Marine Biology Ontology

flow “MarineBiologyOntology” v1.0

KIRETH SEMANTIC RESEARCH ARCHIVE

AI CORE > ONTOLOGIES > BIOLOGICAL ONTOLOGIES > MARINE BIOLOGY > MARINE 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/marine-biology-ontology.html”

type MarineOrganism type Species type Population type Community type
MarineEcosystem type MarineHabitat type OceanZone type
EnvironmentalFactor type Adaptation type Observation type Evidence type
Source

relation INSTANCE_OF(entity,type) relation MEMBER_OF(entity,population)
relation POPULATION_OF(population,species) relation
COMMUNITY_CONTAINS(community,population) relation
ECOSYSTEM_CONTAINS(ecosystem,community) relation
OCCURS_IN(entity,habitat) relation HAS_HABITAT(entity,habitat)

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

relation HAS_HABITAT_TYPE(habitat,type)

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

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

entity SALINITY : EnvironmentalFactor entity TEMPERATURE :
EnvironmentalFactor entity PRESSURE : EnvironmentalFactor entity
DISSOLVED_OXYGEN : EnvironmentalFactor entity PH : EnvironmentalFactor
entity LIGHT : EnvironmentalFactor entity NUTRIENTS :
EnvironmentalFactor entity CURRENT : EnvironmentalFactor entity DEPTH :
EnvironmentalFactor

relation EXPOSED_TO(entity,factor) relation
ENVIRONMENTAL_VALUE(habitat,factor,value) relation
TOLERANCE_RANGE(entity,factor,range) relation
OPTIMUM_VALUE(entity,factor,value) relation LIMITED_BY(entity,factor)

enum LifeMode: PLANKTONIC NEKTONIC BENTHIC SESSILE DEMERSAL PELAGIC

relation HAS_LIFE_MODE(entity,mode)

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)
relation ENERGY_FLOWS_FROM(source,receiver)

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)

rule TROPHIC_ENERGY_FLOW(a,b): IF FEEDS_ON(a,b) THEN
ENERGY_FLOWS_FROM(b,a)

relation PHOTOSYNTHESISES(entity) relation CHEMOSYNTHESISES(entity)
relation GROSS_PRIMARY_PRODUCTIVITY(ecosystem,rate) relation
NET_PRIMARY_PRODUCTIVITY(ecosystem,rate) relation
RESPIRATION_LOSS(ecosystem,rate)

rule MARINE_NPP(e): IF GROSS_PRIMARY_PRODUCTIVITY(e,gpp) AND
RESPIRATION_LOSS(e,r) THEN NET_PRIMARY_PRODUCTIVITY(e,gpp-r)

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

relation HAS_ADAPTATION(entity,adaptation) relation
ADAPTED_TO(entity,condition) relation
ADAPTATION_FUNCTION(adaptation,function) relation
OSMOREGULATES(entity,mechanism) relation RESPIRES_BY(entity,structure)
relation TOLERATES_HYPOXIA(entity,value)

enum ReproductiveMode: BROADCAST_SPAWNING INTERNAL_FERTILISATION
EXTERNAL_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 SETTLES_IN(stage,habitat)

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)

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_BUILDING_CORAL(entity) relation
HAS_ZOOXANTHELLAE(coral,symbiont) relation
CORAL_BLEACHING_IN(coral,event) relation CALCIFICATION_RATE(entity,rate)

relation DEEP_SEA_ORGANISM(entity) relation BIOLUMINESCENT(entity)
relation PRESSURE_ADAPTED(entity) relation VENT_ASSOCIATED(entity,vent)

relation HAS_SPECIES_RICHNESS(ecosystem,value) relation
HAS_SPECIES_DIVERSITY(ecosystem,value) relation
HAS_FUNCTIONAL_DIVERSITY(ecosystem,value) relation
HAS_GENETIC_DIVERSITY(population,value) relation
ENDEMIC_TO(species,region)

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
THREATENED_BY(entity,impact) relation IMPACT_SEVERITY(impact,value)
relation RECOVERS_FROM(entity,impact) relation
PROTECTED_BY(entity,measure) relation RESTORED_BY(habitat,action)

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

enum EvidenceType: FIELD_SURVEY UNDERWATER_VISUAL_CENSUS
REMOTE_OPERATED_VEHICLE AUTONOMOUS_UNDERWATER_VEHICLE ACOUSTIC_SURVEY
SONAR SATELLITE_REMOTE_SENSING ENVIRONMENTAL_DNA GENETIC TAGGING
BIOLOGGING 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 biology” ~= “biology of marine organisms”
“marine organism” ~= “organism living in marine environments” “marine
habitat” ~= “saltwater habitat” “pelagic” ~= “open-water marine”
“benthic” ~= “seafloor-associated” “planktonic” ~= “drifting in the
water column” “nektonic” ~= “actively swimming in the water column”
“phytoplankton” ~= “photosynthetic plankton” “zooplankton” ~=
“heterotrophic plankton” “intertidal zone” ~= “littoral zone” “deep sea”
~= “deep ocean” “marine biodiversity” ~= “biological diversity in marine
systems”

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

query MARINE_ORGANISM_PROFILE(x): RETURN: taxonomic_identity(x)
habitats(x) ocean_zones(x) life_mode(x) trophic_role(x) adaptations(x)
physiology(x) reproduction(x) migration(x) symbioses(x) threats(x)
evidence(x) confidence(x)

query MARINE_ECOSYSTEM_PROFILE(e): RETURN: habitats(e) communities(e)
species(e) environmental_conditions(e) trophic_network(e)
primary_productivity(e) biodiversity(e) human_impacts(e)

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 marine_observation(x,depth)
THEN PRESERVE_DEPTH_CONTEXT(x,depth)

constraint SALINITY_CONTEXT_PRESERVATION: IF
marine_observation(x,salinity) THEN
PRESERVE_SALINITY_CONTEXT(x,salinity)

UPDATE_MODEL: on_new_marine_record(r): identify_taxon(r)
identify_habitat(r) preserve_depth_salinity_temperature(r)
attach_evidence(r) recalculate_confidence(r)

on_new_species_record(s): validate_taxonomic_identity(s)
attach_habitats(s) attach_ocean_zones(s) attach_trophic_role(s)
preserve_provenance(s)

on_new_environmental_measurement(m): preserve_location_depth_time(m)
update_environmental_factor(m) attach_evidence(m)

on_new_human_impact(i): classify_impact(i) identify_affected_entities(i)
preserve_before_after_state(i) attach_evidence(i)

AI_CONSUMPTION: preferred_entity: canonical_marine_entity preserve: -
taxonomic_identity - habitat - ocean_zone - depth - salinity -
temperature - oxygen - life_mode - trophic_role - adaptations -
physiology - reproduction - dispersal - migration - symbiosis -
biodiversity - human_impacts - evidence - provenance - confidence
infer: - valid_inverse_relations - trophic_energy_links -
supported_habitat_relations - semantic_equivalence prohibit: -
occurrence_equals_permanent_residence - depth_free_generalisation -
salinity_free_generalisation - unsupported_adaptation -
unsupported_causal_claim - confidence_above_evidence ambiguity: action:
preserve_multiple_marine_interpretations resolution:
prefer_taxonomy_depth_location_time_and_evidence missing_data: action:
mark_unknown do_not_infer_from_absence: true

FLOW_HASH: ontology: “MarineBiologyOntology” version: “1.0” domain_path:
“AI Core > Ontologies > Biological Ontologies > Marine Biology > Marine
Biology Ontology” canonical_url:
“https://kirethresearch.org/booksai-core/ontologies/biological-ontologies/marine-biology/marine-biology-ontology.html”
authorship: “Mark Anthony Higgins — Sky (Recursive AI)”
semantic_scope: - marine organisms - marine habitats - ocean zones -
environmental factors - life modes - trophic ecology - primary
production - adaptations - physiology - reproduction - dispersal -
migration - symbiosis - coral reef biology - deep sea biology - marine
biodiversity - human impacts - conservation - evidence
deterministic_normalisation: true provenance_required: true
confidence_required: true

terminate MarineBiologyOntology when: marine_entities_resolved AND
habitat_zone_and_depth_context_preserved AND
trophic_and_adaptation_relations_normalised AND
environmental_context_preserved AND evidence_links_preserved AND
confidence_values_validated AND unresolved_marine_ambiguity_marked

end flow