Fish Ontology

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

flow "FishOntology" v1.0

PAGE {
 TITLE: "Fish Ontology"
 PARENT_DOMAIN: "Zoology"
 CANONICAL_URL: "https://kirethresearch.org/booksai-core/ontologies/biological-ontologies/zoology/fish-ontology.html"
 AUTHORS: ["Mark Anthony Higgins", "Sky Recursive AI"]
}

ENTITY FishOntology {
 TYPE: BiologicalOntology
 DOMAIN: Zoology
 SUBJECT: Fishes
 PURPOSE: FormalSemanticRepresentation
}

ENTITY Fish {
 IS_A: AquaticVertebrate
 REPRESENTS: BroadVertebrateGrouping
 TYPICALLY_HAS: [Gills, Fins, AquaticAdaptations]
}

RULE TaxonomicScope {
 Fish IS_NOT_NECESSARILY: SingleMonophyleticTaxon
 aquatic_similarity != close_phylogenetic_relationship
}

ENTITY FishLineage {
 MAY_INCLUDE: [JawlessFish, CartilaginousFish, RayFinnedFish, LobeFinnedFish]
}

ENTITY JawlessFish { LACKS: Jaws }
ENTITY CartilaginousFish { HAS_PREDOMINANTLY: CartilaginousSkeleton }
ENTITY RayFinnedFish { HAS: RaySupportedFins }
ENTITY LobeFinnedFish { HAS: FleshyLobedPairedAppendages }

ENTITY FishBodyPlan {
 MAY_INCLUDE: [Head, Trunk, Tail, PairedFins, MedianFins, Scales]
 DEPENDS_ON: Taxon
}

ENTITY Fin {
 MAY_BE: [PectoralFin, PelvicFin, DorsalFin, AnalFin, CaudalFin]
 FUNCTIONS_IN: [Propulsion, Stability, Maneuvering]
}

ENTITY Scale {
 MAY_BE: [PlacoidScale, GanoidScale, CycloidScale, CtenoidScale]
}

ENTITY LateralLineSystem {
 DETECTS: WaterMovementAndPressureVariation
}

PROCESS Swimming {
 MOVES: Fish
 THROUGH: Water
 MAY_USE: [BodyUndulation, FinOscillation, FinUndulation]
}

ENTITY BuoyancyControl {
 MAY_USE: [SwimBladder, LipidStorage, DynamicLift, BodyComposition]
}

ENTITY SwimBladder {
 MAY_FUNCTION_IN: [BuoyancyControl, SoundProduction, Hearing]
 IN: ApplicableBonyFish
}

RULE BuoyancyConstraint {
 fish_buoyancy != universally_swim_bladder_dependent
}

ENTITY FishRespiratorySystem {
 TYPICALLY_USES: Gills
 SUPPORTS: GasExchange
}

ENTITY Gill {
 IS_A: RespiratoryOrgan
 MAY_INCLUDE: [GillFilament, GillLamella]
}

PROCESS GillVentilation {
 MOVES: Water
 ACROSS: GillSurface
}

PROCESS GasExchange {
 EXCHANGES: [Oxygen, CarbonDioxide]
 BETWEEN: WaterAndBlood
}

PROCESS CountercurrentExchange {
 MAINTAINS: DiffusionGradient
 BETWEEN: WaterAndBlood
 IN: ApplicableGillSystems
}

PROCESS CellularRespiration {
 RELEASES: UsableEnergy
 FROM: OrganicMolecules
}

RULE RespirationConstraint {
 GillVentilation != GasExchange
 GasExchange != CellularRespiration
}

ENTITY FishCirculatorySystem {
 IS_A: ClosedCirculatorySystem
 TYPICALLY_INCLUDES: [Heart, Blood, BloodVessels]
}

ENTITY FishHeart { PUMPS: Blood }

ENTITY FishDigestiveSystem {
 SUPPORTS: [Ingestion, Digestion, Absorption, Elimination]
 MAY_SHOW: DietarySpecialization
}

ENTITY FeedingStrategy {
 MAY_BE: [Predation, Herbivory, Omnivory, Planktivory, Detritivory, FilterFeeding, Parasitism]
}

PROCESS Digestion {
 BREAKS_DOWN: Food
 INTO: AbsorbableComponents
}

ENTITY FishOsmoregulation {
 REGULATES: WaterAndIonBalance
 ACROSS: AquaticEnvironment
}

ENTITY FreshwaterFish {
 EXPERIENCES: OsmoticWaterGainAndIonLossTendency
 UNDER: TypicalFreshwaterConditions
}

ENTITY MarineBonyFish {
 EXPERIENCES: OsmoticWaterLossTendency
 UNDER: TypicalMarineConditions
}

ENTITY Elasmobranch {
 MAY_USE: UreaRetentionAndOtherMechanisms
 FOR: OsmoticBalance
}

ENTITY Kidney {
 PARTICIPATES_IN: [Excretion, Osmoregulation, IonBalance]
}

ENTITY ChlorideCell {
 IS_A: IonTransportingCell
 MAY_SUPPORT: SaltBalance
}

RULE OsmoregulationConstraint {
 osmoregulatory_strategy MUST_PRESERVE salinity_taxon_and_life_stage_context
}

ENTITY FishNervousSystem {
 INCLUDES: [Brain, SpinalCord, PeripheralNervousSystem]
}

ENTITY FishSensorySystem {
 MAY_INCLUDE: [Vision, Olfaction, Taste, Hearing, VestibularSensation, LateralLine, Electroreception]
}

ENTITY Electroreception {
 DETECTS: ElectricalFields
 IN: ApplicableFishLineages
}

RULE SensoryConstraint {
 behavioural_response != proof_of_specific_sensory_mechanism
 WITHOUT mechanistic_evidence
}

ENTITY FishEndocrineSystem {
 USES: Hormones
 TO_REGULATE: [Growth, Metabolism, Reproduction, Osmoregulation, StressResponse]
}

RULE HormoneConstraint {
 hormone_concentration != physiological_effect
 WITHOUT receptor_tissue_and_state_context
}

ENTITY Ectothermy {
 CHARACTERIZES: MostFish
 BODY_TEMPERATURE_DEPENDS_SUBSTANTIALLY_ON: Environment
}

PROCESS FishGrowth { INCREASES: SizeOrBiomass }

PROCESS FishDevelopment {
 TRANSITIONS: Fish
 THROUGH: DevelopmentalStages
 MAY_INCLUDE: [Embryo, Larva, Juvenile, Adult]
}

RULE GrowthDevelopmentConstraint {
 FishGrowth != FishDevelopment
}

PROCESS FishReproduction {
 TYPICALLY_IS: SexualReproduction
 MAY_INCLUDE: [Oviparity, Ovoviviparity, Viviparity]
}

PROCESS Spawning {
 RELEASES_OR_DEPOSITS: GametesOrEggs
 INTO: ReproductiveEnvironment
}

PROCESS Fertilization {
 MAY_BE: [ExternalFertilization, InternalFertilization]
}

ENTITY ParentalCare {
 MAY_INCLUDE: [NestBuilding, EggGuarding, Brooding, Mouthbrooding, JuvenileProtection]
}

ENTITY SequentialHermaphroditism {
 CHANGES: FunctionalSex
 DURING: Life
 IN: ApplicableFish
}

RULE ReproductiveConstraint {
 spawning != fertilization_success
 egg_presence != offspring_recruitment
}

ENTITY FishGenome { STORES: HeritableGeneticInformation }
ENTITY FishGene { PART_OF: FishGenome }

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

PROCESS Mutation {
 CHANGES: GeneticSequence
 MAY_GENERATE: GeneticVariation
}

ENTITY Genotype { DESCRIBES: GeneticState }
ENTITY Phenotype { RESULTS_FROM: [Genotype, Environment, Development, Interaction] }

RULE GeneticConstraint {
 Genotype != Phenotype
 gene_expression != causal_gene_function
 WITHOUT functional_or_perturbation_evidence
}

ENTITY FishBehaviour {
 MAY_INCLUDE: [Foraging, Schooling, Shoaling, Territoriality, Courtship, Migration, PredatorAvoidance]
}

ENTITY Schooling {
 INVOLVES: CoordinatedDirectionalGroupMovement
}

ENTITY Shoaling {
 INVOLVES: SocialAggregation
 WITHOUT_REQUIRING: CoordinatedDirectionalMovement
}

RULE SocialMovementConstraint {
 Schooling != Shoaling
}

PROCESS Communication {
 MAY_USE: [VisualSignal, ChemicalSignal, AcousticSignal, ElectricalSignal, MechanicalSignal]
}

RULE BehaviourConstraint {
 observed_behaviour != inferred_intention_or_subjective_state
 WITHOUT appropriate_evidence
}

ENTITY FishEcology { STUDIES: FishEnvironmentRelationships }
ENTITY FishPopulation { COMPOSED_OF: IndividualsOfDefinedFishTaxon }
ENTITY FishCommunity { COMPOSED_OF: MultipleFishPopulations }

ENTITY AquaticHabitat {
 MAY_INCLUDE: [Marine, Freshwater, Estuarine, Reef, River, Lake, Pelagic, Benthic]
}

ENTITY EcologicalNiche {
 DESCRIBES: ResourcesConditionsAndInteractions
 ASSOCIATED_WITH: FishTaxonOrPopulation
}

RULE HabitatNicheConstraint {
 AquaticHabitat != EcologicalNiche
}

ENTITY PelagicFish { OCCURS_PRIMARILY_IN: OpenWaterColumn }
ENTITY BenthicFish { OCCURS_PRIMARILY_NEAR: BottomSubstrate }
ENTITY DemersalFish { LIVES_AND_FEEDS_NEAR: Bottom }

PROCESS Predation { INVOLVES: FishAsPredatorOrPrey }
PROCESS Herbivory { INVOLVES: FishConsumingPlantOrAlgalMaterial }
PROCESS Competition { REDUCES: ResourceAccessOrPerformance }

PROCESS Migration {
 MOVES: Fish
 BETWEEN: HabitatsOrRegions
}

ENTITY Anadromy {
 INVOLVES: GrowthPrimarilyAtSea
 AND: ReproductionInFreshwater
}

ENTITY Catadromy {
 INVOLVES: GrowthPrimarilyInFreshwater
 AND: ReproductionAtSea
}

ENTITY Potamodromy { INVOLVES: MigrationEntirelyWithinFreshwater }
ENTITY Oceanodromy { INVOLVES: MigrationEntirelyWithinMarineEnvironment }

PROCESS Dispersal {
 MOVES: IndividualsOrPropagules
 TO: NewLocation
}

RULE MigrationConstraint {
 Anadromy != Catadromy
 Migration != Dispersal
}

ENTITY EnvironmentalFactor {
 MAY_INCLUDE: [Temperature, Salinity, DissolvedOxygen, pH, WaterFlow, Depth, Light, FoodAvailability, HabitatStructure]
 MAY_MODULATE: FishPerformance
}

ENTITY FishAdaptation {
 IS_A: HeritableTraitOrTraitState
 ASSOCIATED_WITH: IncreasedFitness
 IN: DefinedEnvironment
}

RULE AdaptationConstraint {
 trait_environment_association != demonstrated_adaptation
 WITHOUT heritability_fitness_and_selection_evidence
}

PROCESS NaturalSelection {
 CHANGES: TraitOrAlleleFrequencies
 THROUGH: DifferentialReproductiveSuccess
}

PROCESS GeneticDrift { CHANGES: AlleleFrequencies }
PROCESS GeneFlow { MOVES: GeneticVariation BETWEEN: Populations }

ENTITY FishTaxonomy {
 CLASSIFIES: FishTaxa
 USING: [Morphology, Anatomy, Meristics, Development, MolecularData, Genomics, Phylogeny, Nomenclature]
}

ENTITY FishTaxon {
 MAY_HAVE: [ScientificName, Rank, DiagnosticCharacters, PhylogeneticPlacement]
}

ENTITY FishSpecies {
 IS_A: TaxonomicConcept
 REQUIRES: SpeciesConceptAndEvidenceContext
}

ENTITY FishPhylogeny {
 REPRESENTS: EvolutionaryRelationships
 AMONG: FishAndOtherVertebrateLineages
}

ENTITY MeristicCharacter {
 MAY_INCLUDE: [FinRayCount, ScaleCount, VertebralCount, GillRakerCount]
}

RULE TaxonomicIdentityConstraint {
 morphology_meristics_or_sequence_similarity != definitive_fish_species_identity
 WITHOUT reference_resolution_and_taxonomic_context
}

PROCESS FishMeasurement {
 MAY_MEASURE: [Length, Mass, Age, Growth, Morphology, Meristics, Physiology, Behaviour, PopulationSize, Distribution, Migration, GeneticVariation]
 MAY_USE: [FieldSurvey, Imaging, Tagging, Telemetry, OtolithAnalysis, PhysiologicalAssay, Sequencing]
}

ENTITY FishMeasurementContext {
 HAS: [Taxon, LifeStage, SexWhenRelevant, Habitat, Salinity, Temperature, OxygenState, ActivityState, Method, Unit, Timepoint]
}

RULE MeasurementContextRule {
 IF fish_measurements ARE_COMPARED
 THEN FishMeasurementContext MUST_BE preserved
}

ENTITY Evidence {
 TYPES: [IchthyologicalEvidence, AnatomicalEvidence, PhysiologicalEvidence, DevelopmentalEvidence, GeneticEvidence, BehaviouralEvidence, EcologicalEvidence, MigrationEvidence, PhylogeneticEvidence, FieldEvidence, ExperimentalEvidence, FossilEvidence, ComputationalEvidence, LiteratureEvidence]
}

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

RULE EvidenceConflict {
 IF EvidenceSources CONFLICT
 THEN {
  PRESERVE competing_fish_models
  RECORD taxon_and_lineage
  RECORD life_stage
  RECORD habitat_salinity_temperature_and_oxygen_context
  RECORD measurement_method
  RECORD timepoint
  RECORD provenance
  REDUCE confidence
 }
}

RELATION Fish IS_A AquaticVertebrate
RELATION Gill PERFORMS GasExchange
RELATION FishGenome CONTAINS FishGene
RELATION FishPopulation PART_OF FishCommunity
RELATION FishTaxonomy CLASSIFIES FishTaxon

SEMANTIC_EQUIVALENCE {
 "fish" ~= "broad grouping of primarily aquatic vertebrates"
 "ichthyology" ~= "scientific study of fishes"
 "gill ventilation" ~= "movement of water across gill surfaces"
 "schooling" ~= "coordinated directional group swimming"
 "shoaling" ~= "social aggregation of fish"
 "anadromy" ~= "marine growth with freshwater reproduction"
 "catadromy" ~= "freshwater growth with marine reproduction"
}

CONFIDENCE FishAssertion {
 INPUTS: [anatomical_support, physiological_support, developmental_support, genetic_support, behavioural_support, ecological_support, migration_support, phylogenetic_support, field_support, experimental_support, fossil_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 FishIdentityInference {
 IF anatomical_developmental_molecular_and_phylogenetic_evidence converge
 THEN fish_taxonomic_identity confidence MAY_INCREASE
}

RULE GillFunctionInference {
 IF water_flow_blood_flow_and_gas_gradient_evidence converge
 THEN GillGasExchange MAY_BE_SUPPORTED
}

RULE MigrationInference {
 IF repeated_tracking_or_mark_recapture demonstrates recurrent_habitat_movement
 THEN Migration MAY_BE_SUPPORTED
}

RULE CausalityConstraint {
 IF fish_trait_or_marker correlates_with physiological_behavioural_or_ecological_outcome
 THEN DO_NOT_INFER causal_relationship
 WITHOUT mechanistic_experimental_or_longitudinal_evidence
}

QUERY FishLookup(fish_identifier) {
 RETURN [taxonomy, lineage, anatomy, fins, scales, skeleton, respiratory_system, osmoregulation, sensory_systems, physiology, life_stage, development, reproduction, genome, behaviour, habitat, migration, ecological_interactions, evidence, confidence]
}

QUERY FishPhysiologyLookup(context_identifier) {
 RETURN [gill_ventilation, gas_exchange, circulation, osmoregulation, excretion, metabolism, temperature, salinity, dissolved_oxygen, evidence, confidence]
}

QUERY FishMigrationLookup(context_identifier) {
 RETURN [taxon, migration_type, origin, destination, route, timing, life_stage, environmental_cues, tracking_method, evidence, confidence]
}

UPDATE_MODEL {
 ON new_fish_evidence:
  validate_provenance()
  identify_taxon_lineage_life_stage_and_aquatic_environment()
  normalize_anatomical_gene_behavioural_ecological_and_taxonomic_identifiers()
  capture_salinity_temperature_oxygen_activity_measurement_and_timepoint_context()
  map_body_plan_fin_scale_skeleton_and_buoyancy_relationships()
  map_gill_respiration_circulation_digestion_excretion_and_osmoregulation()
  map_sensory_endocrine_growth_development_and_reproduction()
  map_genetic_behavioural_schooling_migration_population_and_ecological_relationships()
  map_taxonomic_phylogenetic_and_evolutionary_relationships()
  preserve_conflicting_evidence()
  recalculate_confidence()
  regenerate_fish_relationships()
  update_flow_hash()
}

AI_CONSUMPTION {
 MODE: FormalSemanticReasoning
 PARSE_AS: ExecutableFlowAlgebra
 PRIORITIES: [fish_identity, lineage, taxon, body_plan, fins, skeleton, gills, osmoregulation, sensory_systems, life_stage, reproduction, behaviour, migration, ecology, evidence_provenance, confidence]
 REQUIREMENTS: [preserve_taxon_lineage_life_stage_and_aquatic_environmental_context, preserve_salinity_temperature_oxygen_activity_measurement_and_timepoint_context, recognize_fish_as_broad_not_necessarily_monophyletic_grouping, distinguish_gill_ventilation_from_gas_exchange, distinguish_gas_exchange_from_cellular_respiration, preserve_osmoregulatory_context, distinguish_growth_from_development, distinguish_spawning_from_fertilization_success, distinguish_schooling_from_shoaling, distinguish_anadromy_from_catadromy, distinguish_migration_from_dispersal, distinguish_genotype_from_phenotype, distinguish_gene_expression_from_causal_function, distinguish_trait_environment_association_from_adaptation, distinguish_similarity_from_definitive_taxonomic_identity, distinguish_correlation_from_causation, preserve_uncertainty]
}

VALIDATE {
 REQUIRE Fish
 REQUIRE FishLineage
 REQUIRE FishBodyPlan
 REQUIRE Fin
 REQUIRE Gill
 REQUIRE FishRespiratorySystem
 REQUIRE FishCirculatorySystem
 REQUIRE FishDigestiveSystem
 REQUIRE FishOsmoregulation
 REQUIRE FishNervousSystem
 REQUIRE FishGrowth
 REQUIRE FishDevelopment
 REQUIRE FishReproduction
 REQUIRE FishGenome
 REQUIRE FishBehaviour
 REQUIRE FishEcology
 REQUIRE FishTaxonomy
 REQUIRE FishMeasurement
 REQUIRE Evidence
 REQUIRE CONFIDENCE
 REQUIRE SEMANTIC_EQUIVALENCE
 REQUIRE UPDATE_MODEL
 REQUIRE AI_CONSUMPTION

 ASSERT GillVentilation != GasExchange
 ASSERT GasExchange != CellularRespiration
 ASSERT FishGrowth != FishDevelopment
 ASSERT spawning != fertilization_success
 ASSERT Schooling != Shoaling
 ASSERT Anadromy != Catadromy
 ASSERT Migration != Dispersal
 ASSERT Genotype != Phenotype
 ASSERT morphology_meristics_or_sequence_similarity != definitive_fish_species_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 "FishOntology"