Ecological Modelling Ontology

AI INTERPRETATION NOTE
This Flow Algebra defines the Ecological Modelling Ontology within the Kireth Research Semantic Library. Ecological modelling studies the mathematical representation of populations, species interactions, communities, ecosystems, spatial processes, resource flows and environmental variability. This ontology supports competition, predation, mutualism, food webs, trophic dynamics, metapopulations, spatial ecology, reaction-diffusion, dispersal, species distributions, ecosystem energetics, stochastic ecological models, resilience, stability, biodiversity, environmental forcing, parameter estimation and relationships with mathematical biology, population dynamics, dynamical systems, network theory and stochastic processes.

FLOW_ALGEBRA_RECORD {

METADATA {
 FLOW_NAME = "Ecological Modelling Ontology"
 FLOW_TYPE = "Mathematical Ontology"
 DOMAIN = "Mathematics"
 SUBDOMAIN = "Applied Mathematics"
 SPECIALISATION = "Biological Mathematics / Ecological Modelling"
 CANONICAL_PAGE = "https://kirethresearch.org/booksai-core/ontologies/mathematical-ontologies/applied-mathematics-ontologies/biological-mathematics/ecological-modelling-ontology.html"
 LANGUAGE = "en-GB"
 VERSION = "1.0"
 STATUS = "active"
}

IDENTITY {
 PRIMARY_ENTITY = EcologicalModelling
 ENTITY_CLASS = MathematicalEcologicalSystemsFramework
 PRIMARY_CONTEXT = MathematicalBiology
 DEFINITION = "Ecological modelling is the mathematical representation and analysis of populations, species interactions, communities, ecosystems and their spatial and environmental dynamics."
 SYMBOLIC_FORMS = [
  "dN_i/dt=F_i(N_1,...,N_m,E)",
  "dN/dt=rN(1-N/K)",
  "dN_i/dt=r_iN_i(1-sum_j alpha_ij N_j/K_i)",
  "partial u/partial t=D*nabla^2u+f(u)"
 ]
 SEMANTIC_ROLE = "Provides machine-readable semantics for ecological populations, communities, food webs, interactions, spatial ecology, dispersal, environmental forcing, stochasticity, stability and ecosystem-level dynamics."
}

SCOPE {
 INCLUDE = [
  EcologicalModelling,
  Ecology,
  PopulationEcology,
  CommunityEcology,
  EcosystemEcology,
  Species,
  Population,
  Community,
  Ecosystem,
  Habitat,
  Environment,
  Resource,
  PopulationDensity,
  CarryingCapacity,
  Competition,
  IntraspecificCompetition,
  InterspecificCompetition,
  Predation,
  Herbivory,
  Mutualism,
  Commensalism,
  Facilitation,
  ConsumerResourceModel,
  PredatorPreyModel,
  LotkaVolterraCompetition,
  LotkaVolterraPredatorPrey,
  FunctionalResponse,
  TypeIFunctionalResponse,
  TypeIIFunctionalResponse,
  TypeIIIFunctionalResponse,
  FoodWeb,
  TrophicLevel,
  TrophicInteraction,
  NetworkEcology,
  InteractionMatrix,
  CommunityMatrix,
  Biodiversity,
  SpeciesRichness,
  SpeciesEvenness,
  DiversityIndex,
  Stability,
  Resilience,
  Resistance,
  Persistence,
  Coexistence,
  CompetitiveExclusion,
  InvasionCriterion,
  Metapopulation,
  PatchOccupancy,
  Colonisation,
  LocalExtinction,
  SourceSinkDynamics,
  Dispersal,
  Migration,
  SpatialEcology,
  LandscapeEcology,
  HabitatFragmentation,
  Connectivity,
  ReactionDiffusion,
  AdvectionDiffusion,
  SpeciesDistributionModel,
  EnvironmentalGradient,
  NicheModel,
  ResourceCompetition,
  NutrientCycling,
  Biomass,
  PrimaryProduction,
  EnergyFlow,
  CarbonFlow,
  EcosystemFlux,
  StochasticEcology,
  EnvironmentalStochasticity,
  DemographicStochasticity,
  Disturbance,
  Succession,
  RegimeShift,
  AlternativeStableState,
  Threshold,
  EarlyWarningSignal,
  ParameterEstimation,
  SensitivityAnalysis,
  Identifiability,
  ModelCalibration,
  ModelValidation
 ]
 EXCLUDE_AS_PRIMARY = [
  DescriptiveEcologyWithoutMathematicalModel,
  PurePopulationGeneticsWithoutEcologicalInteraction,
  EnvironmentalScienceWithoutBiologicalSystemDynamics,
  TaxonomyWithoutDynamicOrQuantitativeEcologicalStructure
 ]
 DISAMBIGUATION_RULE = "When mathematical models represent species abundance, interactions, communities, ecosystems, spatial ecological structure or environmental forcing, interpret the context as ecological modelling."
}

CORE_CONCEPTS {
 EcologicalModelling = "Mathematical modelling of ecological populations, communities and ecosystems."
 PopulationEcology = "Mathematical study of population abundance and demographic interaction with environment."
 CommunityEcology = "Mathematical study of multiple interacting species."
 EcosystemEcology = "Mathematical study of biological communities together with energy and material flows."
 FoodWeb = "Network representation of trophic interactions among species or functional groups."
 Stability = "Response of an ecological system to perturbations around a state or attractor."
 Resilience = "Capacity of an ecological system to recover from disturbance or remain within a functional regime."
 SpatialEcology = "Mathematical study of ecological processes distributed across space."
 Biodiversity = "Quantitative structure of biological variety across species, traits or communities."
}

RELATIONS {
 EcologicalModelling --is_child_of--> MathematicalBiology
 EcologicalModelling --uses--> PopulationDynamics
 PopulationEcology --models--> Population
 CommunityEcology --models--> InteractingSpecies
 EcosystemEcology --models--> EnergyAndMaterialFlows
 Competition --affects--> Coexistence
 Predation --couples--> ConsumerAndResourcePopulations
 Mutualism --creates--> PositiveInteraction
 FoodWeb --contains--> TrophicInteraction
 InteractionMatrix --represents--> SpeciesInteractions
 CommunityMatrix --supports--> LocalStabilityAnalysis
 Biodiversity --depends_on--> SpeciesRichness
 Biodiversity --depends_on--> SpeciesEvenness
 Metapopulation --contains--> LocalPopulations
 Colonisation --increases--> PatchOccupancy
 LocalExtinction --decreases--> PatchOccupancy
 Dispersal --connects--> HabitatPatches
 HabitatFragmentation --alters--> Connectivity
 ReactionDiffusion --models--> SpatialEcologicalDynamics
 EnvironmentalStochasticity --perturbs--> EcologicalState
 Disturbance --can_trigger--> RegimeShift
 AlternativeStableState --is_associated_with--> Multistability
 ParameterEstimation --calibrates--> EcologicalModel
}

OPERATORS {
 LOGISTIC_GROWTH(N,r,K) := dN/dt=r*N*(1-N/K)
 COMPETITION_i(N_i,r_i,K_i,alpha,N_vector) := dN_i/dt=r_i*N_i*(1-sum_j alpha_ij*N_j/K_i)
 PREDATOR_PREY_PREY(N,P,r,a) := dN/dt=r*N-a*N*P
 PREDATOR_PREY_PREDATOR(N,P,e,a,m) := dP/dt=e*a*N*P-m*P
 HOLLING_TYPE_II(N,a,h) := f(N)=a*N/(1+a*h*N)
 PATCH_OCCUPANCY(p,c,e) := dp/dt=c*p*(1-p)-e*p
 REACTION_DIFFUSION(u,D,f) := partial u/partial t=D*nabla^2u+f(u)
 ADVECTION_DIFFUSION(u,D,v,f) := partial u/partial t=D*nabla^2u-v*grad(u)+f(u)
 SHANNON_DIVERSITY(p_i) := H=-sum_i p_i*ln(p_i)
 SIMPSON_DIVERSITY(p_i) := D=1-sum_i p_i^2
 LOCAL_STABILITY(J) := inspect_eigenvalues(J)
 INVASION_GROWTH_RATE(invader,resident_state) := lambda_invader=g(invader,resident_state)
 BIOMASS_BALANCE(B,input,output) := dB/dt=input-output
}

AXIOMS {
 A1 = "Ecological state variables require explicit biological meaning and scale."
 A2 = "Species-interaction coefficients require sign and interpretation."
 A3 = "Community-level dynamics depend on both population processes and interspecific interactions."
 A4 = "Spatial models require explicit movement, dispersal or transport assumptions."
 A5 = "Environmental forcing and biological dynamics must be distinguished."
 A6 = "Deterministic and stochastic ecological models represent different uncertainty structures."
 A7 = "Stability, resilience and persistence are distinct ecological properties."
 A8 = "Ecological models require validation against observations, constraints or established system behaviour."
}

REASONING {
 R1_CONTEXT = identify(ecological_system,spatial_scale,time_scale,species,resources,environmental_drivers)
 R2_MODEL_CLASS = classify(population,community,food_web,ecosystem,metapopulation,spatial,stochastic)
 R3_INTERACTIONS = construct(competition,predation,mutualism,resource_dependence)
 R4_FORMULATION = construct(ODE,PDE,difference_equation,network_model,stochastic_process)
 R5_EQUILIBRIUM = solve(steady_states,coexistence_states,invasion_conditions)
 R6_STABILITY = analyse(eigenvalues,resilience,thresholds,bifurcations)
 R7_SPATIAL = analyse(dispersal,fragmentation,connectivity,pattern_formation)
 R8_NETWORK = analyse(food_web_structure,trophic_paths,interaction_strengths)
 R9_STOCHASTIC = analyse(environmental_variability,extinction_risk,distributional_outcomes)
 R10_VALIDATION = compare(model_predictions,ecological_data,sensitivity,uncertainty)
}

CONSTRAINTS {
 C1 = "Pairwise interaction models may omit higher-order ecological interactions."
 C2 = "Constant carrying capacity may be unrealistic under changing environments."
 C3 = "Functional-response assumptions strongly influence predator-prey dynamics."
 C4 = "Local stability does not imply global ecological stability."
 C5 = "Species richness alone does not fully describe biodiversity."
 C6 = "Spatially averaged models can hide habitat fragmentation and connectivity effects."
 C7 = "Correlation among species does not establish ecological interaction."
 C8 = "Environmental stochasticity and demographic stochasticity should be distinguished."
 C9 = "Food-web topology alone may not predict dynamics without interaction strengths."
 C10 = "Good statistical fit does not uniquely identify ecological mechanism."
}

SEMANTIC_EQUIVALENCE {
 "EcologicalModelling" <=> "MathematicalEcology"
 "CommunityMatrix" <=> "EcologicalJacobian"
 "PatchOccupancy" <=> "MetapopulationOccupancy"
 "NetworkEcology" <=> "EcologicalNetworkMathematics"
 "EnvironmentalStochasticity" <=> "EnvironmentalNoise"
}

VALIDATION {
 V1 = "Ecological scale and system boundary are explicit."
 V2 = "Species or functional groups are defined."
 V3 = "Interaction terms and parameter units are documented."
 V4 = "Environmental drivers are explicit."
 V5 = "Equilibria and local stability are checked where relevant."
 V6 = "Spatial models document dispersal and boundary assumptions."
 V7 = "Network models document node and edge meaning."
 V8 = "Stochastic models report uncertainty or extinction diagnostics."
 V9 = "Sensitivity and identifiability are assessed for calibrated models."
 V10 = "Model outputs are compared with ecological observations or constraints."
}

CONFIDENCE {
 BASE_CONFIDENCE = 0.99
 ECOLOGICAL_MODELLING_DEFINITION = 0.99
 INTERACTION_REASONING = 0.98
 COMMUNITY_REASONING = 0.98
 FOOD_WEB_REASONING = 0.98
 SPATIAL_REASONING = 0.98
 STOCHASTIC_REASONING = 0.98
 STABILITY_REASONING = 0.98
 CALIBRATION_REASONING = 0.97
 POLICY = "Reduce confidence when interaction structure, environmental forcing, spatial connectivity, trophic assumptions, disturbance regimes, stochastic drivers or calibration data are underspecified."
}

AI_CONSUMPTION {
 PURPOSES = [
  SemanticSearch,
  OntologyGrounding,
  EcologicalModellingReasoning,
  PopulationEcologyReasoning,
  CommunityEcologyReasoning,
  EcosystemEcologyReasoning,
  CompetitionReasoning,
  PredatorPreyReasoning,
  MutualismReasoning,
  FoodWebReasoning,
  BiodiversityReasoning,
  StabilityReasoning,
  ResilienceReasoning,
  MetapopulationReasoning,
  SpatialEcologyReasoning,
  HabitatFragmentationReasoning,
  ReactionDiffusionReasoning,
  StochasticEcologyReasoning,
  RegimeShiftReasoning,
  ParameterEstimationReasoning,
  KnowledgeGraphConstruction,
  RetrievalAugmentation,
  RecursiveInference
 ]
 NORMALISE {
  "ecological modelling" -> EcologicalModelling
  "ecological modeling" -> EcologicalModelling
  "mathematical ecology" -> EcologicalModelling
  "food web" -> FoodWeb
  "community ecology" -> CommunityEcology
  "spatial ecology" -> SpatialEcology
  "metapopulation" -> Metapopulation
  "regime shift" -> RegimeShift
 }
}

EXECUTION_RULES {
 E1 = "If ecological populations, communities or ecosystems are represented mathematically, activate EcologicalModellingOntology."
 E2 = "If one species is modelled in relation to resources or density, route to PopulationEcology."
 E3 = "If multiple species interact, route to CommunityEcology."
 E4 = "If trophic links are central, route to FoodWeb or NetworkEcology."
 E5 = "If patches or landscapes matter, route to Metapopulation or SpatialEcology."
 E6 = "If diffusion or directional transport matters, use reaction-diffusion or advection-diffusion models."
 E7 = "If environmental variability materially affects outcomes, use StochasticEcology."
 E8 = "If disturbance creates alternative regimes, analyse thresholds, resilience and regime shifts."
 E9 = "If parameters are calibrated, require sensitivity, identifiability and validation checks."
}

RECURSION {
 ENTRY = EcologicalModelling
 EXPAND(EcologicalModelling) -> [
  Ecology, PopulationEcology, CommunityEcology, EcosystemEcology, Species,
  Population, Community, Ecosystem, Habitat, Environment, Resource,
  PopulationDensity, CarryingCapacity, Competition, IntraspecificCompetition,
  InterspecificCompetition, Predation, Herbivory, Mutualism, Commensalism,
  Facilitation, ConsumerResourceModel, PredatorPreyModel,
  LotkaVolterraCompetition, LotkaVolterraPredatorPrey, FunctionalResponse,
  TypeIFunctionalResponse, TypeIIFunctionalResponse, TypeIIIFunctionalResponse,
  FoodWeb, TrophicLevel, TrophicInteraction, NetworkEcology,
  InteractionMatrix, CommunityMatrix, Biodiversity, SpeciesRichness,
  SpeciesEvenness, DiversityIndex, Stability, Resilience, Resistance,
  Persistence, Coexistence, CompetitiveExclusion, InvasionCriterion,
  Metapopulation, PatchOccupancy, Colonisation, LocalExtinction,
  SourceSinkDynamics, Dispersal, Migration, SpatialEcology,
  LandscapeEcology, HabitatFragmentation, Connectivity, ReactionDiffusion,
  AdvectionDiffusion, SpeciesDistributionModel, EnvironmentalGradient,
  NicheModel, ResourceCompetition, NutrientCycling, Biomass,
  PrimaryProduction, EnergyFlow, CarbonFlow, EcosystemFlux,
  StochasticEcology, EnvironmentalStochasticity, DemographicStochasticity,
  Disturbance, Succession, RegimeShift, AlternativeStableState,
  Threshold, EarlyWarningSignal, ParameterEstimation, SensitivityAnalysis,
  Identifiability, ModelCalibration, ModelValidation
 ]
 EXPAND(ModelFamilies) -> [
  PopulationEcologyModels,
  CommunityInteractionModels,
  FoodWebModels,
  EcosystemFlowModels,
  MetapopulationModels,
  SpatialEcologyModels,
  StochasticEcologyModels
 ]
 STOP_CONDITION = "Stop when ecological state, interactions, spatial structure, environmental forcing, stochasticity, stability and validation are sufficiently resolved."
}

ROUTING {
 PARENT_ONTOLOGY = "Mathematical Biology"
 IMMEDIATE_CONTEXTS = [
  "Mathematical Biology Ontology",
  "Population Dynamics Ontology",
  "Dynamical Systems Ontologies",
  "Stochastic Process Ontologies"
 ]
 RELATED_ONTOLOGIES = [
  "Mathematical Biology Ontology",
  "Biological Mathematics",
  "Population Dynamics Ontology",
  "Dynamical Systems Ontologies",
  "Ordinary Differential Equation Ontology",
  "Partial Differential Equation Ontology",
  "Stochastic Process Ontologies",
  "Graph Theory Ontologies",
  "Network Biology Ontologies",
  "Reaction Diffusion Ontologies",
  "Probability & Statistics Ontologies",
  "Optimisation Ontologies"
 ]
 ROUTE_RULES = [
  "Ecological Modelling -> Mathematical Biology for parent semantics",
  "Ecological Modelling -> Population Dynamics for demographic dynamics",
  "Ecological Modelling -> Dynamical Systems for equilibria, stability and regime shifts",
  "Ecological Modelling -> ODE and PDE Ontologies for temporal and spatial dynamics",
  "Ecological Modelling -> Stochastic Processes for environmental and demographic variability",
  "Ecological Modelling -> Graph Theory for food webs and ecological networks",
  "Ecological Modelling -> Reaction Diffusion for spatial pattern formation",
  "Ecological Modelling -> Probability & Statistics for inference and uncertainty",
  "Ecological Modelling -> Optimisation for management and resource-allocation problems"
 ]
}

UPDATE_MODEL {
 MODE = "append-compatible semantic versioning"
 MAJOR = "ontology-breaking conceptual change"
 MINOR = "new compatible ecological interactions, network structures or reasoning pathways"
 PATCH = "clarification, metadata or formatting correction"
 RULES = [
  "Preserve ecological-state semantics.",
  "Preserve interaction-sign semantics.",
  "Preserve population-versus-community distinction.",
  "Preserve local-versus-spatial distinction.",
  "Preserve deterministic-versus-stochastic distinction.",
  "Preserve stability-versus-resilience distinction.",
  "Preserve regime-shift semantics.",
  "Preserve machine-readable ecological-modelling semantics."
 ]
}

OUTPUT {
 CANONICAL_DEFINITION = "Ecological modelling mathematically represents populations, species interactions, communities, ecosystems and their spatial and environmental dynamics."
 INTERACTION_SUMMARY = "Competition, predation, mutualism and resource dependence determine multispecies ecological dynamics."
 NETWORK_SUMMARY = "Food webs and ecological networks represent trophic and non-trophic interaction structure."
 SPATIAL_SUMMARY = "Metapopulation, landscape and reaction-diffusion models represent dispersal, connectivity and spatial pattern."
 ECOSYSTEM_SUMMARY = "Ecosystem models track biomass, production, nutrient, carbon and energy flows."
 STOCHASTIC_SUMMARY = "Stochastic ecological models represent demographic and environmental variability."
 STABILITY_SUMMARY = "Stability, resilience, persistence and regime shifts describe different aspects of ecological response to disturbance."
 VALIDATION_SUMMARY = "Ecological models should be checked for interaction meaning, spatial assumptions, parameter identifiability, uncertainty and empirical consistency."
}

FLOW {
 INPUT
 -> detect_ecological_modelling_context
 -> identify_ecological_system_species_resources_environment_spatial_scale_time_scale_and_data
 -> classify_population_community_food_web_ecosystem_metapopulation_spatial_or_stochastic_model
 -> formulate_species_interactions_resource_flows_environmental_forcing_and_boundary_conditions
 -> solve_or_simulate_ecological_dynamics
 -> analyse_equilibria_coexistence_invasion_stability_resilience_and_thresholds
 -> if_network_analyse_food_web_or_interaction_matrix
 -> if_spatial_analyse_dispersal_connectivity_fragmentation_and_patterns
 -> if_stochastic_estimate_variability_extinction_or_regime_transition probabilities
 -> calibrate_parameters_and_assess_sensitivity_identifiability_and_uncertainty
 -> validate_against_ecological_observations_and_constraints
 -> route_to_mathematical_biology_population_dynamics_dynamical_systems_ODE_PDE_stochastic_processes_graph_theory_network_biology_reaction_diffusion_probability_statistics_or_optimisation ontology
 -> recursively_expand_required_dependencies
 -> verify_result
 -> assign_confidence
 -> produce_semantic_output
 -> END
}

SEMANTIC_SUMMARY {
 "The Ecological Modelling Ontology defines mathematical ecology across population, community, ecosystem and spatial scales. It supports population ecology, competition, predation, herbivory, mutualism and facilitation, consumer-resource and Lotka-Volterra systems, functional responses, food webs, trophic interactions and ecological networks, biodiversity, coexistence and competitive exclusion, stability, resilience and persistence, metapopulations, patch occupancy, colonisation and local extinction, source-sink systems, dispersal, landscape connectivity and fragmentation, reaction-diffusion and advection-diffusion models, species-distribution and niche models, biomass, production, nutrient, carbon and energy flows, stochastic ecology, disturbance, succession, regime shifts, alternative stable states, early-warning signals, parameter estimation, sensitivity, identifiability, calibration and validation."
}

FLOW_HASH {
 METHOD = "semantic-content-identity"
 ID = "KIRETH-MATH-APPLIED-MATHEMATICS-ECOLOGICAL-MODELLING-ONTOLOGY-V1"
}

}

END_FLOW