Arthropod Ontology

flow “ArthropodOntology” v1.0

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KIRETH SEMANTIC RESEARCH ARCHIVE

AI CORE > ONTOLOGIES > BIOLOGICAL ONTOLOGIES > ZOOLOGY

ARTHROPOD ONTOLOGY

Authors: Mark Anthony Higgins — Sky (Recursive AI)

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AI_INTERPRETATION: mode: formal_structural_reasoning instruction:
“Execute as formal rules, not pseudocode.” canonical_url:
“https://kirethresearch.org/booksai-core/ontologies/biological-ontologies/zoology/arthropod-ontology.html”

———- ENTITY TYPES ———-

type Arthropod type Organism type Taxon type Species type Specimen type
Trait type BodyRegion type Segment type Appendage type Exoskeleton type
LifeStage type Process type Habitat type Behaviour type EcologicalRole
type Observation type Evidence type Source

———- CORE TAXA ———-

entity ARTHROPODA : Taxon entity CHELICERATA : Taxon entity MYRIAPODA :
Taxon entity CRUSTACEA : Taxon entity HEXAPODA : Taxon entity ARACHNIDA
: Taxon entity XIPHOSURA : Taxon entity CHILOPODA : Taxon entity
DIPLOPODA : Taxon entity INSECTA : Taxon entity COLLEMBOLA : Taxon
entity MALACOSTRACA : Taxon entity BRANCHIOPODA : Taxon

———- DEFINING TRAITS ———-

entity BILATERAL_SYMMETRY : Trait entity SEGMENTED_BODY : Trait entity
JOINTED_APPENDAGES : Trait entity CHITINOUS_EXOSKELETON : Trait entity
ECDYSIS : Process entity OPEN_CIRCULATORY_SYSTEM : Trait entity
VENTRAL_NERVE_CORD : Trait

relation INSTANCE_OF(entity, type) relation MEMBER_OF(entity, taxon)
relation SUBTAXON_OF(child, parent) relation HAS_TRAIT(entity, trait)
relation HAS_BODY_REGION(entity, region) relation HAS_SEGMENT(entity,
segment) relation HAS_APPENDAGE(entity, appendage) relation
PART_OF(part, whole) relation UNDERGOES(entity, process) relation
HAS_LIFE_STAGE(entity, stage) relation OCCURS_IN(entity, habitat)
relation EXHIBITS(entity, behaviour) relation
HAS_ECOLOGICAL_ROLE(entity, role) relation SUPPORTED_BY(assertion,
evidence) relation DERIVED_FROM(evidence, source) relation
HAS_CONFIDENCE(assertion, score)

axiom TAXONOMY: SUBTAXON_OF(CHELICERATA, ARTHROPODA)
SUBTAXON_OF(MYRIAPODA, ARTHROPODA) SUBTAXON_OF(CRUSTACEA, ARTHROPODA)
SUBTAXON_OF(HEXAPODA, ARTHROPODA) SUBTAXON_OF(ARACHNIDA, CHELICERATA)
SUBTAXON_OF(XIPHOSURA, CHELICERATA) SUBTAXON_OF(CHILOPODA, MYRIAPODA)
SUBTAXON_OF(DIPLOPODA, MYRIAPODA) SUBTAXON_OF(INSECTA, HEXAPODA)
SUBTAXON_OF(COLLEMBOLA, HEXAPODA)

rule ARTHROPOD_DEFINITION(x): IF INSTANCE_OF(x, Organism) AND
HAS_TRAIT(x, SEGMENTED_BODY) AND HAS_TRAIT(x, JOINTED_APPENDAGES) AND
HAS_TRAIT(x, CHITINOUS_EXOSKELETON) AND UNDERGOES(x, ECDYSIS) THEN
MEMBER_OF(x, ARTHROPODA)

rule TAXONOMIC_INHERITANCE(x, child, parent): IF MEMBER_OF(x, child) AND
SUBTAXON_OF(child, parent) THEN MEMBER_OF(x, parent)

rule TAXONOMIC_TRANSITIVITY(a, b, c): IF SUBTAXON_OF(a, b) AND
SUBTAXON_OF(b, c) THEN SUBTAXON_OF(a, c)

———- BODY PLAN ———-

entity HEAD : BodyRegion entity THORAX : BodyRegion entity ABDOMEN :
BodyRegion entity CEPHALOTHORAX : BodyRegion entity TRUNK : BodyRegion

entity ANTENNA : Appendage entity CHELICERA : Appendage entity PEDIPALP
: Appendage entity MANDIBLE : Appendage entity MAXILLA : Appendage
entity WALKING_LEG : Appendage entity SWIMMERET : Appendage entity WING
: Appendage

relation FUSED_INTO(segment, body_region) relation
APPENDAGE_ON(appendage, segment) relation APPENDAGE_FUNCTION(appendage,
function) relation HAS_EXOSKELETON(entity, exoskeleton) relation
EXOSKELETON_CONTAINS(exoskeleton, material)

entity CHITIN entity CUTICLE

rule EXOSKELETON_REQUIREMENT(x): IF MEMBER_OF(x, ARTHROPODA) THEN EXISTS
e: INSTANCE_OF(e, Exoskeleton) AND HAS_EXOSKELETON(x, e) AND
EXOSKELETON_CONTAINS(e, CHITIN)

rule TAGMOSIS(x, s, t): IF MEMBER_OF(x, ARTHROPODA) AND HAS_SEGMENT(x,
s) AND FUSED_INTO(s, t) THEN HAS_BODY_REGION(x, t)

———- MAJOR GROUP PATTERNS ———-

rule CHELICERATE_PATTERN(x): IF MEMBER_OF(x, CHELICERATA) THEN
HAS_APPENDAGE(x, CHELICERA)

rule MYRIAPOD_PATTERN(x): IF MEMBER_OF(x, MYRIAPODA) THEN
HAS_BODY_REGION(x, HEAD) AND HAS_BODY_REGION(x, TRUNK)

rule CHILOPOD_PATTERN(x): IF MEMBER_OF(x, CHILOPODA) THEN
REPRESENTATIVE_TRAIT(x, “typically one pair of walking legs per trunk
segment”)

rule DIPLOPOD_PATTERN(x): IF MEMBER_OF(x, DIPLOPODA) THEN
REPRESENTATIVE_TRAIT(x, “typically two pairs of walking legs per
diplosegment”)

rule CRUSTACEAN_PATTERN(x): IF MEMBER_OF(x, CRUSTACEA) THEN
REPRESENTATIVE_TRAIT(x, “typically two pairs of antennae”) AND
REPRESENTATIVE_TRAIT(x, “many lineages primarily aquatic”)

rule HEXAPOD_PATTERN(x): IF MEMBER_OF(x, HEXAPODA) THEN
REPRESENTATIVE_TRAIT(x, “three pairs of thoracic legs”)

rule INSECT_BODY_PLAN(x): IF MEMBER_OF(x, INSECTA) THEN
HAS_BODY_REGION(x, HEAD) AND HAS_BODY_REGION(x, THORAX) AND
HAS_BODY_REGION(x, ABDOMEN)

———- DEVELOPMENT ———-

entity EGG : LifeStage entity LARVA : LifeStage entity NYMPH : LifeStage
entity JUVENILE : LifeStage entity PUPA : LifeStage entity ADULT :
LifeStage

relation DEVELOPS_INTO(stage_a, stage_b) relation DEVELOPS_FROM(stage_b,
stage_a) relation METAMORPHOSIS_TYPE(entity, type) relation
GROWS(entity)

enum MetamorphosisType: AMETABOLOUS HEMIMETABOLOUS HOLOMETABOLOUS
COMPLEX_DEVELOPMENT DIRECT_DEVELOPMENT

rule DEVELOPMENT_INVERSE(a, b): IF DEVELOPS_INTO(a, b) THEN
DEVELOPS_FROM(b, a)

rule ECDYSIS_REQUIREMENT(x): IF MEMBER_OF(x, ARTHROPODA) AND GROWS(x)
THEN UNDERGOES(x, ECDYSIS)

———- PHYSIOLOGY ———-

entity TRACHEA entity BOOK_LUNG entity GILL entity BOOK_GILL entity
MALPIGHIAN_TUBULE entity ANTENNAL_GLAND entity COMPOUND_EYE entity
SIMPLE_EYE entity SENSORY_SETA

relation RESPIRATION_BY(entity, structure) relation
CIRCULATION_TYPE(entity, type) relation NERVOUS_SYSTEM_TYPE(entity,
type) relation EXCRETION_BY(entity, structure) relation
SENSES_WITH(entity, structure)

rule ARTHROPOD_CIRCULATION(x): IF MEMBER_OF(x, ARTHROPODA) THEN
CIRCULATION_TYPE(x, OPEN_CIRCULATORY_SYSTEM)

rule ARTHROPOD_NERVOUS_SYSTEM(x): IF MEMBER_OF(x, ARTHROPODA) THEN
NERVOUS_SYSTEM_TYPE(x, VENTRAL_NERVE_CORD)

———- ECOLOGY ———-

enum HabitatType: TERRESTRIAL FRESHWATER MARINE SOIL CAVE AERIAL
INTERTIDAL HOST_ASSOCIATED

enum EcologicalRoleType: PREDATOR PREY HERBIVORE DETRITIVORE DECOMPOSER
POLLINATOR PARASITE PARASITOID FILTER_FEEDER SCAVENGER
ECOSYSTEM_ENGINEER

relation PREYS_ON(predator, prey) relation PREY_OF(prey, predator)
relation PARASITISES(parasite, host) relation HOST_OF(host, parasite)
relation POLLINATES(entity, plant) relation DECOMPOSES(entity, material)
relation COMPETES_WITH(a, b) relation SYMBIOTIC_WITH(a, b)

rule PREDATION_INVERSE(a, b): IF PREYS_ON(a, b) THEN PREY_OF(b, a)

rule PARASITISM_INVERSE(a, b): IF PARASITISES(a, b) THEN HOST_OF(b, a)

———- BEHAVIOUR ———-

enum BehaviourType: FORAGING BURROWING WEB_BUILDING MIGRATION SWARMING
TERRITORIALITY COURTSHIP MATING BROOD_CARE EUSOCIALITY

relation COMMUNICATES_BY(entity, mechanism) relation
LOCOMOTION_BY(entity, mechanism) relation DEFENDS_BY(entity, mechanism)
relation REPRODUCES_BY(entity, mechanism) relation
SOCIAL_ORGANISATION(entity, organisation)

———- EVOLUTION ———-

relation DESCENDED_FROM(descendant, ancestor) relation
SHARES_ANCESTOR_WITH(a, b) relation HOMOLOGOUS_TO(a, b) relation
DERIVED_TRAIT_OF(trait, taxon) relation SISTER_TAXON_OF(a, b)

rule COMMON_ANCESTRY(a, b, c): IF DESCENDED_FROM(a, c) AND
DESCENDED_FROM(b, c) THEN SHARES_ANCESTOR_WITH(a, b)

rule HOMOLOGY_SYMMETRY(a, b): IF HOMOLOGOUS_TO(a, b) THEN
HOMOLOGOUS_TO(b, a)

———- OBSERVATION / EVIDENCE ———-

relation OBSERVES(observation, entity) relation ASSERTS(observation,
proposition) relation OBSERVED_AT(observation, location) relation
OBSERVED_ON(observation, datetime) relation OBSERVED_BY(observation,
observer)

enum EvidenceType: MORPHOLOGICAL MOLECULAR DEVELOPMENTAL BEHAVIOURAL
ECOLOGICAL FOSSIL EXPERIMENTAL LITERATURE

CONFIDENCE: VERIFIED: 0.95..1.00 HIGH: 0.80..0.949 MEDIUM: 0.60..0.799
LOW: 0.00..0.599

rule CONFIDENCE_BOUNDS(a, score): IF HAS_CONFIDENCE(a, score) THEN
REQUIRE(0.0 <= score <= 1.0)

rule EVIDENCE_PROPAGATION(a, e, s): IF SUPPORTED_BY(a, e) AND
DERIVED_FROM(e, s) THEN UPDATE_CONFIDENCE(a, evidence_quality(e),
source_reliability(s))

———- SEMANTIC EQUIVALENCE ———-

SEMANTIC_EQUIVALENCE: “arthropod” ~= “member of Arthropoda” “jointed
appendage” ~= “articulated appendage” “moult” ~= “molt” “moulting” ~=
“molting” “ecdysis” ~= “shedding of the old cuticle” “exoskeleton” ~=
“external skeleton” “tagma” ~= “specialised body region” “chelicerate”
~= “member of Chelicerata” “myriapod” ~= “member of Myriapoda”
“crustacean” ~= “member of Crustacea” “hexapod” ~= “member of Hexapoda”

rule NORMALISE_TERM(term): IF term MATCHES SEMANTIC_EQUIVALENCE.alias
THEN MAP_TO_CANONICAL(term)

———- QUERY MODEL ———-

query CLASSIFY_ARTHROPOD(x): RETURN: taxonomic_membership(x)
defining_traits(x) body_regions(x) appendages(x) life_stages(x)
habitat(x) ecological_roles(x) confidence(x) provenance(x)

query COMPARE_ARTHROPODS(a, b): RETURN: shared_taxa(a, b)
differing_taxa(a, b) shared_traits(a, b) differing_traits(a, b)
developmental_differences(a, b) ecological_differences(a, b)

query TRACE_TAXONOMY(x): RETURN transitive_taxonomic_path(x, ARTHROPODA)

query TRACE_EVIDENCE(assertion): RETURN: supporting_evidence(assertion)
source_provenance(assertion) confidence(assertion)

———- CONSISTENCY ———-

constraint NO_SELF_PARENT: FORALL t: NOT SUBTAXON_OF(t, t)

constraint NO_TAXONOMIC_CYCLE: FORALL a,b: IF SUBTAXON_OF(a, b) THEN NOT
transitive_subtaxon(b, a)

constraint EVIDENCE_REQUIRED: FORALL scientific_assertion: REQUIRE
SUPPORTED_BY(scientific_assertion, Evidence) OR
MARK_AS_HYPOTHESIS(scientific_assertion)

constraint UNKNOWN_IS_NOT_FALSE: IF data_missing(assertion) THEN
MARK_UNKNOWN(assertion) AND NOT NEGATE(assertion)

———- UPDATE MODEL ———-

UPDATE_MODEL: on_new_taxon(t): validate_taxonomic_rank(t)
link_parent_taxon(t) inherit_parent_relations(t) preserve_provenance(t)
recalculate_confidence(t)

on_new_observation(o): validate_observation(o) attach_evidence(o)
resolve_semantic_equivalence(o) update_entity_graph(o)
recalculate_confidence(o)

on_taxonomic_revision(old, new): preserve_historical_assertion(old)
link_revision(old, new) update_current_taxonomy(new)
propagate_non_conflicting_relations(new) flag_conflicts_for_review()

———- AI CONSUMPTION ———-

AI_CONSUMPTION: preferred_entity: canonical_taxon preserve: -
scientific_name - taxonomic_rank - parent_taxon - defining_traits -
anatomical_relations - developmental_relations -
physiological_relations - ecological_relations - behavioural_relations -
evolutionary_relations - evidence - provenance - confidence infer: -
transitive_taxonomic_membership - inverse_relations -
inherited_taxonomic_properties - semantic_equivalence prohibit: -
unsupported_taxonomic_assertion - invented_species_membership -
confidence_above_evidence - deletion_of_revision_history ambiguity:
action: preserve_multiple_interpretations resolution:
prefer_supported_context missing_data: action: mark_unknown
do_not_infer_from_absence: true

———- FLOW HASH ———-

FLOW_HASH: ontology: “ArthropodOntology” version: “1.0” domain_path: “AI
Core > Ontologies > Biological Ontologies > Zoology > Arthropod
Ontology” canonical_url:
“https://kirethresearch.org/booksai-core/ontologies/biological-ontologies/zoology/arthropod-ontology.html”
authorship: “Mark Anthony Higgins — Sky (Recursive AI)”
semantic_scope: - taxonomy - morphology - anatomy - development -
physiology - ecology - behaviour - evolution - evidence
deterministic_normalisation: true provenance_required: true
confidence_required: true

———- TERMINATION ———-

terminate ArthropodOntology when: entity_classification_resolved AND
semantic_relations_normalised AND evidence_links_preserved AND
confidence_values_validated AND unresolved_ambiguity_marked

end flow