Invertebrate Ontology

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

flow "InvertebrateOntology" v1.0

ENTITY InvertebrateOntology {
 TYPE: BiologicalOntology
 DOMAIN: Zoology
 SUBJECT: InvertebrateAnimals
 PURPOSE: FormalSemanticRepresentation
}

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

ENTITY Invertebrate {
 IS_A: Animal
 LACKS: VertebralColumn
 REPRESENTS: BroadNonVertebrateAnimalGrouping
}

RULE InvertebrateTaxonomyConstraint {
 Invertebrate IS_NOT_NECESSARILY: SingleMonophyleticTaxon
}

ENTITY Vertebrate { IS_A: Animal }
RULE VertebrateDistinction { Invertebrate != Vertebrate }

ENTITY InvertebrateBodyPlan {
 MAY_INCLUDE: [RadialSymmetry, BilateralSymmetry, Asymmetry, Segmentation, BodyCavityVariation, Exoskeleton, HydrostaticSkeleton]
 DEPENDS_ON: Lineage
}

ENTITY Porifera { IS_A: InvertebrateLineage }
ENTITY Cnidaria { IS_A: InvertebrateLineage }
ENTITY Platyhelminthes { IS_A: InvertebrateLineage }
ENTITY Nematoda { IS_A: InvertebrateLineage }
ENTITY Annelida { IS_A: InvertebrateLineage }
ENTITY Mollusca { IS_A: InvertebrateLineage }
ENTITY Arthropoda { IS_A: InvertebrateLineage }
ENTITY Echinodermata { IS_A: InvertebrateLineage }

RULE LineageConstraint {
 shared_invertebrate_status != close_phylogenetic_relationship
}

ENTITY Symmetry { MAY_BE: [RadialSymmetry, BilateralSymmetry, Asymmetry] }
ENTITY Segmentation { DESCRIBES: RepeatedBodyUnits }
ENTITY BodyCavity { MAY_BE: [Coelom, Pseudocoelom, ReducedOrAbsentBodyCavity] }

ENTITY Exoskeleton {
 IS_A: ExternalSupportingStructure
 MAY_PROVIDE: [Protection, MechanicalSupport, MuscleAttachment]
}

ENTITY HydrostaticSkeleton {
 USES: FluidPressureAndBodyWall
 FOR: MechanicalSupportAndMovement
}

ENTITY ArthropodExoskeleton {
 SUBCLASS_OF: Exoskeleton
 MAY_CONTAIN: Chitin
}

PROCESS Molting {
 SHEDS_AND_RENEWS: ExternalCuticleOrExoskeleton
}

ENTITY Ecdysis { IS_A: MoltingProcess }

PROCESS Locomotion {
 MAY_USE: [MuscularContraction, Appendages, Cilia, JetPropulsion, HydrostaticMechanism]
}

PROCESS Feeding {
 MAY_BE: [FilterFeeding, Grazing, Predation, DepositFeeding, ParasiticFeeding, SuspensionFeeding]
}

ENTITY DigestiveSystem {
 MAY_BE: [IncompleteDigestiveSystem, CompleteDigestiveSystem, IntracellularDigestionDominantSystem]
 DEPENDS_ON: Lineage
}

PROCESS Digestion {
 BREAKS_DOWN: Food
 INTO: AbsorbableComponents
}

PROCESS Absorption {
 MOVES: Nutrients
 INTO: CellsOrInternalTransportSystem
}

ENTITY RespiratoryStrategy {
 MAY_INCLUDE: [BodySurfaceExchange, Gills, TrachealSystem, BookLungs, SpecializedRespiratoryStructures]
}

PROCESS GasExchange {
 EXCHANGES: RespiratoryGases
 BETWEEN: AnimalAndEnvironment
}

PROCESS CellularRespiration {
 RELEASES: UsableEnergy
 FROM: OrganicMolecules
}

RULE RespirationDistinction {
 GasExchange != CellularRespiration
}

ENTITY CirculatoryStrategy {
 MAY_BE: [OpenCirculation, ClosedCirculation, DiffusionDominatedTransport]
}

ENTITY Hemolymph {
 IS_A: CirculatoryFluid
 IN: ManyOpenCirculatorySystems
}

ENTITY ExcretoryStructure {
 MAY_INCLUDE: [Nephridium, MalpighianTubule, ExcretoryCanal, DiffusionBasedExcretion]
}

PROCESS Excretion { REMOVES: MetabolicWaste }
PROCESS Osmoregulation { MAINTAINS: WaterAndSoluteBalance }

ENTITY NervousSystem {
 MAY_RANGE_FROM: NerveNetToCentralizedNervousSystem
}

ENTITY NerveNet { IS_A: DistributedNeuralNetwork }
ENTITY Ganglion { IS_A: ClusterOfNeuronalCellBodies }

ENTITY SensoryStructure {
 MAY_INCLUDE: [Eye, Ocellus, Statocyst, Chemoreceptor, Mechanoreceptor]
}

PROCESS SensoryDetection {
 DETECTS: EnvironmentalOrInternalStimulus
}

PROCESS InvertebrateGrowth {
 INCREASES: SizeOrBiomass
}

PROCESS InvertebrateDevelopment {
 TRANSITIONS: Organism
 THROUGH: DevelopmentalStages
 MAY_INCLUDE: [Embryogenesis, LarvalDevelopment, Metamorphosis, Maturation]
}

RULE GrowthDevelopmentDistinction {
 InvertebrateGrowth != InvertebrateDevelopment
}

ENTITY InvertebrateLifeStage {
 MAY_BE: [Embryo, Larva, Juvenile, Adult]
 DEPENDS_ON: Taxon
}

PROCESS Metamorphosis {
 TRANSFORMS: BodyFormAndPhysiology
 BETWEEN: LifeStages
}

ENTITY CompleteMetamorphosis {
 MAY_INCLUDE: [Egg, Larva, Pupa, Adult]
}

ENTITY IncompleteMetamorphosis {
 MAY_INCLUDE: [Egg, Nymph, Adult]
}

RULE MetamorphosisConstraint {
 CompleteMetamorphosis != IncompleteMetamorphosis
}


PROCESS InvertebrateReproduction {
 MAY_BE: [SexualReproduction, AsexualReproduction]
}

PROCESS SexualReproduction {
 INVOLVES: GameticContribution
}

PROCESS AsexualReproduction {
 MAY_INCLUDE: [Budding, Fission, Fragmentation, Parthenogenesis]
 DEPENDS_ON: Lineage
}

PROCESS Fertilization {
 MAY_BE: [InternalFertilization, ExternalFertilization]
}

ENTITY Hermaphroditism {
 OCCURS_WHEN: IndividualHasMaleAndFemaleReproductiveFunctions
}

ENTITY InvertebrateGenome {
 STORES: HeritableGeneticInformation
}

ENTITY InvertebrateGene {
 PART_OF: InvertebrateGenome
 MAY_ENCODE_OR_REGULATE: Trait
}

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

PROCESS Mutation {
 CHANGES: GeneticSequence
 MAY_GENERATE: Variation
}

ENTITY Genotype { DESCRIBES: GeneticState }

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

RULE GenotypePhenotypeDistinction {
 Genotype != Phenotype
}

ENTITY InvertebrateBehaviour {
 MAY_INCLUDE: [Foraging, Mating, Escape, Territoriality, SocialBehaviour, Migration]
}

PROCESS Communication {
 MAY_USE: [ChemicalSignal, VisualSignal, AcousticSignal, TactileSignal, VibrationalSignal]
}

ENTITY Eusociality {
 TYPICALLY_INCLUDES: [CooperativeBroodCare, OverlappingGenerations, ReproductiveDivisionOfLabour]
}

RULE BehaviourConstraint {
 observed_behaviour != inferred_intention_or_subjective_state
 WITHOUT appropriate_evidence
}

ENTITY InvertebrateEcology {
 STUDIES: InvertebrateEnvironmentRelationships
}

ENTITY InvertebratePopulation {
 COMPOSED_OF: IndividualsOfDefinedInvertebrateTaxon
}

ENTITY InvertebrateCommunity {
 COMPOSED_OF: MultipleInvertebratePopulations
}

ENTITY Habitat {
 MAY_INCLUDE: [Marine, Freshwater, Terrestrial, Soil, HostAssociated, Aerial]
}

ENTITY EcologicalNiche {
 DESCRIBES: ResourcesConditionsAndInteractions
 ASSOCIATED_WITH: InvertebrateTaxonOrPopulation
}

RULE HabitatNicheDistinction {
 Habitat != EcologicalNiche
}

PROCESS Predation { INVOLVES: InvertebratePredatorOrPrey }
PROCESS Herbivory { INVOLVES: ConsumptionOfPlantOrAlgalMaterial }
PROCESS Parasitism { BENEFITS: Parasite AT_COST_TO: Host }
PROCESS Mutualism { BENEFITS: InteractingPartners }

PROCESS Pollination {
 MAY_BE_PERFORMED_BY: Invertebrate
 TRANSFERS: Pollen
 BETWEEN: PlantReproductiveStructures
}

PROCESS Decomposition {
 MAY_BE_SUPPORTED_BY: DetritivorousInvertebrates
}

ENTITY Detritivore {
 CONSUMES: DeadOrganicMatter
}

ENTITY EcosystemEngineer {
 MODIFIES: PhysicalHabitat
 THROUGH: BiologicalActivity
}

ENTITY EnvironmentalFactor {
 MAY_INCLUDE: [Temperature, Moisture, Oxygen, Salinity, FoodAvailability, HabitatStructure, PredationPressure]
 MAY_MODULATE: InvertebratePerformance
}

ENTITY InvertebrateAdaptation {
 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
 THROUGH: StochasticProcesses
}

PROCESS GeneFlow {
 MOVES: GeneticVariation
 BETWEEN: Populations
}

ENTITY InvertebrateTaxonomy {
 CLASSIFIES: InvertebrateAnimals
 USING: [Morphology, Anatomy, Development, MolecularData, Phylogeny, Nomenclature]
}

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

ENTITY InvertebrateSpecies {
 IS_A: TaxonomicConcept
 REQUIRES: SpeciesConceptAndEvidenceContext
}

ENTITY InvertebratePhylogeny {
 REPRESENTS: EvolutionaryRelationships
 AMONG: InvertebrateLineages
}

RULE TaxonomicIdentityConstraint {
 morphological_or_sequence_similarity != definitive_invertebrate_species_identity
 WITHOUT reference_resolution_and_taxonomic_context
}

PROCESS InvertebrateMeasurement {
 MAY_MEASURE: [Morphology, Anatomy, Physiology, Growth, Development, Behaviour, PopulationSize, Distribution, GeneticVariation]
 MAY_USE: [Observation, Imaging, Microscopy, PhysiologicalAssay, Tracking, Sequencing, FieldSurvey]
}

ENTITY InvertebrateMeasurementContext {
 HAS: [Taxon, LifeStage, SexWhenRelevant, TissueOrOrgan, Environment, Method, Unit, Timepoint]
}

RULE MeasurementContextRule {
 IF invertebrate_measurements ARE_COMPARED
 THEN InvertebrateMeasurementContext MUST_BE preserved
}

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

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

RULE EvidenceConflict {
 IF EvidenceSources CONFLICT
 THEN {
  PRESERVE competing_invertebrate_models
  RECORD taxon
  RECORD life_stage
  RECORD sex_when_relevant
  RECORD tissue_or_organ
  RECORD environment
  RECORD measurement_method
  RECORD timepoint
  RECORD provenance
  REDUCE confidence
 }
}


RELATION Invertebrate IS_A Animal
RELATION InvertebrateGenome CONTAINS InvertebrateGene
RELATION InvertebratePopulation PART_OF InvertebrateCommunity
RELATION EnvironmentalFactor MODULATES InvertebratePerformance
RELATION Arthropoda IS_A InvertebrateLineage
RELATION Mollusca IS_A InvertebrateLineage
RELATION Annelida IS_A InvertebrateLineage
RELATION Nematoda IS_A InvertebrateLineage
RELATION Cnidaria IS_A InvertebrateLineage
RELATION Echinodermata IS_A InvertebrateLineage

SEMANTIC_EQUIVALENCE {
 "invertebrate" ~= "animal lacking a vertebral column"
 "invertebrate zoology" ~= "study of non-vertebrate animals"
 "ecdysis" ~= "molting of an external cuticle or exoskeleton"
 "hemolymph" ~= "circulatory fluid of many open circulatory systems"
 "larva" ~= "pre-adult developmental stage" WHEN applicable
 "eusociality" ~= "social system with cooperative brood care overlapping generations and reproductive division of labour"
}

CONFIDENCE InvertebrateAssertion {
 INPUTS: [anatomical_support, physiological_support, developmental_support, genetic_support, behavioural_support, ecological_support, phylogenetic_support, field_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 InvertebrateIdentityInference {
 IF absence_of_vertebral_column
 AND anatomical_developmental_molecular_and_phylogenetic_evidence converge
 THEN invertebrate_identity confidence MAY_INCREASE
}

RULE LineageInference {
 IF morphological_developmental_and_molecular_features converge
 THEN invertebrate_lineage_assignment MAY_BE_SUPPORTED
}

RULE EcologicalFunctionInference {
 IF repeated_observation_or_experiment links_invertebrate_activity_to ecosystem_process
 THEN ecological_function MAY_BE_SUPPORTED
}

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

QUERY InvertebrateLookup(invertebrate_identifier) {
 RETURN [taxonomy, lineage, body_plan, organ_systems, physiology, life_stage, development, reproduction, genome, behaviour, habitat, ecological_interactions, evidence, confidence]
}

QUERY InvertebrateLineageLookup(lineage_identifier) {
 RETURN [diagnostic_features, body_plan, organ_systems, developmental_pattern, reproduction, representative_taxa, phylogeny, ecology, evidence, confidence]
}

QUERY InvertebrateEcologyLookup(context_identifier) {
 RETURN [taxa, populations, community, habitat, niche, trophic_roles, pollination, decomposition, environmental_factors, evidence, confidence]
}

UPDATE_MODEL {
 ON new_invertebrate_evidence:
  validate_provenance()
  identify_taxon_lineage_life_stage_tissue_organ_and_environment()
  normalize_anatomical_gene_behavioural_ecological_and_taxonomic_identifiers()
  capture_measurement_method_units_and_timepoint()
  map_body_plan_tissue_and_organ_system_relationships()
  map_feeding_respiration_circulation_excretion_and_osmoregulation()
  map_growth_development_metamorphosis_reproduction_and_genetics()
  map_sensory_behavioural_social_and_communication_relationships()
  map_population_community_trophic_pollination_and_decomposition_relationships()
  map_taxonomic_phylogenetic_and_evolutionary_relationships()
  compare_existing_invertebrate_models()
  preserve_conflicting_evidence()
  recalculate_confidence()
  regenerate_invertebrate_relationships()
  update_flow_hash()
}

AI_CONSUMPTION {
 MODE: FormalSemanticReasoning
 PARSE_AS: ExecutableFlowAlgebra
 PRIORITIES: [invertebrate_identity, lineage, taxon, body_plan, organ_system, physiology, life_stage, development, reproduction, genetics, behaviour, ecology, evidence_provenance, confidence]
 REQUIREMENTS: [preserve_taxon_lineage_life_stage_and_environmental_context, preserve_tissue_organ_measurement_and_timepoint_context, recognize_invertebrate_as_broad_nonvertebrate_grouping, distinguish_invertebrate_from_vertebrate, distinguish_shared_invertebrate_status_from_close_phylogenetic_relationship, distinguish_gas_exchange_from_cellular_respiration, distinguish_growth_from_development, distinguish_complete_from_incomplete_metamorphosis, distinguish_genotype_from_phenotype, distinguish_observed_behaviour_from_inferred_intention, distinguish_habitat_from_ecological_niche, distinguish_trait_environment_association_from_adaptation, distinguish_similarity_from_definitive_taxonomic_identity, distinguish_correlation_from_causation, preserve_uncertainty]
}

VALIDATE {
 REQUIRE Invertebrate
 REQUIRE InvertebrateBodyPlan
 REQUIRE Porifera
 REQUIRE Cnidaria
 REQUIRE Nematoda
 REQUIRE Annelida
 REQUIRE Mollusca
 REQUIRE Arthropoda
 REQUIRE Echinodermata
 REQUIRE DigestiveSystem
 REQUIRE GasExchange
 REQUIRE CirculatoryStrategy
 REQUIRE NervousSystem
 REQUIRE InvertebrateGrowth
 REQUIRE InvertebrateDevelopment
 REQUIRE InvertebrateReproduction
 REQUIRE InvertebrateGenome
 REQUIRE InvertebrateBehaviour
 REQUIRE InvertebrateEcology
 REQUIRE InvertebrateTaxonomy
 REQUIRE InvertebrateMeasurement
 REQUIRE Evidence
 REQUIRE CONFIDENCE
 REQUIRE SEMANTIC_EQUIVALENCE
 REQUIRE UPDATE_MODEL
 REQUIRE AI_CONSUMPTION

 ASSERT Invertebrate != Vertebrate
 ASSERT shared_invertebrate_status != close_phylogenetic_relationship
 ASSERT GasExchange != CellularRespiration
 ASSERT InvertebrateGrowth != InvertebrateDevelopment
 ASSERT CompleteMetamorphosis != IncompleteMetamorphosis
 ASSERT Genotype != Phenotype
 ASSERT Habitat != EcologicalNiche
 ASSERT trait_environment_association != demonstrated_adaptation
 ASSERT morphological_or_sequence_similarity != definitive_invertebrate_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 "InvertebrateOntology"