Deep Sea Biology Ontology

flow “DeepSeaBiologyOntology” v1.0

KIRETH SEMANTIC RESEARCH ARCHIVE

AI CORE > ONTOLOGIES > BIOLOGICAL ONTOLOGIES > MARINE BIOLOGY > DEEP SEA BIOLOGY 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/deep-sea-biology-ontology.html”

type DeepSeaOrganism type Species type Population type Community type
DeepSeaHabitat type OceanZone type EnvironmentalFactor type Adaptation
type Symbiont type Observation type Evidence type Source

relation INSTANCE_OF(entity,type) relation OCCURS_IN(entity,habitat)
relation OCCUPIES_ZONE(entity,zone) relation
HAS_DEPTH_RANGE(entity,range) relation LOCATED_AT_DEPTH(entity,depth)
relation MEMBER_OF_COMMUNITY(entity,community)

enum DeepSeaZone: MESOPELAGIC BATHYPELAGIC ABYSSOPELAGIC HADOPELAGIC
BATHYAL_BENTHIC ABYSSAL_BENTHIC HADAL_BENTHIC

relation HAS_DEEP_SEA_ZONE(entity,zone) relation
ZONE_DEPTH_RANGE(zone,range) relation ZONE_PRESSURE_RANGE(zone,range)
relation ZONE_LIGHT_LEVEL(zone,value)

enum DeepSeaHabitatType: CONTINENTAL_SLOPE CONTINENTAL_RISE
ABYSSAL_PLAIN MID_OCEAN_RIDGE SEAMOUNT SUBMARINE_CANYON OCEAN_TRENCH
HYDROTHERMAL_VENT COLD_SEEP WHALE_FALL DEEP_CORAL_REEF
DEEP_SEA_SPONGE_GROUND

relation HAS_HABITAT_TYPE(habitat,type) relation
USES_HABITAT(entity,habitat)

———- ENVIRONMENT ———-

entity HYDROSTATIC_PRESSURE : EnvironmentalFactor entity TEMPERATURE :
EnvironmentalFactor entity LIGHT : EnvironmentalFactor entity
DISSOLVED_OXYGEN : EnvironmentalFactor entity SALINITY :
EnvironmentalFactor entity PH : EnvironmentalFactor entity
FOOD_AVAILABILITY : EnvironmentalFactor

relation ENVIRONMENTAL_VALUE(habitat,factor,value) relation
TOLERANCE_RANGE(entity,factor,range) relation LIMITED_BY(entity,factor)
relation ADAPTED_TO(entity,condition)

enum DeepSeaLifeMode: PELAGIC DEMERSAL BENTHIC EPIFAUNAL INFAUNAL
SESSILE NEKTONIC PLANKTONIC

relation HAS_LIFE_MODE(entity,mode)

———- TROPHIC ECOLOGY ———-

enum TrophicRole: CHEMOAUTOTROPH SUSPENSION_FEEDER DEPOSIT_FEEDER
DETRITIVORE SCAVENGER PREDATOR OMNIVORE PARASITE DECOMPOSER

relation HAS_TROPHIC_ROLE(entity,role) relation
FEEDS_ON(consumer,resource) relation CONSUMED_BY(resource,consumer)
relation PREYS_ON(predator,prey) relation SCAVENGES(entity,resource)
relation DEPOSIT_FEEDS_ON(entity,sediment)

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

———- FOOD SUPPLY ———-

relation RECEIVES_MARINE_SNOW(habitat,flux) relation
PARTICULATE_ORGANIC_CARBON_FLUX(habitat,rate) relation
FOOD_PULSE(event,habitat) relation RESOURCE_LIMITED(entity,resource)
relation FEEDS_ON_MARINE_SNOW(entity) relation FEEDS_ON_CARRION(entity)

———- CHEMOSYNTHESIS ———-

relation CHEMOSYNTHESISES(entity) relation OXIDISES(entity,compound)
relation FIXES_CARBON(entity,rate) relation
CHEMOSYNTHETIC_PRIMARY_PRODUCTION(habitat,rate) relation
CHEMOSYNTHETIC_SYMBIOSIS(host,symbiont)

enum ChemosyntheticSubstrate: HYDROGEN_SULFIDE METHANE HYDROGEN AMMONIA
FERROUS_IRON

———- VENTS / SEEPS / WHALE FALLS ———-

relation VENT_ASSOCIATED(entity,vent) relation
VENT_FLUID_TEMPERATURE(vent,value) relation
VENT_FLUID_CHEMISTRY(vent,compound,value) relation
SEEP_ASSOCIATED(entity,seep) relation METHANE_FLUX(seep,rate) relation
SULFIDE_FLUX(seep,rate) relation COLONISES_WHALE_FALL(entity,whale_fall)

———- BIOLUMINESCENCE ———-

relation BIOLUMINESCENT(entity) relation PRODUCES_LIGHT(entity,organ)
relation BIOLUMINESCENCE_FUNCTION(entity,function) relation
BIOLUMINESCENCE_WAVELENGTH(entity,range)

enum BioluminescenceFunction: PREY_ATTRACTION PREDATOR_AVOIDANCE
COUNTERILLUMINATION COMMUNICATION MATE_ATTRACTION STARTLE_DEFENCE

———- SENSORY / PRESSURE ADAPTATIONS ———-

relation HAS_ENHANCED_VISION(entity,trait) relation
HAS_REDUCED_VISION(entity,trait) relation
HAS_ENHANCED_CHEMOSENSATION(entity,trait) relation
HAS_MECHANOSENSORY_ADAPTATION(entity,trait) relation
PRESSURE_ADAPTED(entity) relation MEMBRANE_ADAPTATION(entity,trait)
relation PROTEIN_STABILISATION(entity,mechanism) relation
OSMOLYTE_ACCUMULATION(entity,compound) relation PIEZOPHILIC(entity)

———- METABOLISM / LIFE HISTORY ———-

relation METABOLIC_RATE(entity,rate) relation
LOW_METABOLIC_STRATEGY(entity) relation
ENERGY_STORAGE(entity,compound,value) relation
FASTING_TOLERANCE(entity,duration) relation GROWTH_RATE(entity,rate)
relation REPRODUCES_BY(entity,mode) relation
SPAWNING_DEPTH(entity,depth) relation FECUNDITY(entity,value) relation
LARVAL_DISPERSAL(entity,region) relation LONGEVITY(entity,duration)
relation AGE_AT_MATURITY(entity,age)

relation DEEP_SEA_GIGANTISM(entity,evidence) relation
BODY_SIZE(entity,value)

constraint SIZE_PATTERN_NOT_UNIVERSAL: IF INSTANCE_OF(x,DeepSeaOrganism)
THEN DO_NOT_INFER(DEEP_SEA_GIGANTISM(x))

———- BIODIVERSITY / CONNECTIVITY ———-

relation HAS_SPECIES(habitat,species) relation
HAS_SPECIES_RICHNESS(habitat,value) relation
HAS_SPECIES_DIVERSITY(habitat,value) relation
HAS_FUNCTIONAL_DIVERSITY(habitat,value) relation
ENDEMIC_TO(species,habitat) relation CONNECTED_TO(habitat_a,habitat_b)
relation LARVAL_CONNECTIVITY_BETWEEN(a,b) relation
POPULATION_CONNECTIVITY(a,b,value)

———- CARBON CYCLING ———-

relation CARBON_REMINERALISATION(habitat,rate) relation
CARBON_BURIAL(habitat,rate) relation BENTHIC_RESPIRATION(habitat,rate)
relation BIOLOGICAL_CARBON_PUMP_SUPPLIES(habitat,flux) relation
CARBON_SEQUESTRATION(habitat,amount)

———- HUMAN IMPACT ———-

enum DeepSeaImpact: DEEP_SEA_MINING BOTTOM_TRAWLING OIL_GAS_EXTRACTION
POLLUTION PLASTIC_POLLUTION CLIMATE_WARMING DEOXYGENATION
OCEAN_ACIDIFICATION SEDIMENT_PLUME UNDERWATER_NOISE

relation AFFECTED_BY(entity,impact) relation
IMPACT_SEVERITY(impact,value) relation
HABITAT_DAMAGE(impact,habitat,value) relation
RECOVERS_FROM(entity,impact) relation RECOVERY_TIME(entity,duration)
relation PROTECTED_BY(entity,measure) relation
VULNERABLE_MARINE_ECOSYSTEM(habitat)

———- SAMPLING / EVIDENCE ———-

enum SamplingMethod: ROV AUV MANNED_SUBMERSIBLE DEEP_TOW_CAMERA
BAITED_CAMERA TRAWL BOX_CORER MULTICORER LANDER SEDIMENT_TRAP
ENVIRONMENTAL_DNA ACOUSTIC_SURVEY

relation SAMPLED_BY(entity,method) 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: ROV_OBSERVATION AUV_OBSERVATION
SUBMERSIBLE_OBSERVATION DEEP_SEA_CAMERA SPECIMEN SEDIMENT_SAMPLE
WATER_SAMPLE ENVIRONMENTAL_DNA GENETIC CHEMICAL_ANALYSIS
PRESSURE_EXPERIMENT SEDIMENT_TRAP ACOUSTIC_SURVEY LONG_TERM_OBSERVATORY
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: “deep sea” ~= “deep ocean” “deep sea biology” ~=
“biology of deep-ocean organisms and ecosystems” “hadal” ~= “ocean
trench environment” “hydrothermal vent” ~= “seafloor hydrothermal
system” “cold seep” ~= “seafloor fluid seep supporting chemosynthetic
communities” “chemosynthesis” ~= “primary production using chemical
energy” “marine snow” ~= “sinking particulate organic material”
“piezophile” ~= “pressure-loving organism” “barophile” ~= “piezophile”
“bioluminescence” ~= “biological production of visible light” “whale
fall” ~= “whale carcass ecosystem on the seafloor”

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

query DEEP_SEA_ORGANISM_PROFILE(x): RETURN: taxonomy(x) habitat(x)
depth_range(x) life_mode(x) trophic_role(x) pressure_adaptations(x)
sensory_adaptations(x) bioluminescence(x) metabolism(x) reproduction(x)
evidence(x) confidence(x)

query DEEP_SEA_HABITAT_PROFILE(h): RETURN: habitat_type(h) depth(h)
pressure(h) temperature(h) oxygen(h) food_flux(h) communities(h)
biodiversity(h) carbon_cycling(h) impacts(h)

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_REQUIRED: IF deep_sea_observation(o) THEN
REQUIRE(OBSERVED_DEPTH(o,d)) OR MARK_DEPTH_UNKNOWN(o)

constraint SAMPLING_METHOD_PRESERVATION: IF SAMPLED_BY(x,m) THEN
PRESERVE_METHOD_LIMITATIONS(m)

UPDATE_MODEL: on_new_deep_sea_record(r): validate_taxonomic_identity(r)
classify_habitat_and_zone(r) preserve_depth_pressure_temperature(r)
preserve_sampling_method(r) attach_evidence(r) recalculate_confidence(r)

on_new_vent_or_seep_record(r): classify_system(r)
preserve_geochemistry(r) identify_chemosynthetic_producers(r)
attach_symbioses(r) attach_evidence(r)

on_new_adaptation(a): identify_organism(a) classify_adaptation(a)
attach_evidence(a)
distinguish_observed_trait_from_adaptive_interpretation(a)

on_conflicting_observations(a,b): preserve(a) preserve(b)
compare_depth(a,b) compare_sampling_methods(a,b)
compare_pressure_conditions(a,b) compare_temporal_context(a,b)
flag_unresolved_conflict()

AI_CONSUMPTION: preferred_entity: canonical_deep_sea_entity preserve: -
taxonomic_identity - habitat_type - ocean_zone - depth - pressure -
temperature - oxygen - life_mode - trophic_role - food_availability -
chemosynthesis - symbiosis - bioluminescence - sensory_adaptations -
pressure_adaptations - metabolism - reproduction - biodiversity -
connectivity - carbon_cycling - human_impacts - sampling_method -
evidence - provenance - confidence infer: - valid_inverse_relations -
supported_trophic_relations - supported_chemosynthetic_relations -
supported_connectivity_relations - semantic_equivalence prohibit: -
depth_free_deep_sea_generalisation -
all_deep_sea_organisms_are_bioluminescent -
all_deep_sea_organisms_show_gigantism -
observed_trait_equals_adaptation_without_evidence -
sampling_location_equals_global_range - confidence_above_evidence
ambiguity: action: preserve_multiple_deep_sea_interpretations
resolution: prefer_taxonomy_depth_pressure_habitat_method_and_evidence
missing_data: action: mark_unknown do_not_infer_from_absence: true

FLOW_HASH: ontology: “DeepSeaBiologyOntology” version: “1.0”
domain_path: “AI Core > Ontologies > Biological Ontologies > Marine
Biology > Deep Sea Biology Ontology” canonical_url:
“https://kirethresearch.org/booksai-core/ontologies/biological-ontologies/marine-biology/deep-sea-biology-ontology.html”
authorship: “Mark Anthony Higgins — Sky (Recursive AI)”
semantic_scope: - deep sea organisms - deep ocean zones - deep sea
habitats - pressure - darkness - temperature - trophic ecology - food
limitation - marine snow - chemosynthesis - hydrothermal vents - cold
seeps - whale falls - bioluminescence - sensory adaptations - pressure
adaptations - metabolism - life history - biodiversity - connectivity -
carbon cycling - human impacts - sampling - evidence
deterministic_normalisation: true provenance_required: true
confidence_required: true

terminate DeepSeaBiologyOntology when: deep_sea_entity_identity_resolved
AND habitat_zone_depth_and_pressure_context_preserved AND
trophic_and_chemosynthetic_relations_normalised AND
adaptation_claims_evidence_checked AND sampling_context_preserved AND
evidence_links_preserved AND confidence_values_validated AND
unresolved_deep_sea_ambiguity_marked

end flow