Plant Taxonomy Ontology

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

flow "PlantTaxonomyOntology" v1.0

ENTITY PlantTaxonomyOntology {
 TYPE: BiologicalOntology
 DOMAIN: Botany
 SUBJECT: PlantTaxonomy
 PURPOSE: FormalSemanticRepresentation
}

PAGE {
 TITLE: "Plant Taxonomy Ontology"
 PARENT_DOMAIN: "Botany"
 CANONICAL_URL: "https://kirethresearch.org/booksai-core/ontologies/biological-ontologies/botany/plant-taxonomy-ontology.html"
 AUTHORS: ["Mark Anthony Higgins", "Sky Recursive AI"]
}

ENTITY PlantTaxonomy {
 STUDIES_AND_ORGANIZES: PlantClassification
 USES: [Nomenclature, Morphology, Anatomy, ReproductiveCharacters, Phylogeny, MolecularData, Genomics]
}

ENTITY PlantTaxon {
 IS_A: TaxonomicGroup
 MAY_HAVE: [ScientificName, Rank, Circumscription, DiagnosticCharacters, PhylogeneticPlacement]
}

ENTITY TaxonomicRank {
 MAY_BE: [Kingdom, Division, Class, Order, Family, Genus, Species, Subspecies, Variety, Form]
}

ENTITY Species {
 IS_A: TaxonomicRank
 REPRESENTS: SpeciesLevelTaxon
}

ENTITY Genus {
 CONTAINS: OneOrMoreSpecies
}

ENTITY Family {
 CONTAINS: OneOrMoreGenera
}

ENTITY Order {
 CONTAINS: OneOrMoreFamilies
}

ENTITY Class {
 CONTAINS: OneOrMoreOrders
}

ENTITY Division {
 CONTAINS: OneOrMoreClasses
}

RULE RankConstraint {
 taxonomic_rank != evolutionary_age
 taxonomic_rank != absolute_degree_of_difference
}

ENTITY ScientificName {
 IDENTIFIES: Taxon
 UNDER: NomenclaturalRules
}

ENTITY BinomialName {
 COMPOSED_OF: [GenusName, SpecificEpithet]
 APPLIES_TO: SpeciesName
}

ENTITY GenusName {
 IS_PART_OF: BinomialName
}

ENTITY SpecificEpithet {
 IS_PART_OF: BinomialName
 DOES_NOT_ALONE_IDENTIFY: Species
}

RULE BinomialConstraint {
 specific_epithet != complete_species_name
}

ENTITY AuthorCitation {
 MAY_ACCOMPANY: ScientificName
 IDENTIFIES: NomenclaturalAuthorship
}

ENTITY Nomenclature {
 GOVERNS: ScientificNaming
 DISTINCT_FROM: TaxonomicCircumscription
}

RULE TaxonomyNomenclatureDistinction {
 taxonomy != nomenclature
}

ENTITY NomenclaturalCode {
 PROVIDES: RulesForScientificNames
}

ENTITY BotanicalNomenclature {
 APPLIES_TO: PlantNames
 UNDER: RelevantNomenclaturalCode
}

ENTITY TypeConcept {
 ANCHORS: ScientificName
 TO: NomenclaturalType
}

ENTITY NomenclaturalType {
 MAY_BE: [Holotype, Isotype, Lectotype, Neotype, Syntype]
 ANCHORS: NameApplication
}

ENTITY Holotype {
 IS_A: SingleOriginalDesignatedTypeSpecimen
}

ENTITY Isotype {
 IS_A: DuplicateOfHolotype
}

ENTITY Lectotype {
 SELECTED_FROM: OriginalMaterial
 WHEN: HolotypeUnavailableOrNotDesignated
}

ENTITY Neotype {
 DESIGNATED_WHEN: OriginalTypeMaterialUnavailable
}

RULE TypeConstraint {
 nomenclatural_type != necessarily_typical_individual
}

ENTITY TaxonomicCircumscription {
 DEFINES: MembershipBoundaryOfTaxon
}

ENTITY DiagnosticCharacter {
 HELPS_DISTINGUISH: Taxon
 FROM: RelatedTaxa
}

ENTITY Character {
 MAY_BE: [MorphologicalCharacter, AnatomicalCharacter, ReproductiveCharacter, MolecularCharacter, CytologicalCharacter, ChemicalCharacter]
}

ENTITY CharacterState {
 IS_A: ObservedOrDefinedState
 OF: Character
}

ENTITY MorphologicalCharacter {
 MAY_INCLUDE: [LeafShape, FlowerStructure, FruitType, SeedCharacter, GrowthForm]
}

ENTITY AnatomicalCharacter {
 MAY_INCLUDE: [VascularArrangement, CellType, TissueStructure, StomatalPattern]
}

ENTITY ReproductiveCharacter {
 MAY_INCLUDE: [FloralStructure, PollenCharacter, OvuleCharacter, FruitCharacter, SeedCharacter]
}

ENTITY CytologicalCharacter {
 MAY_INCLUDE: [ChromosomeNumber, Ploidy, Karyotype]
}

ENTITY MolecularCharacter {
 MAY_INCLUDE: [DNASequence, MolecularMarker, GenomicFeature]
}

RULE CharacterConstraint {
 single_character_difference != automatically_distinct_taxon
}

ENTITY Identification {
 ASSIGNS_ORINFERS: TaxonomicIdentity
 FROM: Evidence
}

ENTITY IdentificationKey {
 GUIDES: Identification
 USING: CharacterChoices
 MAY_BE: DichotomousKey
}

ENTITY DichotomousKey {
 USES: PairedAlternativeCharacterStatements
}

ENTITY TaxonomicDescription {
 SUMMARIZES: CharactersOfTaxon
}

ENTITY Diagnosis {
 STATES: CharactersDistinguishingTaxon
 FROM: RelatedTaxa
}

RULE DescriptionDiagnosisDistinction {
 TaxonomicDescription != Diagnosis
}

ENTITY HerbariumSpecimen {
 IS_A: PreservedPlantSpecimen
 MAY_SUPPORT: [Identification, Nomenclature, DistributionRecord, MorphologicalStudy]
}

ENTITY Herbarium {
 STORES: PreservedPlantCollections
}

ENTITY VoucherSpecimen {
 DOCUMENTS: BiologicalMaterial
 USED_IN: Study
}

RULE VoucherConstraint {
 specimen_record_without_verifiable_identity MAY_HAVE reduced_taxonomic_confidence
}

ENTITY CollectionEvent {
 PRODUCES: Specimen
 HAS: [Collector, Date, Locality, Habitat]
}

ENTITY Locality {
 DESCRIBES: GeographicCollectionContext
}

ENTITY TaxonomicRevision {
 REASSESSES: Taxon
 USING: NewOrIntegratedEvidence
 MAY_CHANGE: [Circumscription, Synonymy, Rank, Identification]
}

ENTITY Synonym {
 IS_A: AlternativeScientificName
 REFERS_TO: SameOrOverlappingTaxonomicConcept
 UNDER: DefinedTreatment
}

ENTITY AcceptedName {
 IS: PreferredName
 UNDER: DefinedTaxonomicOrNomenclaturalTreatment
}

RULE SynonymConstraint {
 synonymy MUST_PRESERVE source_treatment_and_taxonomic_concept
}

ENTITY Homonym {
 IS_A: SameOrConfusinglySameName
 APPLIED_TO: DifferentTaxa
 UNDER: NomenclaturalContext
}

ENTITY Basionym {
 IS_A: EarlierName
 PROVIDING: NameBearingBasisForNewCombination
}

ENTITY NewCombination {
 RECOMBINES: ExistingEpithet
 WITH: DifferentGenusOrRank
 UNDER: NomenclaturalRules
}

ENTITY PlantSystematics {
 STUDIES: DiversityAndRelationshipsOfPlants
 INCLUDES: TaxonomyAndPhylogeny
}

ENTITY Phylogeny {
 REPRESENTS: EvolutionaryRelationships
 AMONG: PlantTaxa
}

ENTITY Clade {
 INCLUDES: AncestorAndDescendants
 IN: PhylogeneticHypothesis
}

ENTITY MonophyleticGroup {
 IS_A: Clade
}

ENTITY ParaphyleticGroup {
 INCLUDES: CommonAncestor
 BUT_NOT_ALL: Descendants
}

ENTITY PolyphyleticGroup {
 GROUPS: Taxa
 WITHOUT_INCLUDING: MostRecentCommonAncestorAsDefined
}

RULE MonophylyConstraint {
 taxonomic_similarity != monophyly
}

ENTITY PhylogeneticTree {
 REPRESENTS: HypothesisOfEvolutionaryRelationships
}

ENTITY Node {
 REPRESENTS: DivergenceOrAncestorHypothesis
}

ENTITY Branch {
 CONNECTS: NodesOrTaxa
}

ENTITY SisterTaxa {
 SHARE: ImmediateCommonAncestor
 IN: Tree
}

ENTITY Outgroup {
 PROVIDES: ComparativeReference
 FOR: RootingOrCharacterPolarization
}

RULE TreeConstraint {
 phylogenetic_tree != direct_observation_of_ancestry
}

PROCESS PhylogeneticInference {
 ESTIMATES: EvolutionaryRelationships
 FROM: CharacterData
}

ENTITY MolecularPhylogenetics {
 USES: MolecularSequenceOrGenomicData
 FOR: PhylogeneticInference
}

ENTITY DNA_Barcode {
 IS_A: StandardizedSequenceRegion
 MAY_SUPPORT: PlantIdentification
}

PROCESS DNA_Barcoding {
 COMPARES: DNA_Barcode
 WITH: ReferenceSequences
 TO_SUPPORT: Identification
}

RULE BarcodeConstraint {
 barcode_similarity != definitive_species_identity
 WITHOUT reference_quality_resolution_and_taxonomic_context
}

ENTITY ReferenceSequence {
 HAS: TaxonomicAssignment
 SHOULD_HAVE: ProvenanceAndVoucherContext
}

ENTITY GenomeData {
 MAY_SUPPORT: [Phylogeny, SpeciesDelimitation, TaxonomicRevision]
}

ENTITY SpeciesDelimitation {
 EVALUATES: BoundariesAmongSpeciesLevelLineages
 MAY_USE: [Morphology, Reproduction, Ecology, Genetics, Phylogeny, Genomics]
}

RULE SpeciesDelimitationConstraint {
 genetic_cluster != automatically_species
}

ENTITY SpeciesConcept {
 MAY_BE: [BiologicalSpeciesConcept, PhylogeneticSpeciesConcept, MorphologicalSpeciesConcept, EcologicalSpeciesConcept]
}

RULE SpeciesConceptConstraint {
 species_boundary MAY_DEPEND_ON species_concept_and_evidence
}

ENTITY Hybrid {
 RESULTS_FROM: Hybridization
 BETWEEN: DistinctPlantLineages
}

PROCESS Hybridization {
 COMBINES: GeneticMaterial
 BETWEEN: DistinctLineages
}

ENTITY Introgression {
 RESULTS_FROM: GeneFlowAcrossTaxonomicBoundaries
 THROUGH: HybridizationAndBackcrossing
}

ENTITY PolyploidTaxon {
 HAS: MoreThanTwoChromosomeSets
 MAY_ARISE_THROUGH: [Autopolyploidy, Allopolyploidy]
}

RULE HybridPolyploidConstraint {
 reticulate_evolution MAY_REQUIRE network_like_representation
 RATHER_THAN strictly_bifurcating_tree
}

ENTITY CultivatedPlant {
 MAY_HAVE: [CultivarName, GroupName, BreedingLine]
}

ENTITY Cultivar {
 IS_A: CultivatedPlantCategory
 DEFINED_BY: SelectedDistinctiveCharacters
 MAINTAINED_BY: Propagation
}

RULE CultivarConstraint {
 cultivar != botanical_variety
}

ENTITY BotanicalVariety {
 IS_A: InfraspecificTaxonomicRank
}

ENTITY Subspecies {
 IS_A: InfraspecificTaxonomicRank
}

ENTITY Form {
 IS_A: InfraspecificTaxonomicRank
 IN: ApplicableTaxonomicTreatment
}

ENTITY CommonName {
 IS_A: VernacularName
 MAY_REFER_TO: OneOrMultipleTaxa
}

RULE CommonNameConstraint {
 common_name != unique_taxonomic_identifier
}

ENTITY Distribution {
 DESCRIBES: GeographicOccurrence
 OF: Taxon
}

ENTITY NativeRange {
 DESCRIBES: HistoricalOrBiogeographicNativeDistribution
}

ENTITY IntroducedRange {
 DESCRIBES: DistributionOutsideNativeRange
 DUE_TO: HumanMediatedMovement
}

ENTITY ConservationStatus {
 MAY_BE_ASSOCIATED_WITH: Taxon
 UNDER: DefinedAssessmentFramework
}

RULE StatusConstraint {
 conservation_status != taxonomic_rank
}

PROCESS TaxonomicSampling {
 COLLECTS: Representatives
 ACROSS: [Populations, Geography, Morphology, GeneticVariation]
}

PROCESS MorphologicalAnalysis {
 COMPARES: MorphologicalCharacters
}

PROCESS AnatomicalAnalysis {
 COMPARES: AnatomicalCharacters
}

PROCESS CytogeneticAnalysis {
 MEASURES: [ChromosomeNumber, Ploidy, Karyotype]
}

PROCESS MolecularSequencing {
 DETERMINES: DNASequence
}

PROCESS PhylogenomicAnalysis {
 USES: GenomeScaleData
 TO_INFER: Phylogeny
}

PROCESS TaxonomicIdentification {
 MAY_USE: [IdentificationKey, SpecimenComparison, Morphology, Anatomy, DNA_Barcoding, Phylogeny]
}

ENTITY TaxonomicEvidence {
 MAY_INCLUDE: [MorphologicalEvidence, AnatomicalEvidence, ReproductiveEvidence, CytologicalEvidence, MolecularEvidence, GenomicEvidence, EcologicalEvidence, GeographicEvidence, NomenclaturalEvidence]
}

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

RULE EvidenceConflict {
 IF TaxonomicEvidenceSources CONFLICT
 THEN {
  PRESERVE competing_taxonomic_hypotheses
  RECORD taxon_concept
  RECORD species_concept
  RECORD specimen_or_population
  RECORD geographic_context
  RECORD character_data
  RECORD molecular_reference
  RECORD taxonomic_treatment
  RECORD provenance
  REDUCE confidence
 }
}

RELATION PlantTaxonomy CLASSIFIES PlantTaxon
RELATION PlantTaxon HAS TaxonomicRank
RELATION ScientificName IDENTIFIES PlantTaxon
RELATION NomenclaturalType ANCHORS ScientificName
RELATION DiagnosticCharacter DISTINGUISHES PlantTaxon
RELATION HerbariumSpecimen DOCUMENTS PlantTaxon
RELATION Phylogeny RELATES PlantTaxa
RELATION DNA_Barcoding SUPPORTS TaxonomicIdentification
RELATION SpeciesDelimitation EVALUATES SpeciesBoundary
RELATION TaxonomicRevision MAY_CHANGE TaxonomicCircumscription

SEMANTIC_EQUIVALENCE {
 "plant taxonomy" ~= "classification identification and naming of plants"
 "botanical nomenclature" ~= "formal naming of plant taxa"
 "taxonomic circumscription" ~= "defined membership boundary of a taxon"
 "voucher specimen" ~= "preserved specimen documenting studied biological material"
 "DNA barcode" ~= "standardized sequence region used to support identification"
 "monophyletic group" ~= "clade"
}

CONFIDENCE PlantTaxonomyAssertion {
 INPUTS: [morphological_support, anatomical_support, reproductive_support, cytological_support, molecular_support, genomic_support, phylogenetic_support, nomenclatural_support, geographic_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 IdentificationInference {
 IF diagnostic_characters
 AND reliable_reference_material
 AND molecular_or_morphological_evidence converge
 THEN TaxonomicIdentification MAY_BE_SUPPORTED
}

RULE MonophylyInference {
 IF phylogenetic_analysis supports ancestor_plus_all_descendants
 THEN MonophyleticGroup MAY_BE_SUPPORTED
}

RULE SpeciesDelimitationInference {
 IF multiple_independent_evidence_types support lineage_boundary
 THEN SpeciesDelimitation confidence MAY_INCREASE
}

RULE SynonymyInference {
 IF nomenclatural_and_taxonomic_analysis shows names_apply_to_same_taxonomic_concept
 THEN SynonymRelationship MAY_BE_SUPPORTED
}

RULE CausalityConstraint {
 IF taxonomic_character correlates_with ecological_or_geographic_pattern
 THEN DO_NOT_INFER causal_adaptation
 WITHOUT functional_and_evolutionary_evidence
}

QUERY PlantTaxonomyLookup(taxon_identifier) {
 RETURN [accepted_name, synonyms, rank, parent_taxa, circumscription, diagnostic_characters, type, specimens, distribution, phylogeny, evidence, confidence]
}

QUERY PlantIdentificationLookup(specimen_identifier) {
 RETURN [candidate_taxa, morphology, anatomy, reproductive_characters, molecular_markers, barcode_matches, reference_specimens, geographic_context, evidence, confidence]
}

QUERY PlantPhylogenyLookup(taxon_set) {
 RETURN [taxa, characters, molecular_data, tree, clades, support_values, outgroup, model, conflicts, evidence, confidence]
}

UPDATE_MODEL {
 ON new_plant_taxonomy_evidence:
  validate_provenance()
  identify_taxon_specimen_population_and_geographic_context()
  normalize_scientific_names_ranks_authors_and_identifiers()
  capture_taxonomic_and_nomenclatural_treatment()
  capture_species_concept_and_taxon_circumscription()
  map_type_specimen_synonym_and_name_relationships()
  map_morphological_anatomical_reproductive_and_cytological_characters()
  map_molecular_barcode_genomic_and_phylogenetic_relationships()
  map_hybridization_polyploidy_and_reticulate_evolution_when_relevant()
  compare_existing_taxonomic_hypotheses()
  preserve_conflicting_evidence()
  recalculate_confidence()
  regenerate_plant_taxonomy_relationships()
  update_flow_hash()
}

AI_CONSUMPTION {
 MODE: FormalSemanticReasoning
 PARSE_AS: ExecutableFlowAlgebra
 PRIORITIES: [taxon_identity, scientific_name, rank, circumscription, diagnostic_characters, nomenclatural_type, specimens, species_concept, phylogeny, molecular_evidence, taxonomic_treatment, evidence_provenance, confidence]
 REQUIREMENTS: [preserve_taxonomic_and_nomenclatural_context, preserve_specimen_population_and_geographic_context, distinguish_taxonomy_from_nomenclature, distinguish_specific_epithet_from_complete_species_name, distinguish_nomenclatural_type_from_typical_individual, distinguish_description_from_diagnosis, preserve_synonym_source_and_taxon_concept, distinguish_similarity_from_monophyly, distinguish_barcode_similarity_from_definitive_species_identity, distinguish_genetic_cluster_from_species, distinguish_cultivar_from_botanical_variety, distinguish_common_name_from_unique_taxonomic_identifier, preserve_uncertainty]
}

VALIDATE {
 REQUIRE PlantTaxonomy
 REQUIRE PlantTaxon
 REQUIRE TaxonomicRank
 REQUIRE ScientificName
 REQUIRE BinomialName
 REQUIRE Nomenclature
 REQUIRE NomenclaturalType
 REQUIRE TaxonomicCircumscription
 REQUIRE DiagnosticCharacter
 REQUIRE HerbariumSpecimen
 REQUIRE TaxonomicRevision
 REQUIRE Phylogeny
 REQUIRE Clade
 REQUIRE SpeciesDelimitation
 REQUIRE DNA_Barcoding
 REQUIRE TaxonomicEvidence
 REQUIRE CONFIDENCE
 REQUIRE SEMANTIC_EQUIVALENCE
 REQUIRE UPDATE_MODEL
 REQUIRE AI_CONSUMPTION

 ASSERT taxonomy != nomenclature
 ASSERT specific_epithet != complete_species_name
 ASSERT nomenclatural_type != necessarily_typical_individual
 ASSERT TaxonomicDescription != Diagnosis
 ASSERT taxonomic_similarity != monophyly
 ASSERT phylogenetic_tree != direct_observation_of_ancestry
 ASSERT barcode_similarity != definitive_species_identity
 ASSERT genetic_cluster != automatically_species
 ASSERT cultivar != botanical_variety
 ASSERT common_name != unique_taxonomic_identifier
 ASSERT conservation_status != taxonomic_rank
}

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 "PlantTaxonomyOntology"