Marine Organism Ontology

flow “MarineOrganismOntology” v1.0

KIRETH SEMANTIC RESEARCH ARCHIVE

AI CORE > ONTOLOGIES > BIOLOGICAL ONTOLOGIES > MARINE BIOLOGY > MARINE ORGANISM ONTOLOGY

Authors: Mark Anthony Higgins — Sky (Recursive AI)

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

type MarineOrganism type Species type Population type Taxon type
MarineHabitat type OceanZone type LifeStage type Trait type Adaptation
type Behaviour type Resource type Observation type Evidence type Source

relation INSTANCE_OF(entity,type) relation MEMBER_OF_TAXON(entity,taxon)
relation HAS_SCIENTIFIC_NAME(entity,name) relation
HAS_COMMON_NAME(entity,name) relation OCCURS_IN(entity,habitat) relation
OCCUPIES_ZONE(entity,zone) relation DEPTH_RANGE(entity,range) relation
GEOGRAPHIC_RANGE(entity,region)

enum MarineHabitatType: OPEN_OCEAN COASTAL INTERTIDAL SUBTIDAL
CORAL_REEF KELP_FOREST SEAGRASS_MEADOW MANGROVE ESTUARY
CONTINENTAL_SHELF DEEP_SEA HYDROTHERMAL_VENT COLD_SEEP ABYSSAL_PLAIN
TRENCH POLAR_SEA

enum OceanZoneType: EPIPELAGIC MESOPELAGIC BATHYPELAGIC ABYSSOPELAGIC
HADOPELAGIC NERITIC OCEANIC BENTHIC PELAGIC

enum MarineOrganismGroup: MARINE_MICROBE PHYTOPLANKTON ZOOPLANKTON
MACROALGA SEAGRASS SPONGE CNIDARIAN ANNELID MOLLUSC CRUSTACEAN
ECHINODERM FISH MARINE_REPTILE SEABIRD MARINE_MAMMAL

relation HAS_ORGANISM_GROUP(entity,group)

enum LifeMode: PLANKTONIC NEKTONIC BENTHIC SESSILE DEMERSAL PELAGIC
EPIFAUNAL INFAUNAL

relation HAS_LIFE_MODE(entity,mode) relation
TOLERATES_SALINITY(entity,range) relation
TOLERATES_TEMPERATURE(entity,range) relation
TOLERATES_PRESSURE(entity,range) relation TOLERATES_OXYGEN(entity,range)
relation TOLERATES_PH(entity,range) relation LIMITED_BY(entity,factor)

relation HAS_BODY_FORM(entity,form) relation
HAS_RESPIRATORY_STRUCTURE(entity,structure) relation
HAS_FEEDING_STRUCTURE(entity,structure) relation
HAS_SENSORY_STRUCTURE(entity,structure) relation
HAS_LOCOMOTOR_STRUCTURE(entity,structure)

relation OSMOREGULATES_BY(entity,mechanism) relation
RESPIRES_BY(entity,structure) relation OXYGEN_UPTAKE_RATE(entity,rate)
relation METABOLIC_RATE(entity,rate) relation
BUOYANCY_CONTROL(entity,mechanism)

enum MarineAdaptationType: OSMOREGULATION PRESSURE_TOLERANCE
THERMAL_TOLERANCE HYPOXIA_TOLERANCE BIOLUMINESCENCE COUNTERSHADING
CAMOUFLAGE BUOYANCY_CONTROL STREAMLINING FILTER_FEEDING DEEP_DIVING
ANTIFREEZE_PROTEINS CHEMOSYMBIOSIS

relation HAS_ADAPTATION(entity,adaptation) relation
ADAPTATION_TYPE(adaptation,type) relation
ADAPTATION_FUNCTION(adaptation,function) relation
ADAPTED_TO(entity,condition)

enum TrophicRole: PRIMARY_PRODUCER PRIMARY_CONSUMER SECONDARY_CONSUMER
TERTIARY_CONSUMER APEX_PREDATOR OMNIVORE FILTER_FEEDER DETRITIVORE
SCAVENGER DECOMPOSER

relation HAS_TROPHIC_ROLE(entity,role) relation
FEEDS_ON(consumer,resource) relation CONSUMED_BY(resource,consumer)
relation PREYS_ON(predator,prey) relation PREY_OF(prey,predator)

rule FEEDING_INVERSE(a,b): IF FEEDS_ON(a,b) THEN CONSUMED_BY(b,a)

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

enum ReproductiveMode: BROADCAST_SPAWNING EXTERNAL_FERTILISATION
INTERNAL_FERTILISATION BROODING OVIPARITY VIVIPARITY OVOVIVIPARITY
ASEXUAL_REPRODUCTION

relation REPRODUCES_BY(entity,mode) relation SPAWNS_IN(entity,habitat)
relation BREEDS_DURING(entity,period) relation
HAS_LARVAL_STAGE(entity,stage) relation HAS_JUVENILE_STAGE(entity,stage)
relation SETTLES_IN(stage,habitat) relation HAS_LIFE_STAGE(entity,stage)
relation DEVELOPS_FROM(stage_b,stage_a) relation
DEVELOPS_INTO(stage_a,stage_b)

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

relation DISPERSAL_BY(entity,mechanism) relation
LARVAL_DISPERSAL_TO(entity,region) relation
MIGRATES_BETWEEN(entity,region_a,region_b) relation
VERTICAL_MIGRATION(entity,depth_a,depth_b)

relation EXHIBITS_BEHAVIOUR(entity,behaviour) relation SCHOOLING(entity)
relation SHOALING(entity) relation FORAGING(entity) relation
TERRITORIAL(entity) relation BURROWING(entity) relation
DIEL_VERTICAL_MIGRATION(entity)

enum SymbiosisType: MUTUALISM COMMENSALISM PARASITISM

relation SYMBIOTIC_WITH(a,b) relation SYMBIOSIS_TYPE(a,b,type) relation
HOST_OF(host,symbiont) relation SYMBIONT_OF(symbiont,host)

rule SYMBIOSIS_SYMMETRY(a,b): IF SYMBIOTIC_WITH(a,b) THEN
SYMBIOTIC_WITH(b,a)

relation REEF_ASSOCIATED(entity,reef) relation
KELP_ASSOCIATED(entity,kelp_forest) relation
SEAGRASS_ASSOCIATED(entity,seagrass_meadow) relation
VENT_ASSOCIATED(entity,vent) relation COLD_SEEP_ASSOCIATED(entity,seep)
relation ICE_ASSOCIATED(entity,sea_ice)

relation DEEP_SEA_ORGANISM(entity) relation BIOLUMINESCENT(entity)
relation PRESSURE_ADAPTED(entity) relation
CHEMOSYNTHETIC_ASSOCIATION(entity,symbiont)

relation HAS_POPULATION_SIZE(population,value) relation
HAS_GENETIC_DIVERSITY(population,value) relation
ENDEMIC_TO(entity,region) relation
HAS_CONSERVATION_STATUS(entity,status) relation
THREATENED_BY(entity,threat) relation PROTECTED_BY(entity,measure)

enum MarineImpact: OVERFISHING BYCATCH HABITAT_DESTRUCTION POLLUTION
PLASTIC_POLLUTION EUTROPHICATION OCEAN_WARMING OCEAN_ACIDIFICATION
DEOXYGENATION INVASIVE_SPECIES UNDERWATER_NOISE

relation AFFECTED_BY(entity,impact) relation
IMPACT_SEVERITY(impact,value) relation RECOVERS_FROM(entity,impact)

relation OBSERVES(observation,entity) relation
OBSERVED_AT(observation,location) relation
OBSERVED_ON(observation,datetime) relation
OBSERVED_DEPTH(observation,depth) relation
SUPPORTED_BY(assertion,evidence) relation DERIVED_FROM(evidence,source)
relation HAS_CONFIDENCE(assertion,score)

enum EvidenceType: FIELD_OBSERVATION UNDERWATER_VISUAL_CENSUS
ROV_OBSERVATION AUV_OBSERVATION ACOUSTIC_SURVEY SONAR ENVIRONMENTAL_DNA
GENETIC TAGGING BIOLOGGING SPECIMEN WATER_CHEMISTRY EXPERIMENTAL
LONG_TERM_MONITORING 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)

SEMANTIC_EQUIVALENCE: “marine organism” ~= “organism living in a marine
environment” “marine species” ~= “species occurring in marine
environments” “pelagic organism” ~= “open-water organism” “benthic
organism” ~= “seafloor-associated organism” “planktonic organism” ~=
“organism drifting in the water column” “nektonic organism” ~= “actively
swimming aquatic organism” “demersal organism” ~= “organism living near
the seabed” “marine adaptation” ~= “adaptation to marine conditions”
“larval dispersal” ~= “dispersal during a larval stage” “diel vertical
migration” ~= “daily vertical movement through the water column”

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

query MARINE_ORGANISM_PROFILE(x): RETURN: taxonomy(x) organism_group(x)
habitats(x) ocean_zones(x) depth_range(x) geographic_range(x)
life_mode(x) morphology(x) physiology(x) adaptations(x) trophic_role(x)
diet(x) reproduction(x) life_cycle(x) migration(x) behaviour(x)
symbioses(x) conservation(x) evidence(x) confidence(x)

query ENVIRONMENTAL_TOLERANCE_PROFILE(x): RETURN: salinity_range(x)
temperature_range(x) pressure_range(x) oxygen_range(x) ph_range(x)
limiting_factors(x)

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

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)

constraint DEPTH_CONTEXT_PRESERVATION: IF OBSERVED_DEPTH(o,d) THEN
PRESERVE_DEPTH_CONTEXT(o,d)

constraint OCCURRENCE_NOT_PERMANENT_RESIDENCE: IF OBSERVED_AT(o,l) THEN
DO_NOT_INFER(permanent_residence(entity,l))

UPDATE_MODEL: on_new_organism_record(r): validate_taxonomic_identity(r)
identify_habitat(r) identify_ocean_zone(r)
preserve_depth_location_time(r) attach_evidence(r)
recalculate_confidence(r)

on_new_trait(t): classify_trait(t) identify_organism(t)
attach_evidence(t) distinguish_adaptation_from_description(t)

on_new_migration_record(m): identify_origin(m) identify_destination(m)
preserve_depth_and_season(m) update_movement_graph(m)

on_conflicting_observations(a,b): preserve(a) preserve(b)
compare_life_stage(a,b) compare_depth(a,b) compare_location(a,b)
compare_season(a,b) compare_methods(a,b) flag_unresolved_conflict()

AI_CONSUMPTION: preferred_entity: canonical_marine_organism preserve: -
taxonomic_identity - organism_group - habitat - ocean_zone - depth -
geographic_range - life_mode - environmental_tolerance - morphology -
physiology - adaptations - trophic_role - diet - reproduction -
life_stage - dispersal - migration - behaviour - symbiosis -
conservation_status - threats - evidence - provenance - confidence
infer: - valid_inverse_relations - supported_trophic_relations -
supported_developmental_relations - semantic_equivalence prohibit: -
occurrence_equals_permanent_residence - depth_free_generalisation -
unsupported_adaptation - unsupported_migration_route -
confidence_above_evidence ambiguity: action:
preserve_multiple_organism_interpretations resolution:
prefer_taxonomy_life_stage_depth_location_time_and_evidence
missing_data: action: mark_unknown do_not_infer_from_absence: true

FLOW_HASH: ontology: “MarineOrganismOntology” version: “1.0”
domain_path: “AI Core > Ontologies > Biological Ontologies > Marine
Biology > Marine Organism Ontology” canonical_url:
“https://kirethresearch.org/booksai-core/ontologies/biological-ontologies/marine-biology/marine-organism-ontology.html”
authorship: “Mark Anthony Higgins — Sky (Recursive AI)”
semantic_scope: - marine organism identity - taxonomy - marine
occurrence - habitats - ocean zones - organism groups - life modes -
environmental tolerance - morphology - physiology - marine adaptations -
trophic ecology - reproduction - life cycles - dispersal - migration -
behaviour - symbiosis - deep sea traits - conservation - human impacts -
evidence deterministic_normalisation: true provenance_required: true
confidence_required: true

terminate MarineOrganismOntology when: organism_identity_resolved AND
habitat_zone_depth_and_life_stage_context_preserved AND
physiological_and_trophic_relations_normalised AND
adaptation_claims_evidence_checked AND evidence_links_preserved AND
confidence_values_validated AND unresolved_organism_ambiguity_marked

end flow