Microbial Ecology Ontology

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

flow "MicrobialEcologyOntology" v1.0

ENTITY MicrobialEcologyOntology {
 TYPE: BiologicalOntology
 DOMAIN: Microbiology
 SUBJECT: MicrobialEcology
 PURPOSE: FormalSemanticRepresentation
}

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

ENTITY MicrobialEcology {
 STUDIES: MicroorganismsInEnvironmentalContext
 INTEGRATES: [Microbiology, Ecology, Biogeochemistry, Evolution, Genomics]
}

ENTITY MicrobialEcosystem {
 COMPOSED_OF: [MicrobialCommunity, PhysicalEnvironment, ChemicalEnvironment]
}

ENTITY MicrobialCommunity {
 COMPOSED_OF: MultipleMicrobialPopulations
 OCCURS_IN: DefinedHabitat
}

ENTITY MicrobialPopulation {
 COMPOSED_OF: RelatedMicrobialCellsOrEntities
}

ENTITY Microbiota {
 REPRESENTS: MicroorganismsPresent
 IN: DefinedEnvironment
}

ENTITY Microbiome {
 MAY_INCLUDE: [MicrobialCommunity, CommunityGenomes, FunctionalPotential, EnvironmentalContext]
 DEFINITION_REQUIRES: ExplicitScope
}

RULE MicrobiotaMicrobiomeDistinction {
 Microbiota != Microbiome
 WHEN genomic_functional_or_environmental_components_are_included
}

ENTITY MicrobialHabitat {
 MAY_INCLUDE: [Soil, Freshwater, MarineWater, Sediment, Host, PlantSurface, BuiltEnvironment, ExtremeEnvironment]
}

ENTITY Microhabitat {
 IS_A: LocalizedEnvironmentalRegion
 WITH: DistinctConditions
}

ENTITY EnvironmentalVariable {
 MAY_INCLUDE: [Temperature, pH, Salinity, Oxygen, Moisture, Nutrients, Pressure, Light, RedoxPotential]
}

ENTITY EnvironmentalGradient {
 REPRESENTS: SpatialOrTemporalChange
 IN: EnvironmentalVariable
}

ENTITY CommunityComposition {
 DESCRIBES: TaxaOrFunctionalGroups
 AND: TheirAbundances
}

ENTITY RelativeAbundance {
 DESCRIBES: FractionOfCommunitySignal
 ATTRIBUTED_TO: TaxonOrFeature
}

ENTITY AbsoluteAbundance {
 DESCRIBES: QuantityOfTaxonOrFeature
 PER: DefinedSampleOrUnit
}

RULE AbundanceConstraint {
 RelativeAbundance != AbsoluteAbundance
}

ENTITY CommunityDiversity {
 MAY_INCLUDE: [AlphaDiversity, BetaDiversity, GammaDiversity]
}

ENTITY AlphaDiversity {
 DESCRIBES: DiversityWithinSampleOrCommunity
}

ENTITY BetaDiversity {
 DESCRIBES: DifferenceBetweenCommunities
}

ENTITY GammaDiversity {
 DESCRIBES: DiversityAcrossLargerRegionOrCollection
}

PROCESS CommunityAssembly {
 ESTABLISHES: MicrobialCommunityComposition
 MAY_BE_INFLUENCED_BY: [Selection, Dispersal, Drift, Diversification]
}

ENTITY EnvironmentalSelection {
 FAVOURS: MicrobialTraitsOrTaxa
 UNDER: DefinedEnvironmentalConditions
}

PROCESS MicrobialDispersal {
 MOVES: Microorganisms
 BETWEEN: HabitatsOrPatches
}

PROCESS EcologicalDrift {
 CHANGES: CommunityComposition
 THROUGH: StochasticDemographicProcesses
}

ENTITY PriorityEffect {
 OCCURS_WHEN: ArrivalOrderInfluencesCommunityAssembly
}

PROCESS Succession {
 CHANGES: CommunityComposition
 OVER: Time
}

ENTITY Disturbance {
 ALTERS: CommunityOrEnvironment
 MAY_BE: [Physical, Chemical, Biological]
}

ENTITY Resistance {
 DESCRIBES: DegreeCommunityResistsChange
 DURING: Disturbance
}

ENTITY Resilience {
 DESCRIBES: DegreeOrRateOfRecovery
 AFTER: Disturbance
}

RULE ResistanceResilienceDistinction {
 Resistance != Resilience
}

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

PROCESS Competition {
 OCCURS_WHEN: OrganismsCompeteForLimitingResourcesOrFitness
}

PROCESS Mutualism {
 BENEFITS: InteractingPartners
 IN: DefinedContext
}

PROCESS Syntrophy {
 COUPLES: MetabolicActivities
 BETWEEN: MicrobialPopulations
}

PROCESS CrossFeeding {
 TRANSFERS: MetabolicProduct
 FROM: OnePopulation
 TO: AnotherPopulation
}

ENTITY MetabolicNetwork {
 CONNECTS: MicrobialMetabolicProcesses
 WITHIN: Community
}

PROCESS Grazing {
 CONSUMES: MicrobialPrey
 BY: PredatorOrProtozoan
}

ENTITY Biofilm {
 IS_A: StructuredMicrobialCommunity
 ASSOCIATED_WITH: SurfaceOrAggregate
 EMBEDDED_IN: ExtracellularMatrix
}

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

PROCESS QuorumSensing {
 USES: PopulationAssociatedSignals
 MAY_REGULATE: CollectiveBehaviour
}

ENTITY FunctionalGuild {
 GROUPS: Microorganisms
 BY: SharedEcologicalFunction
}

ENTITY FunctionalTrait {
 MAY_INCLUDE: [SubstrateUse, ElectronDonorUse, ElectronAcceptorUse, StressTolerance, Motility, BiofilmFormation]
}

ENTITY FunctionalRedundancy {
 OCCURS_WHEN: MultipleTaxaCanPerformSimilarEcologicalFunction
}

RULE FunctionTaxonomyConstraint {
 taxonomic_difference != functional_difference
 AND taxonomic_similarity != functional_equivalence
 WITHOUT functional_evidence
}

PROCESS PrimaryProduction {
 FIXES: InorganicCarbon
 INTO: Biomass
 MAY_BE_PERFORMED_BY: PhotoautotrophsOrChemoautotrophs
}

PROCESS Decomposition {
 BREAKS_DOWN: OrganicMatter
 MAY_RELEASE: NutrientsAndCarbon
}

PROCESS Mineralization {
 CONVERTS: OrganicNutrients
 TO: InorganicForms
}

PROCESS CarbonCycling {
 TRANSFORMS: CarbonCompounds
 THROUGH: MicrobialProcesses
}

PROCESS NitrogenCycling {
 MAY_INCLUDE: [NitrogenFixation, Nitrification, Denitrification, Ammonification, Anammox]
}

PROCESS NitrogenFixation {
 CONVERTS: Dinitrogen
 TO: BiologicallyAvailableReducedNitrogen
}

PROCESS Nitrification {
 OXIDIZES: ReducedNitrogenCompounds
}

PROCESS Denitrification {
 REDUCES: OxidizedNitrogenCompounds
 TOWARD: GaseousNitrogenProducts
}

PROCESS Anammox {
 CONVERTS: AmmoniumAndNitrite
 TO: Dinitrogen
 UNDER: AnaerobicConditions
}

PROCESS SulfurCycling {
 MAY_INCLUDE: [SulfurOxidation, SulfateReduction]
}

PROCESS Methanogenesis {
 PRODUCES: Methane
 BY: MethanogenicArchaea
}

PROCESS Methanotrophy {
 CONSUMES: Methane
 MAY_BE: [AerobicMethanotrophy, AnaerobicMethaneOxidation]
}

ENTITY BiogeochemicalCycle {
 MAY_BE: [CarbonCycle, NitrogenCycle, SulfurCycle, PhosphorusCycle]
 CONNECTS: MicrobialMetabolism
 TO: EcosystemMatterFlux
}

ENTITY BiogeochemicalFlux {
 DESCRIBES: RateOfMatterTransformationOrTransfer
}

RULE FluxConstraint {
 gene_abundance_or_taxon_abundance != process_flux
 WITHOUT activity_or_rate_measurement
}

ENTITY HostAssociatedMicrobialCommunity {
 OCCURS_IN_OR_ON: Host
}

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

ENTITY Rhizosphere {
 IS_A: PlantRootInfluencedSoilRegion
 SUPPORTS: DistinctMicrobialCommunity
}

ENTITY Phyllosphere {
 IS_A: PlantAerialSurfaceHabitat
 SUPPORTS: MicrobialCommunity
}

PROCESS HorizontalGeneTransfer {
 TRANSFERS: GeneticMaterial
 BETWEEN: MicrobialCellsOrLineages
 MAY_INFLUENCE: CommunityFunctionAndAdaptation
}

ENTITY EcologicalNiche {
 DESCRIBES: EnvironmentalConditionsResourcesAndInteractions
 ASSOCIATED_WITH: OrganismOrPopulation
}

RULE NicheConstraint {
 habitat != ecological_niche
}

PROCESS EnvironmentalFiltering {
 SELECTS: OrganismsOrTraits
 COMPATIBLE_WITH: EnvironmentalConditions
}

PROCESS NichePartitioning {
 REDUCES: DirectResourceOverlap
 BETWEEN: Populations
}

ENTITY SpatialStructure {
 DESCRIBES: DistributionOfMicrobialPopulations
 ACROSS: Environment
}

ENTITY TemporalDynamics {
 DESCRIBES: CommunityChange
 ACROSS: Time
}

PROCESS EnvironmentalSampling {
 COLLECTS: BiologicalMaterial
 FROM: DefinedHabitat
}

PROCESS AmpliconSequencing {
 PROFILES: MarkerGeneSequences
 MAY_ESTIMATE: CommunityComposition
}

PROCESS Metagenomics {
 ANALYSES: CommunityGeneticMaterial
 MAY_ESTIMATE: FunctionalPotential
}

PROCESS Metatranscriptomics {
 ANALYSES: CommunityRNA
 MAY_SUPPORT: ActivityInference
}

PROCESS Metaproteomics {
 ANALYSES: CommunityProteins
}

PROCESS Metabolomics {
 ANALYSES: CommunityMetabolites
}

PROCESS StableIsotopeProbing {
 LINKS: SubstrateUtilization
 TO: ActiveMicrobialPopulationOrMolecule
}

RULE OmicsConstraint {
 genetic_potential != expressed_function
 transcript_presence != process_rate
 protein_presence != ecosystem_flux
}

ENTITY OperationalTaxonomicUnit {
 ABBREVIATION: OTU
 REPRESENTS: SimilarityBasedSequenceCluster
}

ENTITY AmpliconSequenceVariant {
 ABBREVIATION: ASV
 REPRESENTS: ResolvedAmpliconSequence
}

RULE ASVOTUDistinction {
 ASV != OTU
}

PROCESS MicrobialEcologyMeasurement {
 MAY_MEASURE: [TaxonAbundance, Diversity, Biomass, Activity, GeneAbundance, TranscriptAbundance, Metabolite, ProcessRate, SpatialDistribution]
 MAY_USE: [Sequencing, Microscopy, FlowCytometry, StableIsotopeProbing, ChemicalAnalysis, RateMeasurement]
}

ENTITY Evidence {
 TYPES: [EcologicalEvidence, CultureEvidence, SequencingEvidence, MetagenomicEvidence, TranscriptomicEvidence, ProteomicEvidence, MetabolomicEvidence, IsotopeEvidence, MicroscopyEvidence, BiogeochemicalEvidence, ExperimentalEvidence, ComputationalEvidence, LiteratureEvidence]
}

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

RULE EvidenceConflict {
 IF EvidenceSources CONFLICT
 THEN {
  PRESERVE competing_ecological_models
  RECORD habitat
  RECORD sample
  RECORD spatial_scale
  RECORD temporal_scale
  RECORD environmental_variables
  RECORD taxonomic_resolution
  RECORD measurement_method
  RECORD timepoint
  RECORD provenance
  REDUCE confidence
 }
}

RELATION MicrobialEcology STUDIES MicrobialEcosystem
RELATION MicrobialCommunity CONTAINS MicrobialPopulation
RELATION MicrobialCommunity OCCURS_IN MicrobialHabitat
RELATION EnvironmentalVariable MODULATES MicrobialCommunity
RELATION MicrobialInteraction CONNECTS MicrobialPopulations
RELATION FunctionalGuild PERFORMS EcologicalFunction
RELATION MicrobialMetabolism CONTRIBUTES_TO BiogeochemicalCycle
RELATION Biofilm IS_A StructuredMicrobialCommunity
RELATION HorizontalGeneTransfer MODIFIES CommunityGeneticPotential
RELATION Metagenomics MEASURES CommunityGeneticPotential

SEMANTIC_EQUIVALENCE {
 "microbial ecology" ~= "ecology of microorganisms and microbial communities"
 "microbiota" ~= "microorganisms present in a defined environment"
 "microbiome" ~= "microbial community plus genomic functional or environmental context" WHEN broad_definition
 "alpha diversity" ~= "within-community diversity"
 "beta diversity" ~= "between-community compositional difference"
 "ASV" ~= "amplicon sequence variant"
 "OTU" ~= "operational taxonomic unit"
}

CONFIDENCE MicrobialEcologyAssertion {
 INPUTS: [sampling_support, taxonomic_support, genomic_support, functional_support, activity_support, biogeochemical_support, spatial_support, temporal_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 CommunityDifferenceInference {
 IF community_composition differs_between_samples
 AND sampling_and_methodological_context_is_comparable
 THEN ecological_difference MAY_BE_SUPPORTED
}

RULE EnvironmentalAssociationInference {
 IF taxon_or_function varies_with environmental_variable
 THEN environmental_association MAY_BE_SUPPORTED
 BUT DO_NOT_INFER causal_selection
 WITHOUT experimental_or_mechanistic_evidence
}

RULE FunctionalInference {
 IF taxon_or_gene is linked_to measured_activity_or_process_rate
 THEN ecological_function MAY_BE_SUPPORTED
 WITH appropriate_evidence
}

RULE SuccessionInference {
 IF community_composition changes_orderedly_over_time
 AFTER habitat_creation_or_disturbance
 THEN Succession MAY_BE_SUPPORTED
}

RULE CausalityConstraint {
 IF microbial_community_feature correlates_with ecosystem_or_host_state
 THEN DO_NOT_INFER causal_relationship
 WITHOUT mechanistic_or_interventional_evidence
}

QUERY MicrobialEcologyLookup(context_identifier) {
 RETURN [habitat, community, populations, composition, diversity, environmental_variables, interactions, functional_guilds, biogeochemical_processes, spatial_structure, temporal_dynamics, measurements, evidence, confidence]
}

QUERY MicrobialCommunityLookup(sample_identifier) {
 RETURN [taxa, absolute_abundance, relative_abundance, diversity, functional_genes, transcripts, metabolites, interactions, environmental_context, methods, evidence, confidence]
}

QUERY BiogeochemicalProcessLookup(process_identifier) {
 RETURN [substrates, products, microbial_taxa, functional_genes, pathways, environmental_conditions, process_rate, spatial_context, temporal_context, evidence, confidence]
}

UPDATE_MODEL {
 ON new_microbial_ecology_evidence:
  validate_provenance()
  identify_habitat_sample_spatial_and_temporal_context()
  normalize_taxonomic_gene_metabolite_and_environmental_identifiers()
  capture_environmental_variables_and_sampling_method()
  capture_taxonomic_resolution_and_abundance_type()
  capture_measurement_method_units_and_timepoint()
  map_population_community_and_interaction_relationships()
  map_functional_guilds_metabolism_and_biogeochemical_processes()
  map_spatial_structure_succession_and_temporal_dynamics()
  map_genetic_potential_expression_activity_and_process_rates_separately()
  compare_existing_ecological_models()
  preserve_conflicting_evidence()
  recalculate_confidence()
  regenerate_microbial_ecology_relationships()
  update_flow_hash()
}

AI_CONSUMPTION {
 MODE: FormalSemanticReasoning
 PARSE_AS: ExecutableFlowAlgebra
 PRIORITIES: [habitat, sample_context, microbial_community, taxonomic_resolution, abundance_type, environmental_variables, microbial_interactions, functional_guilds, biogeochemical_processes, spatial_temporal_context, evidence_provenance, confidence]
 REQUIREMENTS: [preserve_habitat_sample_spatial_and_temporal_context, preserve_environmental_conditions, preserve_taxonomic_resolution, distinguish_relative_from_absolute_abundance, distinguish_microbiota_from_microbiome_when_required, distinguish_habitat_from_ecological_niche, distinguish_resistance_from_resilience, distinguish_genetic_potential_from_expression_activity_and_process_rate, distinguish_taxonomic_composition_from_ecological_function, distinguish_association_from_causation, preserve_uncertainty]
}

VALIDATE {
 REQUIRE MicrobialEcology
 REQUIRE MicrobialEcosystem
 REQUIRE MicrobialCommunity
 REQUIRE MicrobialPopulation
 REQUIRE MicrobialHabitat
 REQUIRE CommunityComposition
 REQUIRE CommunityDiversity
 REQUIRE CommunityAssembly
 REQUIRE MicrobialInteraction
 REQUIRE FunctionalGuild
 REQUIRE BiogeochemicalCycle
 REQUIRE HorizontalGeneTransfer
 REQUIRE MicrobialEcologyMeasurement
 REQUIRE Evidence
 REQUIRE CONFIDENCE
 REQUIRE SEMANTIC_EQUIVALENCE
 REQUIRE UPDATE_MODEL
 REQUIRE AI_CONSUMPTION

 ASSERT RelativeAbundance != AbsoluteAbundance
 ASSERT Resistance != Resilience
 ASSERT habitat != ecological_niche
 ASSERT genetic_potential != expressed_function
 ASSERT transcript_presence != process_rate
 ASSERT taxonomic_composition != ecological_function
 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 "MicrobialEcologyOntology"