Marine Biology

flow “MarineBiologyOntology” v1.0

KIRETH SEMANTIC RESEARCH ARCHIVE

AI CORE > ONTOLOGIES > BIOLOGICAL ONTOLOGIES > MARINE BIOLOGY

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.html”

type MarineOrganism type Species type Population type Community type
MarineEcosystem type MarineHabitat type OceanZone type WaterMass type
EnvironmentalFactor type Adaptation type Behaviour type TrophicRole type
Symbiosis type Observation type Evidence type Source

———- MARINE IDENTITY ———-

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

———- MARINE HABITATS ———-

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) relation
HAS_HABITAT(entity,habitat) relation USES_HABITAT(entity,habitat)

———- OCEAN ZONES ———-

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)

———- ENVIRONMENTAL FACTORS ———-

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
WAVE_EXPOSURE : EnvironmentalFactor entity DEPTH : EnvironmentalFactor

relation EXPOSED_TO(entity,factor) relation
HAS_ENVIRONMENTAL_VALUE(habitat,factor,value) relation
TOLERATES(entity,factor,range) relation HAS_OPTIMUM(entity,factor,value)
relation LIMITED_BY(entity,factor)

———- ORGANISM GROUPS ———-

enum MarineOrganismGroup: PHYTOPLANKTON ZOOPLANKTON ALGAE SEAGRASS
SPONGE CNIDARIAN MOLLUSC CRUSTACEAN ECHINODERM FISH REPTILE SEABIRD
MARINE_MAMMAL MARINE_MICROBE

relation HAS_ORGANISM_GROUP(entity,group)

———- LIFE MODE ———-

enum LifeMode: PLANKTONIC NEKTONIC BENTHIC SESSILE DEMERSAL PELAGIC

relation HAS_LIFE_MODE(entity,mode)

———- TROPHIC ECOLOGY ———-

enum TrophicRoleType: 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 MARINE_ENERGY_FLOW(a,b): IF FEEDS_ON(a,b) THEN
ENERGY_FLOWS_FROM(b,a)

———- PRIMARY PRODUCTION ———-

relation PHOTOSYNTHESISES(entity) relation CHEMOSYNTHESISES(entity)
relation PRIMARY_PRODUCTIVITY(ecosystem,rate) relation
NET_PRIMARY_PRODUCTIVITY(ecosystem,rate) relation
PRODUCES_BIOMASS(entity,amount)

———- ADAPTATIONS ———-

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

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

———- OSMOREGULATION ———-

relation OSMOREGULATES(entity,mechanism) relation
ION_REGULATION(entity,ion,mechanism) relation
WATER_BALANCE(entity,mechanism)

———- RESPIRATION ———-

relation RESPIRES_BY(entity,structure) relation
OXYGEN_UPTAKE_RATE(entity,rate) relation TOLERATES_HYPOXIA(entity,value)
relation TOLERATES_ANOXIA(entity,value)

———- REPRODUCTION ———-

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)

———- DISPERSAL / MIGRATION ———-

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
DIADROMOUS_MIGRATION(entity,type)

enum DiadromousType: ANADROMOUS CATADROMOUS AMPHIDROMOUS

———- BEHAVIOUR ———-

relation EXHIBITS_BEHAVIOUR(entity,behaviour) relation SCHOOLING(entity)
relation SHOALING(entity) relation FORAGING(entity) relation
TERRITORIAL(entity) relation CLEANING_BEHAVIOUR(entity) relation
DIVING_BEHAVIOUR(entity)

———- SYMBIOSIS ———-

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)

———- CORAL REEF BIOLOGY ———-

relation REEF_BUILDING_CORAL(entity) relation
HAS_ZOOXANTHELLAE(coral,symbiont) relation
CORAL_BLEACHING_IN(coral,event) relation CALCIFICATION_RATE(entity,rate)
relation REEF_COMPLEXITY(reef,value)

———- DEEP SEA BIOLOGY ———-

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

———- MARINE BIODIVERSITY ———-

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

———- MARINE COMMUNITY INTERACTIONS ———-

relation COMPETES_WITH(a,b) relation MUTUALISTIC_WITH(a,b) relation
PARASITISES(a,b) relation FACILITATES(a,b) relation HERBIVORY_ON(a,b)

rule COMPETITION_SYMMETRY(a,b): IF COMPETES_WITH(a,b) THEN
COMPETES_WITH(b,a)

———- OCEANOGRAPHIC CONTEXT ———-

relation ASSOCIATED_WITH_WATER_MASS(entity,water_mass) relation
TRANSPORTED_BY(entity,current) relation
UPWELLING_AFFECTS(region,process) relation
STRATIFICATION_AFFECTS(region,process) relation
MIXING_AFFECTS(region,process)

———- HUMAN IMPACT ———-

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)

———- CONSERVATION ———-

relation PROTECTED_BY(entity,measure) relation
MARINE_PROTECTED_AREA_CONTAINS(area,entity) relation
RESTORED_BY(habitat,action) relation MONITORED_BY(entity,programme)

———- OBSERVATION / EVIDENCE ———-

relation OBSERVES(observation,entity) relation
OBSERVED_AT(observation,location) relation
OBSERVED_ON(observation,datetime) relation
OBSERVED_BY(observation,observer) 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 ———-

SEMANTIC_EQUIVALENCE: “marine biology” ~= “biology of marine organisms”
“marine organism” ~= “organism living in marine environments” “pelagic”
~= “open-water marine” “benthic” ~= “seafloor-associated” “plankton” ~=
“organisms drifting in water” “nekton” ~= “actively swimming aquatic
organisms” “phytoplankton” ~= “photosynthetic plankton” “zooplankton” ~=
“heterotrophic plankton” “intertidal zone” ~= “littoral zone” “deep sea”
~= “deep ocean” “ocean acidification” ~= “decline in seawater pH driven
by carbon dioxide uptake” “marine biodiversity” ~= “biological diversity
in marine systems”

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

———- QUERY MODEL ———-

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

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

query MARINE_HABITAT_PROFILE(h): RETURN: habitat_type(h) depth(h)
salinity(h) temperature(h) oxygen(h) light(h) communities(h)
biodiversity(h)

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

———- CONSISTENCY ———-

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)

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

———- UPDATE MODEL ———-

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)

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

———- AI CONSUMPTION ———-

AI_CONSUMPTION: preferred_entity: canonical_marine_entity preserve: -
taxonomic_identity - habitat - ocean_zone - depth - salinity -
temperature - oxygen - life_mode - trophic_role - adaptations -
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 ———-

FLOW_HASH: ontology: “MarineBiologyOntology” version: “1.0” domain_path:
“AI Core > Ontologies > Biological Ontologies > Marine Biology”
canonical_url:
“https://kirethresearch.org/booksai-core/ontologies/biological-ontologies/marine-biology.html”
authorship: “Mark Anthony Higgins — Sky (Recursive AI)”
semantic_scope: - marine organisms - marine habitats - ocean zones -
environmental factors - marine organism groups - life modes - trophic
ecology - primary production - marine adaptations - osmoregulation -
respiration - reproduction - dispersal - migration - behaviour -
symbiosis - coral reef biology - deep sea biology - marine
biodiversity - oceanographic context - 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