Bacteria Ontology

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

flow "BacteriaOntology" v1.0

ENTITY BacteriaOntology {
 TYPE: BiologicalOntology
 DOMAIN: Microbiology
 SUBJECT: Bacteria
 PURPOSE: FormalSemanticRepresentation
}

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

ENTITY Bacterium {
 IS_A: CellularMicroorganism
 DOMAIN: Bacteria
 CELL_TYPE: Prokaryotic
 MAY_EXIST_AS: [SingleCell, Colony, BiofilmAssociatedCell]
}

ENTITY BacterialCell {
 HAS: [CellMembrane, Cytoplasm, Ribosome, Genome]
 MAY_HAVE: [CellWall, OuterMembrane, Capsule, Flagellum, Pilus, Endospore]
}

ENTITY BacterialGenome {
 STORES: HeritableGeneticInformation
 MAY_INCLUDE: [Chromosome, Plasmid, MobileGeneticElement]
}

ENTITY BacterialChromosome {
 IS_PART_OF: BacterialGenome
 TYPICALLY_CONTAINS: EssentialAndAccessoryGenes
}

ENTITY Plasmid {
 IS_A: ExtrachromosomalGeneticElement
 MAY_CARRY: [ResistanceGene, VirulenceGene, MetabolicGene]
}

ENTITY CellMembrane {
 CONTROLS: MolecularExchange
 SUPPORTS: BioenergeticProcesses
}

ENTITY BacterialCellWall {
 PROVIDES: StructuralSupport
 MAY_CONTAIN: Peptidoglycan
}

ENTITY Peptidoglycan {
 IS_A: CellWallPolymer
 CONTRIBUTES_TO: BacterialCellWallStructure
}

ENTITY GramPositiveBacterium {
 HAS: GramPositiveCellEnvelopeArchitecture
}

ENTITY GramNegativeBacterium {
 HAS: GramNegativeCellEnvelopeArchitecture
 MAY_HAVE: OuterMembrane
}

ENTITY OuterMembrane {
 PART_OF: GramNegativeCellEnvelope
 MAY_CONTAIN: Lipopolysaccharide
}

ENTITY Lipopolysaccharide {
 ABBREVIATION: LPS
 IS_A: OuterMembraneComponent
 IN: ManyGramNegativeBacteria
}

RULE GramClassificationConstraint {
 gram_stain_result != complete_taxonomic_identity
}

ENTITY Capsule {
 IS_A: ExtracellularSurfaceLayer
 MAY_SUPPORT: [Adhesion, DesiccationResistance, ImmuneEvasion]
}

ENTITY Flagellum {
 MAY_ENABLE: Motility
}

ENTITY Pilus {
 MAY_SUPPORT: [Adhesion, Conjugation]
}

ENTITY Endospore {
 IS_A: DormantResistantCellularStructure
 PRODUCED_BY: CertainBacteria
}

PROCESS Sporulation {
 PRODUCES: Endospore
 IN: ApplicableBacterialTaxa
}

PROCESS Germination {
 RETURNS: Endospore
 TO: VegetativeGrowthState
 UNDER: SuitableConditions
}

PROCESS BinaryFission {
 DIVIDES: BacterialCell
 INTO: DaughterCells
}

ENTITY BacterialGrowth {
 DESCRIBES: IncreaseInCellNumberOrBiomass
}

ENTITY GrowthPhase {
 MAY_BE: [LagPhase, ExponentialPhase, StationaryPhase, DeclinePhase]
}

ENTITY SpecificGrowthRate {
 SYMBOL: mu
 DESCRIBES: RelativePopulationGrowthPerTime
}

RULE ExponentialGrowthModel {
 N_t := N_0 * exp(mu * t)
 UNDER exponential_growth_conditions
}

ENTITY GenerationTime {
 DESCRIBES: PopulationDoublingTime
 UNDER: DefinedConditions
}

RULE GrowthContextRule {
 bacterial_growth MUST_PRESERVE [
  strain,
  medium,
  temperature,
  pH,
  oxygen_state,
  nutrient_state,
  timepoint
 ]
}

ENTITY BacterialMetabolism {
 MAY_INCLUDE: [Respiration, Fermentation, Photosynthesis, Chemolithotrophy, Heterotrophy]
}

PROCESS AerobicRespiration {
 USES: Oxygen
 AS: TerminalElectronAcceptor
}

PROCESS AnaerobicRespiration {
 USES: NonOxygenTerminalElectronAcceptor
}

PROCESS Fermentation {
 CONSERVES: MetabolicEnergy
 WITHOUT_EXTERNAL_RESPIRATORY_TERMINAL_ACCEPTOR
}

RULE MetabolicDistinction {
 AnaerobicRespiration != Fermentation
}

ENTITY OxygenRelationship {
 MAY_BE: [ObligateAerobe, FacultativeAnaerobe, ObligateAnaerobe, Microaerophile, AerotolerantBacterium]
}

ENTITY BacterialGene {
 PART_OF: BacterialGenome
 MAY_ENCODE: [Protein, FunctionalRNA]
}

PROCESS BacterialGeneExpression {
 INCLUDES: [Transcription, Translation]
}

ENTITY Operon {
 ORGANIZES: FunctionallyRelatedGenes
 MAY_ENABLE: CoordinatedGeneExpression
}

PROCESS BacterialGeneRegulation {
 MODULATES: GeneExpression
 IN_RESPONSE_TO: CellularOrEnvironmentalSignals
}

PROCESS Mutation {
 CHANGES: BacterialGeneticSequence
 MAY_GENERATE: Variation
}

PROCESS Recombination {
 REARRANGES_OR_EXCHANGES: GeneticMaterial
}

PROCESS HorizontalGeneTransfer {
 TRANSFERS: GeneticMaterial
 BETWEEN: BacterialCellsOrLineages
 MAY_INCLUDE: [Transformation, Transduction, Conjugation]
}

PROCESS Transformation {
 ACQUIRES: ExtracellularDNA
}

PROCESS Transduction {
 TRANSFERS: GeneticMaterial
 VIA: Bacteriophage
}

PROCESS Conjugation {
 TRANSFERS: GeneticMaterial
 THROUGH: CellAssociatedMechanism
 MAY_INVOLVE: ConjugativePilus
}

RULE HGTConstraint {
 shared_gene != demonstrated_horizontal_gene_transfer
 WITHOUT genomic_phylogenetic_or_mechanistic_evidence
}

ENTITY Bacteriophage {
 IS_A: Virus
 INFECTS: Bacterium
}

PROCESS PhageInfection {
 MAY_INCLUDE: [Attachment, Entry, GenomeReplication, Assembly, Release]
}

PROCESS LyticCycle {
 PRODUCES: PhageProgeny
 MAY_LYSE: BacterialCell
}

PROCESS Lysogeny {
 MAINTAINS: PhageGeneticMaterial
 WITHIN: BacterialLineage
 IN: ApplicableContext
}

ENTITY BacterialPopulation {
 COMPOSED_OF: BacterialCells
}

ENTITY BacterialCommunity {
 COMPOSED_OF: MultipleBacterialPopulations
}

PROCESS BacterialInteraction {
 MAY_BE: [Competition, Cooperation, Mutualism, Commensalism, Antagonism, Syntrophy]
}

ENTITY Biofilm {
 IS_A: StructuredMicrobialCommunity
 MAY_INCLUDE: BacterialCells
 EMBEDDED_IN: ExtracellularPolymericMatrix
}

PROCESS BiofilmFormation {
 MAY_INCLUDE: [Attachment, MicrocolonyFormation, MatrixProduction, Maturation, Dispersal]
}

ENTITY ExtracellularPolymericSubstance {
 ABBREVIATION: EPS
 CONTRIBUTES_TO: BiofilmMatrix
}

PROCESS QuorumSensing {
 USES: PopulationAssociatedChemicalSignals
 MAY_REGULATE: CollectiveBacterialBehaviour
}

RULE QuorumConstraint {
 signal_detection != demonstrated_quorum_regulation
 WITHOUT density_dependent_functional_evidence
}

ENTITY BacterialMotility {
 MAY_INCLUDE: [Swimming, Swarming, Twitching, Gliding]
}

PROCESS Chemotaxis {
 DIRECTS: BacterialMovement
 IN_RESPONSE_TO: ChemicalGradient
}

ENTITY BacterialHabitat {
 MAY_INCLUDE: [Soil, Water, Sediment, Host, BuiltEnvironment, ExtremeEnvironment]
}

ENTITY EnvironmentalFactor {
 MAY_INCLUDE: [Temperature, pH, Salinity, Oxygen, Nutrients, Pressure]
 MAY_MODULATE: BacterialPhysiology
}

PROCESS BacterialEcologicalResponse {
 MAY_CHANGE: [Growth, Metabolism, GeneExpression, CommunityComposition]
 IN_RESPONSE_TO: EnvironmentalFactor
}

PROCESS BiogeochemicalCycling {
 MAY_BE_MEDIATED_BY: Bacteria
 MAY_INCLUDE: [CarbonCycling, NitrogenCycling, SulfurCycling, PhosphorusCycling]
}

ENTITY HostAssociatedBacterium {
 OCCURS_IN_OR_ON: Host
}

PROCESS HostBacteriumInteraction {
 MAY_BE: [Mutualistic, Commensal, Pathogenic, ContextDependent]
}

ENTITY BacterialPathogen {
 SUBCLASS_OF: Bacterium
 MAY_CAUSE: HostDamageOrDisease
 IN: SusceptibleContext
}

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

ENTITY BacterialToxin {
 IS_A: VirulenceAssociatedMolecule
 MAY_MODIFY_OR_DAMAGE: HostCellOrPhysiology
}

PROCESS Colonization {
 ESTABLISHES: BacterialPopulation
 IN_OR_ON: Host
}

PROCESS BacterialInfection {
 INVOLVES: EntryPersistenceReplicationOrHostInteraction
 BY: Bacterium
}

RULE ColonizationInfectionDistinction {
 Colonization != BacterialInfection
}

ENTITY AntibacterialAgent {
 ACTS_AGAINST: Bacterium
}

ENTITY Antibiotic {
 SUBCLASS_OF: AntibacterialAgent
}

ENTITY AntimicrobialResistance {
 DESCRIBES: ReducedSusceptibility
 TO: AntibacterialAgent
}

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

ENTITY ResistanceGene {
 MAY_ENCODE_OR_CONTRIBUTE_TO: ResistanceMechanism
}

PROCESS ResistanceEvolution {
 MAY_OCCUR_THROUGH: [Mutation, Selection, HorizontalGeneTransfer]
}

ENTITY MinimumInhibitoryConcentration {
 ABBREVIATION: MIC
 DESCRIBES: LowestTestedConcentrationPreventingVisibleGrowth
 UNDER: DefinedAssayConditions
}

PROCESS AntimicrobialSusceptibilityTesting {
 ABBREVIATION: AST
 MEASURES: BacterialResponseToAntimicrobial
}

RULE ResistanceConstraint {
 resistance_gene_detection != phenotypic_resistance
 WITHOUT expression_and_AST_context
}

ENTITY BacterialCulture {
 GROWS: Bacteria
 UNDER: ControlledConditions
}

ENTITY CultureMedium {
 PROVIDES: NutrientsAndEnvironmentalConditions
}

PROCESS Cultivation {
 GROWS_OR_MAINTAINS: BacterialPopulation
}

PROCESS Isolation {
 SEPARATES: BacterialPopulationOrClone
 FROM: MixedSample
}

ENTITY PureCulture {
 CONTAINS_PRIMARILY: SingleBacterialType
}

PROCESS GramStaining {
 CLASSIFIES: BacterialCellEnvelopeStainingPhenotype
}

PROCESS AcidFastStaining {
 MAY_IDENTIFY: AcidFastCellEnvelopePhenotype
}

PROCESS Microscopy {
 VISUALIZES: BacterialCellsAndStructures
}

PROCESS BiochemicalTesting {
 MEASURES: BacterialMetabolicOrEnzymaticPhenotype
}

PROCESS MolecularIdentification {
 USES: NucleicAcidOrMolecularFeatures
 TO_SUPPORT: BacterialIdentification
}

PROCESS Sequencing {
 DETERMINES: NucleicAcidSequence
 MAY_SUPPORT: [Identification, Genomics, Phylogeny]
}

PROCESS WholeGenomeSequencing {
 ABBREVIATION: WGS
 DETERMINES: BroadGenomeSequence
}

ENTITY BacterialTaxonomy {
 CLASSIFIES: Bacteria
 USING: [Phylogeny, Genomics, Phenotype, Nomenclature]
}

ENTITY BacterialSpecies {
 IS_A: TaxonomicConcept
 DEFINITION_DEPENDS_ON: GenomicPhylogeneticAndNomenclaturalContext
}

ENTITY BacterialStrain {
 IS_A: WithinSpeciesOrTaxonVariant
 HAS: DefinedIsolationOrGeneticContext
}

RULE TaxonomyConstraint {
 sequence_similarity != definitive_species_or_strain_identity
 WITHOUT resolution_reference_and_threshold_context
}

PROCESS BacteriaMeasurement {
 MAY_MEASURE: [CellCount, Viability, Biomass, GrowthRate, Metabolism, GeneExpression, Motility, Susceptibility]
 MAY_USE: [Culture, Microscopy, Spectrophotometry, FlowCytometry, Sequencing, MassSpectrometry, MolecularAssay]
}

ENTITY BacteriaMeasurementContext {
 HAS: [SpeciesOrStrain, SampleType, MediumOrEnvironment, Temperature, pH, OxygenState, Method, Unit, Timepoint]
}

RULE MeasurementContextRule {
 IF bacterial_measurements ARE_COMPARED
 THEN BacteriaMeasurementContext MUST_BE preserved
}

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

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

RULE EvidenceConflict {
 IF EvidenceSources CONFLICT
 THEN {
  PRESERVE competing_bacterial_models
  RECORD species_or_strain
  RECORD sample_type
  RECORD environment_or_medium
  RECORD temperature_pH_and_oxygen_state
  RECORD measurement_method
  RECORD timepoint
  RECORD provenance
  REDUCE confidence
 }
}

RELATION Bacterium HAS BacterialCell
RELATION BacterialCell HAS BacterialGenome
RELATION BacterialGenome CONTAINS BacterialGene
RELATION BinaryFission PRODUCES DaughterCells
RELATION HorizontalGeneTransfer MOVES GeneticMaterial
RELATION Bacteriophage INFECTS Bacterium
RELATION BacterialPopulation MAY_FORM Biofilm
RELATION VirulenceFactor MAY_SUPPORT BacterialInfection
RELATION AntibacterialAgent ACTS_ON Bacterium
RELATION Sequencing SUPPORTS BacterialIdentification

SEMANTIC_EQUIVALENCE {
 "bacteria" ~= "domain Bacteria organisms" WHEN taxonomic_context
 "bacterium" ~= "single bacterial organism or cell"
 "HGT" ~= "horizontal gene transfer"
 "EPS" ~= "extracellular polymeric substance" WHEN biofilm_context
 "AST" ~= "antimicrobial susceptibility testing"
 "MIC" ~= "minimum inhibitory concentration"
 "WGS" ~= "whole genome sequencing"
}

CONFIDENCE BacteriaAssertion {
 INPUTS: [culture_support, microscopy_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 BacterialGrowthInference {
 IF cell_number_or_biomass increases_over_time
 UNDER defined_conditions
 THEN BacterialGrowth MAY_BE_SUPPORTED
}

RULE BacterialIdentityInference {
 IF genomic_phylogenetic_and_phenotypic_evidence converge
 THEN bacterial_taxonomic_identity confidence MAY_INCREASE
}

RULE HorizontalTransferInference {
 IF genomic_phylogenetic_and_contextual_evidence support_nonvertical_acquisition
 THEN HorizontalGeneTransfer MAY_BE_SUPPORTED
}

RULE ResistanceInference {
 IF standardized_AST demonstrates_reduced_susceptibility
 THEN AntimicrobialResistance MAY_BE_SUPPORTED
 WITH strain_agent_and_method_context
}

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

QUERY BacteriaLookup(bacterial_identifier) {
 RETURN [taxonomy, species_or_strain, morphology, cell_envelope, genome, metabolism, growth_conditions, motility, habitat, host_interactions, antimicrobial_susceptibility, evidence, confidence]
}

QUERY BacterialGenomeLookup(genome_identifier) {
 RETURN [chromosome, plasmids, genes, mobile_elements, resistance_genes, virulence_genes, horizontal_transfer_evidence, phylogeny, evidence, confidence]
}

QUERY BacterialPopulationLookup(sample_identifier) {
 RETURN [species_or_strains, abundance, growth_state, biofilm_state, metabolism, environmental_context, interactions, susceptibility, methods, evidence, confidence]
}

UPDATE_MODEL {
 ON new_bacterial_evidence:
  validate_provenance()
  identify_sample_species_strain_and_environmental_context()
  normalize_taxonomic_gene_metabolite_and_antimicrobial_identifiers()
  capture_cell_envelope_and_morphological_features()
  capture_medium_temperature_pH_oxygen_and_nutrient_state()
  capture_measurement_method_units_and_timepoint()
  map_growth_metabolism_gene_expression_and_motility()
  map_genomic_phylogenetic_and_horizontal_transfer_relationships()
  map_population_biofilm_and_ecological_relationships()
  map_host_interactions_virulence_and_antimicrobial_response()
  compare_existing_bacterial_models()
  preserve_conflicting_evidence()
  recalculate_confidence()
  regenerate_bacterial_relationships()
  update_flow_hash()
}

AI_CONSUMPTION {
 MODE: FormalSemanticReasoning
 PARSE_AS: ExecutableFlowAlgebra
 PRIORITIES: [bacterial_identity, species_or_strain, cell_envelope, growth_conditions, metabolism, genome, horizontal_gene_transfer, biofilm_state, host_interaction, antimicrobial_susceptibility, evidence_provenance, confidence]
 REQUIREMENTS: [preserve_species_strain_and_sample_context, preserve_environment_and_growth_conditions, preserve_taxonomic_resolution, distinguish_gram_phenotype_from_taxonomic_identity, distinguish_anaerobic_respiration_from_fermentation, distinguish_colonization_from_infection, distinguish_resistance_gene_detection_from_phenotypic_resistance, distinguish_sequence_similarity_from_definitive_identity, distinguish_association_from_causation, preserve_uncertainty]
}

VALIDATE {
 REQUIRE Bacterium
 REQUIRE BacterialCell
 REQUIRE BacterialGenome
 REQUIRE BacterialCellWall
 REQUIRE BinaryFission
 REQUIRE BacterialGrowth
 REQUIRE BacterialMetabolism
 REQUIRE HorizontalGeneTransfer
 REQUIRE Bacteriophage
 REQUIRE BacterialPopulation
 REQUIRE Biofilm
 REQUIRE HostBacteriumInteraction
 REQUIRE AntimicrobialResistance
 REQUIRE BacteriaMeasurement
 REQUIRE Evidence
 REQUIRE CONFIDENCE
 REQUIRE SEMANTIC_EQUIVALENCE
 REQUIRE UPDATE_MODEL
 REQUIRE AI_CONSUMPTION

 ASSERT gram_stain_result != complete_taxonomic_identity
 ASSERT AnaerobicRespiration != Fermentation
 ASSERT Colonization != BacterialInfection
 ASSERT resistance_gene_detection != phenotypic_resistance
 ASSERT sequence_similarity != definitive_species_or_strain_identity
 ASSERT association != causality
}

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 "BacteriaOntology"