Microbiology

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

flow "MicrobiologyOntology" v1.0

ENTITY MicrobiologyOntology {
 TYPE: BiologicalOntology
 DOMAIN: Microbiology
 SUBJECT: Microbiology
 PURPOSE: FormalSemanticRepresentation
}

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

ENTITY Microbiology {
 STUDIES: MicroorganismsAndMicrobialSystems
 INCLUDES: [Bacteriology, ArchaealBiology, Mycology, Protozoology, Virology, MicrobialEcology]
 INTEGRATES: [CellBiology, Genetics, Biochemistry, Evolution, Ecology, Immunology]
}

ENTITY Microorganism {
 IS_A: MicroscopicBiologicalEntity
 MAY_INCLUDE: [Bacterium, Archaeon, MicroscopicFungus, Protozoan, Microalga]
}

ENTITY Bacterium { IS_A: ProkaryoticCellularOrganism }
ENTITY Archaeon { IS_A: ProkaryoticCellularOrganism }
ENTITY Fungus { IS_A: EukaryoticOrganism }
ENTITY Protozoan { IS_A: MicrobialEukaryote }

ENTITY Virus {
 IS_A: AcellularInfectiousEntity
 REQUIRES: HostCell
 FOR: Replication
}

RULE VirusConstraint {
 Virus != CellularMicroorganism
}

ENTITY MicrobialCell {
 MAY_HAVE: [CellMembrane, CellWall, Cytoplasm, Genome, Ribosome]
}

ENTITY MicrobialGenome {
 STORES: GeneticInformation
}

ENTITY Plasmid {
 IS_A: ExtrachromosomalGeneticElement
 MAY_CARRY: AccessoryGenes
}

PROCESS MicrobialReplication {
 INCREASES: MicrobialPopulation
}

PROCESS BinaryFission {
 DIVIDES: ProkaryoticCell
 INTO: DaughterCells
}

ENTITY MicrobialGrowth {
 DESCRIBES: IncreaseInCellNumberOrBiomass
}

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

ENTITY MicrobialMetabolism {
 INCLUDES: [Catabolism, Anabolism, EnergyConservation, Biosynthesis]
}

PROCESS AerobicRespiration {
 USES: Oxygen
 AS: TerminalElectronAcceptor
}

PROCESS AnaerobicRespiration {
 USES: NonOxygenTerminalElectronAcceptor
}

PROCESS Fermentation {
 GENERATES: MetabolicEnergy
 WITHOUT_REQUIRING: RespiratoryElectronTransportToExternalTerminalAcceptor
}

RULE RespirationFermentationDistinction {
 AnaerobicRespiration != Fermentation
}

ENTITY MicrobialGene {
 PART_OF: MicrobialGenome
 MAY_ENCODE: [Protein, FunctionalRNA]
}

PROCESS GeneExpression {
 INCLUDES: [Transcription, Translation]
}

PROCESS GeneRegulation {
 MODULATES: MicrobialGeneExpression
 MAY_RESPOND_TO: EnvironmentalSignal
}

PROCESS Mutation {
 CHANGES: GeneticSequence
 MAY_GENERATE: GeneticVariation
}

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

PROCESS Transformation {
 ACQUIRES: ExtracellularGeneticMaterial
}

PROCESS Transduction {
 TRANSFERS: GeneticMaterial
 VIA: VirusOrPhage
}

PROCESS Conjugation {
 TRANSFERS: GeneticMaterial
 THROUGH: CellAssociatedTransferMechanism
}

ENTITY Bacteriophage {
 SUBCLASS_OF: Virus
 INFECTS: Bacterium
}

PROCESS ViralInfection {
 INVOLVES: [Attachment, Entry, GenomeReplication, GeneExpression, Assembly, Release]
}

ENTITY MicrobialCommunity {
 COMPOSED_OF: MultipleMicrobialPopulations
 OCCURS_IN: EnvironmentOrHost
}

ENTITY Microbiota {
 REPRESENTS: MicroorganismsPresentInDefinedEnvironment
}

ENTITY Microbiome {
 REPRESENTS: MicrobialCommunityAndAssociatedGeneticOrFunctionalContext
}

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

ENTITY Biofilm {
 IS_A: AggregatedMicrobialCommunity
 EMBEDDED_IN: ExtracellularMatrix
}

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

ENTITY QuorumSensing {
 IS_A: CellDensityAssociatedSignallingProcess
 MAY_REGULATE: CollectiveMicrobialBehaviour
}

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

ENTITY EnvironmentalFactor {
 MAY_INCLUDE: [Temperature, pH, Salinity, Oxygen, Nutrients, Pressure, Light]
 MAY_SHAPE: MicrobialCommunity
}

PROCESS BiogeochemicalCycling {
 MAY_INCLUDE: [CarbonCycle, NitrogenCycle, SulfurCycle, PhosphorusCycle]
 MAY_BE_MEDIATED_BY: Microorganisms
}

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

ENTITY Pathogen {
 MAY_CAUSE: Disease
 IN: SusceptibleHostContext
}

ENTITY VirulenceFactor {
 CONTRIBUTES_TO: PathogenicProcess
 MAY_SUPPORT: [Adhesion, Invasion, ToxinActivity, ImmuneEvasion, NutrientAcquisition]
}

PROCESS Colonization {
 ESTABLISHES: MicrobialPopulation
 IN_OR_ON: HostOrEnvironment
}

PROCESS Infection {
 INVOLVES: MicrobialOrViralEntryPersistenceOrReplication
 IN: Host
}

RULE ColonizationInfectionDistinction {
 Colonization != Infection
}

ENTITY AntimicrobialAgent {
 INHIBITS_OR_KILLS: Microorganism
}

ENTITY AntimicrobialResistance {
 DESCRIBES: ReducedSusceptibility
 TO: AntimicrobialAgent
}

ENTITY ResistanceGene {
 MAY_CONFER_OR_CONTRIBUTE_TO: AntimicrobialResistance
}

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

PROCESS AntimicrobialSusceptibilityTesting {
 MEASURES: MicrobialResponseToAntimicrobial
}

ENTITY Culture {
 IS_A: LaboratoryMicrobialPopulation
 GROWN_UNDER: DefinedConditions
}

PROCESS Cultivation {
 GROWS: Microorganism
 UNDER: ControlledConditions
}

PROCESS Isolation {
 SEPARATES: MicroorganismOrPopulation
 FROM: MixedSample
}

ENTITY GramStain {
 IS_A: DifferentialStainingMethod
 CLASSIFIES: BacteriaByCellEnvelopeStainingPhenotype
}

RULE GramConstraint {
 gram_stain_result != complete_taxonomic_identity
}

PROCESS Microscopy {
 VISUALIZES: MicrobialCellsOrStructures
}

PROCESS Sequencing {
 DETERMINES: NucleicAcidSequence
 MAY_SUPPORT: IdentificationAndGenomicAnalysis
}

PROCESS Metagenomics {
 SEQUENCES: CommunityGeneticMaterial
 WITHOUT_REQUIRING: IsolationOfEachOrganism
}

PROCESS Metatranscriptomics {
 MEASURES: CommunityRNA
}

PROCESS MicrobialIdentification {
 MAY_USE: [Culture, Microscopy, BiochemicalTesting, MassSpectrometry, Sequencing]
}

ENTITY MicrobialTaxonomy {
 CLASSIFIES: Microorganisms
 USING: [Phylogeny, Genomics, Phenotype, Nomenclature]
}

ENTITY OperationalTaxonomicUnit {
 ABBREVIATION: OTU
 IS_A: SequenceBasedGrouping
}

ENTITY AmpliconSequenceVariant {
 ABBREVIATION: ASV
 IS_A: ResolvedAmpliconSequenceEntity
}

PROCESS Sterilization {
 AIMS_TO_REMOVE_OR_INACTIVATE: AllViableMicroorganisms
 INCLUDING: ResistantForms
}

PROCESS Disinfection {
 REDUCES_OR_INACTIVATES: Microorganisms
 ON: InanimateSurfaceOrMaterial
}

PROCESS Antisepsis {
 REDUCES_OR_INACTIVATES: Microorganisms
 ON: LivingTissue
}

PROCESS MicrobiologyMeasurement {
 MAY_MEASURE: [CellCount, Biomass, GrowthRate, Viability, Metabolite, GeneExpression, CommunityComposition, Susceptibility]
 MAY_USE: [Culture, Microscopy, Spectrophotometry, FlowCytometry, Sequencing, MassSpectrometry, MolecularAssay]
}

ENTITY Evidence {
 TYPES: [MicrobiologicalEvidence, CultureEvidence, MicroscopyEvidence, BiochemicalEvidence, GenomicEvidence, MetagenomicEvidence, PhylogeneticEvidence, FunctionalEvidence, SusceptibilityEvidence, ExperimentalEvidence, ComputationalEvidence, LiteratureEvidence]
}

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

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

RELATION Microbiology STUDIES Microorganism
RELATION Microbiology STUDIES Virus
RELATION MicrobialGenome CONTAINS MicrobialGene
RELATION HorizontalGeneTransfer MOVES GeneticMaterial
RELATION MicrobialCommunity OCCURS_IN MicrobialHabitat
RELATION Biofilm CONTAINS MicrobialCells
RELATION Pathogen MAY_CAUSE Infection
RELATION AntimicrobialAgent ACTS_ON Microorganism
RELATION Sequencing MAY_SUPPORT MicrobialIdentification

SEMANTIC_EQUIVALENCE {
 "microbiology" ~= "study of microorganisms and microbial systems"
 "microbiota" ~= "microorganisms in a defined environment"
 "microbiome" ~= "microbial community and associated genetic or functional context"
 "HGT" ~= "horizontal gene transfer"
 "MIC" ~= "minimum inhibitory concentration"
 "ASV" ~= "amplicon sequence variant"
 "OTU" ~= "operational taxonomic unit"
}

CONFIDENCE MicrobiologyAssertion {
 INPUTS: [culture_support, microscopy_support, biochemical_support, genomic_support, phylogenetic_support, functional_support, ecological_support, experimental_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 GrowthInference {
 IF cell_number_or_biomass increases_over_time
 UNDER defined_conditions
 THEN MicrobialGrowth MAY_BE_SUPPORTED
}

RULE ResistanceInference {
 IF standardized_susceptibility_testing demonstrates_reduced_susceptibility
 THEN AntimicrobialResistance MAY_BE_SUPPORTED
 WITH organism_drug_and_method_context
}

RULE CommunityAssociationInference {
 IF microbial_taxon_abundance correlates_with environmental_or_host_state
 THEN preserve_association
 AND DO_NOT_INFER causality
 WITHOUT functional_or_interventional_evidence
}

QUERY MicrobiologyLookup(context_identifier) {
 RETURN [organisms, viruses, cellular_features, growth, metabolism, genetics, community, ecology, host_interactions, antimicrobial_response, measurements, evidence, confidence]
}

QUERY MicroorganismLookup(organism_identifier) {
 RETURN [taxonomy, morphology, genome, metabolism, growth_conditions, habitat, interactions, virulence_context, antimicrobial_susceptibility, evidence, confidence]
}

QUERY MicrobialCommunityLookup(sample_identifier) {
 RETURN [sample_type, taxa, relative_or_absolute_abundance, diversity, functional_genes, environment, interactions, methods, evidence, confidence]
}

UPDATE_MODEL {
 ON new_microbiology_evidence:
  validate_provenance()
  identify_sample_organism_or_community_context()
  normalize_taxonomic_gene_metabolite_and_antimicrobial_identifiers()
  capture_environment_medium_temperature_pH_and_oxygen_state()
  capture_measurement_method_and_timepoint()
  map_growth_metabolism_and_gene_expression()
  map_genomic_phylogenetic_and_horizontal_transfer_relationships()
  map_community_ecology_and_host_interactions()
  map_antimicrobial_susceptibility_and_resistance()
  compare_existing_microbiological_models()
  preserve_conflicting_evidence()
  recalculate_confidence()
  regenerate_microbiology_relationships()
  update_flow_hash()
}

AI_CONSUMPTION {
 MODE: FormalSemanticReasoning
 PARSE_AS: ExecutableFlowAlgebra
 PRIORITIES: [microbial_identity, taxonomy, cellular_or_viral_status, growth_conditions, metabolism, genome, community_context, host_interaction, antimicrobial_susceptibility, evidence_provenance, confidence]
 REQUIREMENTS: [preserve_organism_and_sample_context, preserve_environment_and_growth_conditions, preserve_taxonomic_resolution, distinguish_virus_from_cellular_microorganism, distinguish_anaerobic_respiration_from_fermentation, distinguish_microbiota_from_microbiome_when_definition_requires, distinguish_colonization_from_infection, distinguish_resistance_gene_detection_from_phenotypic_resistance, distinguish_association_from_causation, preserve_uncertainty]
}

VALIDATE {
 REQUIRE Microbiology
 REQUIRE Microorganism
 REQUIRE Bacterium
 REQUIRE Archaeon
 REQUIRE Fungus
 REQUIRE Virus
 REQUIRE MicrobialGrowth
 REQUIRE MicrobialMetabolism
 REQUIRE MicrobialGenome
 REQUIRE HorizontalGeneTransfer
 REQUIRE MicrobialCommunity
 REQUIRE Biofilm
 REQUIRE HostMicrobeInteraction
 REQUIRE AntimicrobialResistance
 REQUIRE MicrobiologyMeasurement
 REQUIRE Evidence
 REQUIRE CONFIDENCE
 REQUIRE SEMANTIC_EQUIVALENCE
 REQUIRE UPDATE_MODEL
 REQUIRE AI_CONSUMPTION

 ASSERT Virus != CellularMicroorganism
 ASSERT AnaerobicRespiration != Fermentation
 ASSERT Colonization != Infection
 ASSERT resistance_gene_detection != phenotypic_resistance
 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 "MicrobiologyOntology"