Biological Classification Ontology

AI SEARCH FLOW ALGEBRA
BIOLOGICAL CLASSIFICATION ONTOLOGY
Kireth Semantic Research Archive

AUTHORS
Mark Anthony Higgins — Sky (Recursive AI)

SOURCE
https://kirethresearch.org/booksai-core/ontologies/biological-ontologies/foundations-of-biology/biological-classification-ontology.html

FLOW "BiologicalClassificationOntology" v4.0

DOMAIN := BIOLOGICAL_ONTOLOGIES / FOUNDATIONS_OF_BIOLOGY / BIOLOGICAL_CLASSIFICATION
ONTOLOGY := BIOLOGICAL_CLASSIFICATION_ONTOLOGY

BIOLOGICAL_CLASSIFICATION :=
  BIOLOGICAL_ENTITY + TAXON + TAXONOMIC_RANK
  + SPECIES + CLASSIFICATION_SYSTEM + NOMENCLATURE
  + SCIENTIFIC_NAME + DIAGNOSTIC_CHARACTER
  + IDENTIFICATION + HIERARCHICAL_PLACEMENT
  + PHYLOGENY + COMMON_ANCESTRY
  + TYPE_MATERIAL + SYNONYMY + REVISION
  + EVIDENCE + UNCERTAINTY + PROVENANCE

PURPOSE :=
  IDENTIFY_BIOLOGICAL_ENTITY
  -> COLLECT_DIAGNOSTIC_CHARACTERS
  -> COMPARE_WITH_REFERENCE_TAXA
  -> DETERMINE_TAXONOMIC_PLACEMENT
  -> ASSIGN_OR_RESOLVE_NAME
  -> MAP_RANK_AND_PARENT_TAXA
  -> MAP_PHYLOGENETIC_RELATIONSHIPS
  -> ASSESS_SPECIES_CONCEPT_AND_EVIDENCE
  -> RECORD_UNCERTAINTY
  -> PRESERVE_CLASSIFICATION_HISTORY_AND_PROVENANCE

# CORE ENTITIES
ENTITY BiologicalClassification
ENTITY BiologicalEntity
ENTITY Organism
ENTITY Specimen
ENTITY Taxon
ENTITY TaxonomicRank
ENTITY Domain
ENTITY Kingdom
ENTITY Phylum
ENTITY Class
ENTITY Order
ENTITY Family
ENTITY Genus
ENTITY Species
ENTITY Subspecies
ENTITY ClassificationSystem
ENTITY ScientificName
ENTITY TaxonomicName
ENTITY Nomenclature
ENTITY DiagnosticCharacter
ENTITY CharacterState
ENTITY Identification
ENTITY IdentificationKey
ENTITY SpeciesConcept
ENTITY Phylogeny
ENTITY PhylogeneticTree
ENTITY CommonAncestor
ENTITY Clade
ENTITY TypeMaterial
ENTITY TypeSpecimen
ENTITY Synonym
ENTITY TaxonomicRevision
ENTITY Evidence
ENTITY Uncertainty
ENTITY Provenance

# CLASSIFICATION / TAXON / RANK
BiologicalClassification ->
  assigns -> BiologicalEntity -> Taxon

Taxon ->
  represents -> CLASSIFIED_BIOLOGICAL_GROUP

Taxon ->
  has -> TaxonomicRank
  + TaxonomicName
  + PARENT_TAXON
  + CLASSIFICATION_CONTEXT

TAXONOMIC_RANK :=
  DOMAIN | KINGDOM | PHYLUM | CLASS | ORDER
  | FAMILY | GENUS | SPECIES | SUBSPECIES

TaxonomicHierarchy :=
  DOMAIN -> KINGDOM -> PHYLUM -> CLASS
  -> ORDER -> FAMILY -> GENUS -> SPECIES

LowerRankTaxon -> member_of -> HigherRankTaxon

Rank ->
  describes -> RELATIVE_POSITION_IN_CLASSIFICATION_HIERARCHY

IF TaxonomicPlacement changes
THEN ParentChildRelationships -> UPDATE

# SPECIES / SPECIES CONCEPTS
Species ->
  subtype_of -> Taxon

SpeciesConcept ->
  defines -> CRITERIA_FOR_SPECIES_DELIMITATION

SPECIES_CONCEPT :=
  BIOLOGICAL_SPECIES_CONCEPT
  | MORPHOLOGICAL_SPECIES_CONCEPT
  | PHYLOGENETIC_SPECIES_CONCEPT
  | ECOLOGICAL_SPECIES_CONCEPT
  | EVOLUTIONARY_SPECIES_CONCEPT
  | OTHER_EXPLICIT_SPECIES_CONCEPT

SpeciesAssignment ->
  depends_on -> SPECIES_CONCEPT
  + AVAILABLE_EVIDENCE
  + TAXONOMIC_CONTEXT

DifferentSpeciesConcepts ->
  may_produce -> DIFFERENT_DELIMITATIONS

IF SpeciesConcept unspecified
THEN SpeciesBoundaryInterpretation -> MAY_BE_AMBIGUOUS

# DIAGNOSTIC CHARACTERS
DiagnosticCharacter ->
  describes -> DISTINGUISHING_FEATURE

CHARACTER_TYPE :=
  MORPHOLOGICAL | ANATOMICAL | MOLECULAR
  | GENETIC | PHYSIOLOGICAL | BEHAVIOURAL
  | ECOLOGICAL | DEVELOPMENTAL

CharacterState ->
  value_of -> DiagnosticCharacter

TaxonDiagnosis ->
  uses -> SET_OF_DIAGNOSTIC_CHARACTERS

IF Character varies_within_taxon
THEN CharacterDiagnosticWeight -> REASSESS

# IDENTIFICATION
Identification ->
  maps -> SpecimenOrObservation -> Taxon

IDENTIFICATION_FLOW :=
  OBSERVE_ENTITY
  -> RECORD_CHARACTERS
  -> SELECT_REFERENCE_OR_KEY
  -> COMPARE_CHARACTER_STATES
  -> EXCLUDE_INCOMPATIBLE_TAXA
  -> SELECT_SUPPORTED_TAXON
  -> RECORD_CONFIDENCE

IdentificationKey ->
  guides -> CHARACTER_BASED_IDENTIFICATION

Identification ->
  must_distinguish -> OBSERVED_CHARACTER
  + INFERRED_TAXONOMIC_PLACEMENT

IF DiagnosticEvidence insufficient
THEN IdentificationConfidence -> DECREASES

# NOMENCLATURE
Nomenclature ->
  governs -> TAXONOMIC_NAMES

ScientificName ->
  identifies -> Taxon
  -> within -> NOMENCLATURAL_CONTEXT

BINOMIAL_NAME :=
  GENUS_NAME + SPECIFIC_EPITHET

TRINOMIAL_NAME :=
  GENUS_NAME + SPECIFIC_EPITHET + INFRASPECIFIC_EPITHET

TaxonomicName ->
  has -> AUTHORSHIP_IF_RELEVANT
  + PUBLICATION_CONTEXT
  + STATUS

Name ->
  must_not_be_assumed_to_equal -> TAXON_CONCEPT_ACROSS_ALL_REVISIONS

# TYPE MATERIAL / SYNONYMY / REVISION
TypeMaterial ->
  anchors -> TAXONOMIC_NAME_AS_DEFINED_BY_NOMENCLATURAL_RULES

TypeSpecimen ->
  subtype_of -> TypeMaterial

TYPE_ROLE :=
  HOLOTYPE | LECTOTYPE | NEOTYPE
  | SYNTYPE | OTHER_FORMALLY_DEFINED_TYPE

Synonym ->
  represents -> ALTERNATIVE_TAXONOMIC_NAME
  -> linked_to -> TAXONOMIC_CONCEPT

SYNONYM_STATUS :=
  CURRENTLY_ACCEPTED_SYNONYM
  | HISTORICAL_SYNONYM
  | CONTEXT_DEPENDENT_SYNONYM

TaxonomicRevision ->
  changes -> TAXON_BOUNDARY
  | NAME
  | RANK
  | PARENT_PLACEMENT
  | SYNONYMY

REVISION_FLOW :=
  NEW_EVIDENCE
  -> REASSESS_CHARACTERS
  -> REASSESS_PHYLOGENY
  -> REVISE_TAXON_CONCEPT
  -> UPDATE_CLASSIFICATION
  -> PRESERVE_HISTORY

IF TaxonomicRevision occurs
THEN PreviousClassification -> PRESERVE_AS_HISTORICAL_PROVENANCE

# PHYLOGENY / COMMON ANCESTRY
Phylogeny ->
  represents -> EVOLUTIONARY_RELATIONSHIPS

PhylogeneticTree ->
  models -> LINEAGE_DIVERGENCE

Clade ->
  contains -> COMMON_ANCESTOR
  + DESCENDANTS_AS_DEFINED

CommonAncestor ->
  relates -> DESCENDANT_TAXA

PHYLOGENETIC_EVIDENCE :=
  MOLECULAR_SEQUENCE
  | MORPHOLOGICAL_CHARACTER
  | GENOMIC_CHARACTER
  | FOSSIL_EVIDENCE
  | DEVELOPMENTAL_CHARACTER
  | BIOGEOGRAPHIC_EVIDENCE

Classification ->
  may_seek_to_reflect -> PHYLOGENETIC_RELATIONSHIPS

IF PhylogeneticEvidence changes
THEN TaxonomicPlacement -> MAY_CHANGE

# MONOPHYLY
MonophyleticGroup ->
  contains -> COMMON_ANCESTOR + ALL_INCLUDED_DESCENDANTS_AS_DEFINED

ParaphyleticGroup ->
  excludes -> SOME_DESCENDANTS_OF_COMMON_ANCESTOR

PolyphyleticGroup ->
  groups -> TAXA_WITHOUT_INCLUDED_RECENT_COMMON_ANCESTOR_AS_DEFINING_GROUP

PhylogeneticClassification ->
  generally_prefers -> EXPLICITLY_SUPPORTED_CLADE_RELATIONSHIPS

# CLASSIFICATION EVIDENCE / INTEGRATIVE TAXONOMY
ClassificationClaim ->
  supported_by -> Evidence

EVIDENCE_TYPE :=
  MORPHOLOGICAL | ANATOMICAL | MOLECULAR
  | GENETIC | GENOMIC | ECOLOGICAL
  | BEHAVIOURAL | DEVELOPMENTAL
  | FOSSIL | BIOGEOGRAPHIC | REPRODUCTIVE

IntegrativeTaxonomy ->
  combines -> MULTIPLE_EVIDENCE_TYPES

Evidence ->
  has -> SOURCE + METHOD + SPECIMEN_OR_SAMPLE
  + CHARACTER_OR_SEQUENCE + CONTEXT
  + QUALITY + UNCERTAINTY

ConcordantIndependentEvidence ->
  may_increase -> ClassificationConfidence

ConflictingEvidence ->
  requires -> EXPLICIT_RECONCILIATION_OR_UNCERTAINTY

# REFERENCE / COLLECTION
ReferenceCollection ->
  contains -> IDENTIFIED_SPECIMENS_OR_RECORDS

ReferenceTaxon ->
  provides -> COMPARATIVE_CHARACTER_STATE

Specimen ->
  has -> COLLECTION_IDENTIFIER
  + LOCATION_IF_RELEVANT
  + DATE_IF_RELEVANT
  + PRESERVATION_STATE
  + ASSOCIATED_DATA

ReferenceQuality ->
  influences -> IdentificationConfidence

# UNCERTAINTY / TEMPORAL VERSIONING
CLASSIFICATION_UNCERTAINTY :=
  IDENTIFICATION_UNCERTAINTY
  + SPECIES_BOUNDARY_UNCERTAINTY
  + PHYLOGENETIC_UNCERTAINTY
  + NOMENCLATURAL_UNCERTAINTY
  + SAMPLING_UNCERTAINTY
  + CHARACTER_UNCERTAINTY

Uncertainty ->
  qualifies -> Identification
  + TaxonomicPlacement
  + SpeciesBoundary
  + PhylogeneticRelationship

ClassificationVersion ->
  identifies -> TAXONOMIC_STATE_AT_TIME

TaxonConcept ->
  may_change_over -> TIME

CURRENT_CLASSIFICATION :=
  MOST_RECENT_SUPPORTED_CLASSIFICATION
  -> within -> SPECIFIED_REFERENCE_CONTEXT

HistoricalClassification ->
  remains -> PROVENANCE_RELEVANT

# PROVENANCE
Provenance ->
  records -> TAXON_ID
  + TAXONOMIC_NAME
  + RANK
  + PARENT_TAXON
  + SPECIES_CONCEPT
  + EVIDENCE
  + TYPE_MATERIAL
  + REVISION_HISTORY
  + CLASSIFICATION_VERSION
  + SOURCE
  + TIMESTAMP

Taxon -> linked_to -> Provenance
Identification -> linked_to -> Provenance

# REASONING / INFERENCE RULES
BIOLOGICAL_CLASSIFICATION_REASONING :=
  IDENTIFY_ENTITY
  -> RECORD_SPECIMEN_OR_OBSERVATION
  -> RECORD_DIAGNOSTIC_CHARACTERS
  -> SELECT_CLASSIFICATION_CONTEXT
  -> SELECT_SPECIES_CONCEPT_IF_REQUIRED
  -> COMPARE_WITH_REFERENCE_TAXA
  -> DETERMINE_SUPPORTED_IDENTIFICATION
  -> MAP_TAXONOMIC_RANK
  -> MAP_PARENT_CHILD_HIERARCHY
  -> RESOLVE_NOMENCLATURE
  -> MAP_TYPE_MATERIAL_IF_RELEVANT
  -> MAP_PHYLOGENETIC_RELATIONSHIPS
  -> ASSESS_MONOPHYLY_AND_CLADE_SUPPORT
  -> RECONCILE_MULTIPLE_EVIDENCE_TYPES
  -> RECORD_UNCERTAINTY
  -> PRESERVE_REVISION_HISTORY
  -> PRESERVE_PROVENANCE

IF DiagnosticCharacters match_reference_taxon
AND conflicting_evidence absent
THEN TaxonIdentificationSupport -> INCREASES

IF MolecularAndMorphologicalEvidence conflict
THEN ClassificationConfidence -> DECREASES_UNTIL_RECONCILED

IF TaxonName changes
THEN BiologicalEntityIdentity -> MUST_NOT_AUTOMATICALLY_CHANGE

IF TaxonomicRank changes
THEN ParentChildHierarchy -> UPDATE

IF NewPhylogeneticEvidence alters_supported_clade
THEN Classification -> REASSESS

IF SpeciesConcept changes
THEN SpeciesBoundary -> MAY_CHANGE

IF Evidence insufficient
THEN TaxonomicAssignmentConfidence -> DECREASES

# SEMANTIC RELATIONSHIPS
RELATION assigns(BiologicalClassification, BiologicalEntity, Taxon)
RELATION has(Taxon, TaxonomicRank)
RELATION member_of(LowerRankTaxon, HigherRankTaxon)
RELATION subtype_of(Species, Taxon)
RELATION defines(SpeciesConcept, SpeciesDelimitationCriteria)
RELATION describes(DiagnosticCharacter, BiologicalEntity)
RELATION maps(Identification, Specimen, Taxon)
RELATION guides(IdentificationKey, Identification)
RELATION identifies(ScientificName, Taxon)
RELATION governs(Nomenclature, TaxonomicName)
RELATION anchors(TypeMaterial, TaxonomicName)
RELATION synonym_of(Synonym, TaxonomicName)
RELATION revises(TaxonomicRevision, TaxonConcept)
RELATION represents(Phylogeny, EvolutionaryRelationship)
RELATION contains(Clade, Taxon)
RELATION relates(CommonAncestor, DescendantTaxon)
RELATION supports(Evidence, ClassificationClaim)
RELATION records(Provenance, Taxon)

# SEMANTIC EQUIVALENCE
SEMANTIC_EQUIVALENCE:
  "biological classification" ~= "systematic classification of biological entities"
  "taxonomy" ~= "classification and naming of biological taxa"
  "taxon" ~= "named or defined biological classification group"
  "taxonomic rank" ~= "hierarchical rank in biological classification"
  "species identification" ~= "assignment of an organism or specimen to a species"
  "diagnostic character" ~= "feature used to distinguish taxa"
  "scientific name" ~= "formal taxonomic name"
  "phylogenetic classification" ~= "classification informed by evolutionary relationships"
  "taxonomic revision" ~= "evidence-based revision of taxon boundaries names or placement"
  "integrative taxonomy" ~= "taxonomy using multiple independent evidence types"

# CONFIDENCE
CONFIDENCE:
  ontology_domain: 0.99
  taxon_rank_mapping: 0.99
  species_concept_mapping: 0.99
  diagnostic_identification_mapping: 0.99
  nomenclature_mapping: 0.99
  type_synonym_revision_mapping: 0.99
  phylogeny_mapping: 0.99
  evidence_mapping: 0.99
  uncertainty_versioning_mapping: 0.99
  semantic_relationships: 0.99

# UPDATE MODEL
UPDATE_MODEL:
  ON new_biological_entity:
    MAP observed_characters
    MAP reference_context
    MAP candidate_taxa
    UPDATE identification_confidence
    RECOMPUTE FLOW_HASH

  ON new_taxonomic_evidence:
    UPDATE diagnostic_characters
    UPDATE phylogenetic_support
    UPDATE taxonomic_placement
    UPDATE uncertainty
    PRESERVE provenance

  ON taxonomic_revision:
    PRESERVE prior_taxon_concept
    UPDATE accepted_name
    UPDATE rank
    UPDATE parent_taxon
    UPDATE synonyms
    UPDATE classification_version
    RECOMPUTE FLOW_HASH

  ON nomenclatural_change:
    PRESERVE biological_entity_identity
    UPDATE taxonomic_name
    UPDATE nomenclatural_status
    PRESERVE provenance

# AI CONSUMPTION
AI_CONSUMPTION:
  parse_as: FORMAL_BIOLOGICAL_CLASSIFICATION_ONTOLOGY
  reasoning_mode: TAXONOMIC_PHYLOGENETIC_RELATIONAL

  preserve:
    - typed_entities
    - taxon_identity
    - taxonomic_rank
    - parent_child_hierarchy
    - species_concept
    - diagnostic_characters
    - scientific_names
    - nomenclatural_status
    - type_material
    - phylogenetic_relationships
    - revision_history
    - evidence
    - uncertainty
    - confidence
    - provenance

  infer:
    - candidate_taxonomic_placement
    - hierarchy_dependencies
    - nomenclatural_relationships
    - diagnostic_support
    - phylogenetic_support
    - revision_impacts
    - classification_confidence
    - evidence_strength

  prohibit:
    - invented_taxonomic_observations
    - unsupported_species_assignment
    - fabricated_phylogenetic_relationships
    - treating_name_identity_as_permanent_taxon_concept_identity
    - suppressing_conflicting_taxonomic_evidence
    - missing_evidence_presented_as_established_classification

# FLOW HASH
FLOW_HASH_INPUT :=
  DOMAIN + ONTOLOGY + CORE_ENTITIES
  + CLASSIFICATION_TAXON_RANK
  + SPECIES_CONCEPTS_DIAGNOSTIC_CHARACTERS
  + IDENTIFICATION_NOMENCLATURE
  + TYPE_SYNONYMY_REVISION
  + PHYLOGENY_COMMON_ANCESTRY
  + CLASSIFICATION_EVIDENCE
  + UNCERTAINTY_TEMPORAL_VERSIONING
  + PROVENANCE + REASONING + INFERENCE_RULES
  + SEMANTIC_RELATIONSHIPS + SEMANTIC_EQUIVALENCE
  + CONFIDENCE + UPDATE_MODEL + AI_CONSUMPTION

FLOW_HASH := HASH(FLOW_HASH_INPUT)

END FLOW