_BE: [SeptateHypha, CoenocyticHypha]
}

ENTITY Mycelium {
 IS_A: NetworkOfHyphae
}

ENTITY DimorphicFungus {
 MAY_TRANSITION_BETWEEN: DistinctMorphologicalForms
 IN_RESPONSE_TO: EnvironmentalOrHostConditions
}

RULE DimorphismConstraint {
 fungal_dimorphism MUST_PRESERVE species_environment_and_temperature_context
}

PROCESS FungalGrowth {
 INCREASES: FungalBiomassOrCellNumber
 MAY_USE: [HyphalExtension, Branching, Budding, CellDivision]
}

PROCESS HyphalExtension { EXTENDS: HyphalTip }
PROCESS HyphalBranching { GENERATES: NewHyphalBranches }
PROCESS YeastBudding { PRODUCES: DaughterCell FROM: ParentYeastCell }

RULE GrowthContextRule {
 fungal_growth MUST_PRESERVE [
  species_or_strain,
  substrate_or_medium,
  temperature,
  pH,
  oxygen_state,
  water_activity,
  timepoint
 ]
}

ENTITY FungalMetabolism {
 INCLUDES: [Catabolism, Anabolism, Respiration, Fermentation, SecondaryMetabolism]
}

PROCESS AerobicRespiration {
 USES: Oxygen
 AS: TerminalElectronAcceptor
}

PROCESS FungalFermentation {
 CONSERVES: MetabolicEnergy
 WITHOUT_REQUIRING: AerobicRespiration
}

PROCESS ExtracellularDigestion {
 BREAKS_DOWN: ComplexSubstrate
 OUTSIDE: FungalCell
}

PROCESS NutrientAbsorption {
 MOVES: SolubleNutrients
 INTO: FungalCell
}

ENTITY FungalGenome {
 STORES: HeritableGeneticInformation
 ORGANIZED_IN: EukaryoticChromosomes
}

ENTITY FungalGene {
 PART_OF: FungalGenome
 MAY_ENCODE: [Protein, FunctionalRNA]
}

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

PROCESS FungalGeneRegulation {
 MODULATES: GeneExpression
 IN_RESPONSE_TO: [Development, Nutrients, Stress, HostSignals]
}

PROCESS Mutation {
 CHANGES: FungalGeneticSequence
 MAY_GENERATE: GeneticVariation
}

PROCESS FungalReproduction {
 MAY_BE: [AsexualReproduction, SexualReproduction]
}

PROCESS AsexualReproduction {
 MAY_PRODUCE: [AsexualSpore, BuddedCell, Fragment]
}

PROCESS SexualReproduction {
 INVOLVES: [CompatibleCellFusion, NuclearProcesses, Meiosis]
 MAY_PRODUCE: SexualSpore
}

ENTITY FungalSpore {
 IS_A: ReproductiveOrDispersalCell
 MAY_BE: [AsexualSpore, SexualSpore]
}

PROCESS Sporulation {
 PRODUCES: FungalSpores
}

PROCESS SporeGermination {
 INITIATES: NewFungalGrowth
 UNDER: SuitableConditions
}

RULE SporeConstraint {
 fungal_spore != bacterial_endospore
}

ENTITY FungalLifeCycle {
 MAY_INCLUDE: [HaploidStage, DiploidStage, DikaryoticStage, AsexualStage]
 DEPENDS_ON: FungalLineage
}

ENTITY FungalPopulation {
 COMPOSED_OF: FungalIndividualsOrCells
}

ENTITY FungalCommunity {
 MAY_INCLUDE: MultipleFungalTaxa
 OCCURS_IN: DefinedEnvironment
}

ENTITY Mycobiome {
 REPRESENTS: FungalComponentOfMicrobialCommunity
 IN: DefinedEnvironment
}

PROCESS FungalInteraction {
 MAY_BE: [Competition, Mutualism, Commensalism, Parasitism, Predation]
}

ENTITY Mycorrhiza {
 IS_A: SymbioticAssociation
 BETWEEN: Fungus
 AND: PlantRoot
}

ENTITY Lichen {
 IS_A: SymbioticAssociation
 INVOLVES: FungusAndPhotosyntheticPartner
}

ENTITY SaprotrophicFungus {
 OBTAINS_NUTRIENTS_FROM: DeadOrganicMatter
}

PROCESS Decomposition {
 BREAKS_DOWN: OrganicMatter
 MAY_BE_MEDIATED_BY: Fungi
}

ENTITY FungalHabitat {
 MAY_INCLUDE: [Soil, PlantSurface, PlantTissue, AnimalHost, Freshwater, MarineEnvironment, BuiltEnvironment]
}

ENTITY EnvironmentalFactor {
 MAY_INCLUDE: [Temperature, pH, Moisture, WaterActivity, Oxygen, Nutrients, Light]
 MAY_MODULATE: FungalPhysiology
}

ENTITY HostAssociatedFungus {
 OCCURS_IN_OR_ON: Host
 MAY_BE: [Commensal, Mutualist, Pathogen]
}

ENTITY FungalPathogen {
 SUBCLASS_OF: Fungus
 MAY_CAUSE: Disease
 IN: SusceptibleHostContext
}

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

PROCESS FungalColonization {
 ESTABLISHES: FungalPopulation
 IN_OR_ON: Host
}

PROCESS FungalInfection {
 INVOLVES: FungalGrowthPersistenceOrTissueInteraction
 IN: Host
}

RULE ColonizationInfectionDistinction {
 FungalColonization != FungalInfection
}

ENTITY Mycotoxin {
 IS_A: FungalSecondaryMetabolite
 MAY_HAVE: ToxicBiologicalEffects
}

RULE MycotoxinConstraint {
 presence_of_toxigenic_species != demonstrated_mycotoxin_exposure
 WITHOUT toxin_measurement
}

ENTITY AntifungalAgent {
 ACTS_AGAINST: Fungus
 MAY_TARGET: [CellMembrane, CellWall, NucleicAcidSynthesis, Mitosis]
}

ENTITY AntifungalResistance {
 DESCRIBES: ReducedSusceptibility
 TO: AntifungalAgent
}

ENTITY ResistanceMechanism {
 MAY_INCLUDE: [TargetModification, Efflux, TargetOverexpression, PathwayAlteration, BiofilmAssociatedTolerance]
}

PROCESS AntifungalSusceptibilityTesting {
 MEASURES: FungalResponseToAntifungalAgent
}

ENTITY MinimumInhibitoryConcentration {
 ABBREVIATION: MIC
 DESCRIBES: LowestTestedConcentrationPreventingDefinedGrowth
 UNDER: StandardizedAssayConditions
}

RULE ResistanceConstraint {
 resistance_variant_detection != phenotypic_antifungal_resistance
 WITHOUT expression_and_susceptibility_context
}

ENTITY FungalBiofilm {
 IS_A: StructuredFungalOrMixedMicrobialCommunity
 ASSOCIATED_WITH: SurfaceOrTissue
}

PROCESS FungalBiofilmFormation {
 MAY_INCLUDE: [Adhesion, Growth, MatrixProduction, Maturation, Dispersal]
}

PROCESS FungalCulture {
 GROWS: Fungus
 UNDER: ControlledConditions
}

PROCESS FungalIsolation {
 SEPARATES: FungalPopulationOrClone
 FROM: MixedSample
}

PROCESS FungalMicroscopy {
 VISUALIZES: [YeastCells, Hyphae, Spores, ReproductiveStructures]
}

PROCESS MolecularIdentification {
 USES: NucleicAcidOrMolecularFeatures
 TO_SUPPORT: FungalIdentification
}

PROCESS FungalSequencing {
 DETERMINES: FungalNucleicAcidSequence
 MAY_SUPPORT: [Identification, Genomics, Phylogeny]
}

PROCESS FungalMetagenomics {
 ANALYSES: FungalGeneticMaterial
 WITHIN: MixedCommunity
}

ENTITY FungalTaxonomy {
 CLASSIFIES: Fungi
 USING: [Morphology, Reproduction, Phylogeny, Genomics, Nomenclature]
}

ENTITY FungalSpecies {
 IS_A: TaxonomicConcept
 REQUIRES: PhylogeneticGenomicMorphologicalAndNomenclaturalContext
}

ENTITY FungalStrain {
 IS_A: WithinSpeciesOrTaxonVariant
 HAS: DefinedIsolationOrGeneticContext
}

RULE TaxonomyConstraint {
 sequence_similarity != definitive_fungal_species_or_strain_identity
 WITHOUT reference_resolution_and_threshold_context
}

PROCESS FungiMeasurement {
 MAY_MEASURE: [CellCount, Biomass, HyphalGrowth, SporeCount, Viability, Metabolism, GeneExpression, AntifungalSusceptibility]
 MAY_USE: [Culture, Microscopy, Imaging, Sequencing, MassSpectrometry, MolecularAssay, SusceptibilityTesting]
}

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

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

RULE EvidenceConflict {
 IF EvidenceSources CONFLICT
 THEN {
  PRESERVE competing_fungal_models
  RECORD species_or_strain
  RECORD sample_type
  RECORD substrate_or_medium
  RECORD temperature_pH_water_activity_and_oxygen_state
  RECORD measurement_method
  RECORD timepoint
  RECORD provenance
  REDUCE confidence
 }
}

RELATION Fungus HAS FungalCell
RELATION FilamentousFungus FORMS Hypha
RELATION Hyphae FORM Mycelium
RELATION FungalGenome CONTAINS FungalGene
RELATION FungalReproduction PRODUCES FungalSpore
RELATION Fungus MAY_FORM FungalBiofilm
RELATION Mycorrhiza CONNECTS Fungus TO PlantRoot
RELATION FungalPathogen MAY_CAUSE FungalInfection
RELATION AntifungalAgent ACTS_ON Fungus
RELATION FungalSequencing SUPPORTS FungalIdentification

SEMANTIC_EQUIVALENCE {
 "fungi" ~= "organisms of kingdom Fungi" WHEN taxonomic_context
 "fungus" ~= "single fungal organism"
 "hypha" ~= "filamentous fungal growth structure"
 "mycelium" ~= "network of fungal hyphae"
 "mycobiome" ~= "fungal component of a microbiome"
 "MIC" ~= "minimum inhibitory concentration"
}

CONFIDENCE FungiAssertion {
 INPUTS: [culture_support, microscopy_support, morphological_support, biochemical_support, molecular_support, genomic_support, phylogenetic_support, ecological_support, functional_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 FungalGrowthInference {
 IF biomass_cell_number_or_hyphal_extent increases_over_time
 UNDER defined_conditions
 THEN FungalGrowth MAY_BE_SUPPORTED
}

RULE FungalIdentityInference {
 IF morphological_molecular_genomic_and_phylogenetic_evidence converge
 THEN fungal_taxonomic_identity confidence MAY_INCREASE
}

RULE DimorphismInference {
 IF same_fungal_lineage reproducibly_changes_morphological_form
 WITH environmental_or_host_condition
 THEN fungal_dimorphism MAY_BE_SUPPORTED
}

RULE ResistanceInference {
 IF standardized_susceptibility_testing demonstrates_reduced_susceptibility
 THEN AntifungalResistance MAY_BE_SUPPORTED
 WITH species_agent_and_method_context
}

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

QUERY FungiLookup(fungal_identifier) {
 RETURN [taxonomy, species_or_strain, morphology, cell_wall, membrane, genome, metabolism, reproduction, growth_conditions, habitat, host_interactions, antifungal_susceptibility, evidence, confidence]
}

QUERY FungalGrowthLookup(context_identifier) {
 RETURN [growth_form, hyphal_extension, branching, budding, biomass, sporulation, substrate, environmental_conditions, measurements, evidence, confidence]
}

QUERY FungalCommunityLookup(sample_identifier) {
 RETURN [fungal_taxa, abundance, diversity, growth_forms, ecological_functions, environmental_context, interactions, methods, evidence, confidence]
}

UPDATE_MODEL {
 ON new_fungal_evidence:
  validate_provenance()
  identify_sample_species_strain_and_environmental_context()
  normalize_taxonomic_gene_metabolite_and_antifungal_identifiers()
  capture_morphology_cell_wall_membrane_and_growth_form()
  capture_substrate_temperature_pH_water_activity_oxygen_and_nutrient_state()
  capture_measurement_method_units_and_timepoint()
  map_growth_metabolism_gene_expression_and_reproduction()
  map_genomic_phylogenetic_and_life_cycle_relationships()
  map_population_biofilm_symbiosis_and_ecological_relationships()
  map_host_interactions_virulence_mycotoxins_and_antifungal_response()
  compare_existing_fungal_models()
  preserve_conflicting_evidence()
  recalculate_confidence()
  regenerate_fungal_relationships()
  update_flow_hash()
}

AI_CONSUMPTION {
 MODE: FormalSemanticReasoning
 PARSE_AS: ExecutableFlowAlgebra
 PRIORITIES: [fungal_identity, species_or_strain, growth_form, cell_wall_and_membrane, growth_conditions, metabolism, genome, reproduction, ecological_context, host_interaction, antifungal_susceptibility, evidence_provenance, confidence]
 REQUIREMENTS: [preserve_species_strain_and_sample_context, preserve_substrate_and_environmental_conditions, preserve_taxonomic_resolution, distinguish_fungus_from_bacterium, distinguish_yeast_from_filamentous_growth_form, distinguish_fungal_spore_from_bacterial_endospore, preserve_dimorphism_context, distinguish_colonization_from_infection, distinguish_toxigenic_species_presence_from_mycotoxin_exposure, distinguish_resistance_variant_from_phenotypic_resistance, distinguish_sequence_similarity_from_definitive_identity, distinguish_correlation_from_causation, preserve_uncertainty]
}

VALIDATE {
 REQUIRE Fungus
 REQUIRE FungalCell
 REQUIRE FungalCellWall
 REQUIRE FungalMembrane
 REQUIRE Yeast
 REQUIRE FilamentousFungus
 REQUIRE Hypha
 REQUIRE Mycelium
 REQUIRE FungalGrowth
 REQUIRE FungalMetabolism
 REQUIRE FungalGenome
 REQUIRE FungalReproduction
 REQUIRE FungalSpore
 REQUIRE FungalCommunity
 REQUIRE FungalPathogen
 REQUIRE AntifungalResistance
 REQUIRE FungiMeasurement
 REQUIRE Evidence
 REQUIRE CONFIDENCE
 REQUIRE SEMANTIC_EQUIVALENCE
 REQUIRE UPDATE_MODEL
 REQUIRE AI_CONSUMPTION

 ASSERT Fungus != Bacterium
 ASSERT FungalCell != ProkaryoticCell
 ASSERT fungal_spore != bacterial_endospore
 ASSERT FungalColonization != FungalInfection
 ASSERT resistance_variant_detection != phenotypic_antifungal_resistance
 ASSERT sequence_similarity != definitive_fungal_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 "FungiOntology"