Marine Ecosystem Ontology

flow “MarineEcosystemOntology” v1.0

KIRETH SEMANTIC RESEARCH ARCHIVE

AI CORE > ONTOLOGIES > BIOLOGICAL ONTOLOGIES > MARINE BIOLOGY > MARINE ECOSYSTEM 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-ecosystem-ontology.html”

type MarineEcosystem type MarineHabitat type MarineOrganism type Species
type Population type Community type WaterMass type EnvironmentalFactor
type TrophicNetwork type Disturbance type Observation type Evidence type
Source

relation INSTANCE_OF(entity,type) relation CONTAINS(ecosystem,entity)
relation PART_OF(entity,ecosystem) relation
HAS_HABITAT(ecosystem,habitat) relation
HAS_COMMUNITY(ecosystem,community) relation
COMMUNITY_CONTAINS(community,population) relation
POPULATION_OF(population,species) relation OCCURS_IN(entity,ecosystem)
relation LOCATED_IN(ecosystem,region)

enum MarineEcosystemType: OPEN_OCEAN CONTINENTAL_SHELF COASTAL ESTUARINE
INTERTIDAL CORAL_REEF KELP_FOREST SEAGRASS_MEADOW MANGROVE SALT_MARSH
DEEP_SEA HYDROTHERMAL_VENT COLD_SEEP ABYSSAL POLAR_MARINE

relation HAS_ECOSYSTEM_TYPE(ecosystem,type) relation
HAS_AREA(ecosystem,area) relation HAS_DEPTH_RANGE(ecosystem,range)

———- PELAGIC / BENTHIC ———-

relation HAS_PELAGIC_COMPONENT(ecosystem,community) relation
HAS_BENTHIC_COMPONENT(ecosystem,community) relation
PELAGIC_BENTHIC_COUPLING(ecosystem,process) relation
PARTICULATE_FLUX_TO_BENTHOS(ecosystem,rate) relation
BENTHIC_REMINERALISATION(ecosystem,rate)

———- ENVIRONMENT ———-

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

relation ENVIRONMENTAL_VALUE(ecosystem,factor,value) relation
HAS_RANGE(ecosystem,factor,range) relation LIMITED_BY(entity,factor)
relation ASSOCIATED_WITH_WATER_MASS(ecosystem,water_mass) relation
MIXING_IN(ecosystem,rate) relation STRATIFICATION_IN(ecosystem,value)
relation UPWELLING_IN(region,event)

———- PRIMARY PRODUCTION ———-

relation GROSS_PRIMARY_PRODUCTIVITY(ecosystem,rate) relation
NET_PRIMARY_PRODUCTIVITY(ecosystem,rate) relation
RESPIRATION_LOSS(ecosystem,rate) relation
CHEMOSYNTHETIC_PRODUCTIVITY(ecosystem,rate)

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

———- TROPHIC NETWORK ———-

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
ENERGY_FLOWS_FROM(source,receiver) relation
HAS_TROPHIC_NETWORK(ecosystem,network)

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

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

———- DETRITUS / NUTRIENT CYCLING ———-

relation PRODUCES_DETRITUS(entity,detritus) relation
DETRITUS_SINKS_TO(detritus,habitat) relation
FEEDS_ON_DETRITUS(entity,detritus) relation DECOMPOSES(entity,detritus)
relation REMINERALISES(entity,nutrient) relation
NUTRIENT_UPTAKE(entity,nutrient,rate) relation
NUTRIENT_REGENERATION(ecosystem,nutrient,rate)

enum MarineCycle: CARBON_CYCLE NITROGEN_CYCLE PHOSPHORUS_CYCLE
SILICA_CYCLE SULFUR_CYCLE OXYGEN_CYCLE

relation HAS_BIOGEOCHEMICAL_CYCLE(ecosystem,cycle)

———- CARBON PUMP ———-

relation BIOLOGICAL_CARBON_PUMP(ecosystem,process) relation
PARTICULATE_ORGANIC_CARBON_EXPORT(ecosystem,rate) relation
DISSOLVED_ORGANIC_CARBON_EXPORT(ecosystem,rate) relation
CARBON_SEQUESTRATION(ecosystem,amount) relation
MARINE_SNOW_FLUX(ecosystem,rate)

———- BIODIVERSITY ———-

relation HAS_SPECIES(ecosystem,species) 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)

———- CONNECTIVITY ———-

relation CONNECTED_TO(ecosystem_a,ecosystem_b) relation
LARVAL_CONNECTIVITY_BETWEEN(a,b) relation ORGANISM_MOVEMENT_BETWEEN(a,b)
relation MATERIAL_EXCHANGE_BETWEEN(a,b)

rule CONNECTIVITY_SYMMETRY(a,b): IF CONNECTED_TO(a,b) THEN
CONNECTED_TO(b,a)

———- HABITAT FORMERS ———-

relation HABITAT_FORMED_BY(habitat,organism) relation
REEF_BUILDING(entity) relation KELP_CANOPY_FORMING(entity) relation
SEAGRASS_MEADOW_FORMING(entity) relation MANGROVE_FOREST_FORMING(entity)
relation STRUCTURAL_COMPLEXITY(ecosystem,value)

———- DISTURBANCE / RESILIENCE ———-

enum DisturbanceType: MARINE_HEATWAVE TROPICAL_CYCLONE STORM HYPOXIA
ANOXIA HARMFUL_ALGAL_BLOOM DISEASE_OUTBREAK POLLUTION_EVENT
SEDIMENTATION_EVENT INVASIVE_SPECIES

relation EXPERIENCES(ecosystem,disturbance) relation
DISTURBANCE_TYPE(disturbance,type) relation
DISTURBANCE_INTENSITY(disturbance,value) relation
DISTURBANCE_DURATION(disturbance,duration) relation
HAS_RESISTANCE(ecosystem,value) relation HAS_RESILIENCE(ecosystem,value)
relation RECOVERS_FROM(ecosystem,disturbance) relation
RECOVERY_TIME(ecosystem,duration)

———- HUMAN IMPACT ———-

enum HumanImpact: OVERFISHING BYCATCH BOTTOM_TRAWLING DREDGING
COASTAL_DEVELOPMENT POLLUTION PLASTIC_POLLUTION NUTRIENT_LOADING
OCEAN_WARMING OCEAN_ACIDIFICATION DEOXYGENATION UNDERWATER_NOISE
INVASIVE_SPECIES

relation AFFECTED_BY(ecosystem,impact) relation
IMPACT_SEVERITY(impact,value) relation CHANGES_HABITAT(impact,habitat)
relation CHANGES_TROPHIC_STRUCTURE(impact,ecosystem) relation
CHANGES_BIODIVERSITY(impact,ecosystem)

———- ECOSYSTEM SERVICES ———-

enum MarineEcosystemService: FOOD_PROVISION CARBON_STORAGE
COASTAL_PROTECTION NUTRIENT_CYCLING HABITAT_PROVISION RECREATION
CULTURAL_VALUE

relation PROVIDES_SERVICE(ecosystem,service) relation
SERVICE_DEPENDS_ON(service,component) relation
PROTECTED_BY(ecosystem,measure) relation RESTORED_BY(ecosystem,action)
relation MONITORED_BY(ecosystem,programme)

———- EVIDENCE ———-

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

enum EvidenceType: FIELD_SURVEY UNDERWATER_VISUAL_CENSUS ROV_SURVEY
AUV_SURVEY ACOUSTIC_SURVEY SONAR SATELLITE_REMOTE_SENSING
ENVIRONMENTAL_DNA WATER_CHEMISTRY SEDIMENT_SAMPLE FLUX_MEASUREMENT
PRIMARY_PRODUCTIVITY_MEASUREMENT ECOSYSTEM_MODEL 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 ecosystem” ~= “ecological system in a
marine environment” “pelagic ecosystem” ~= “open-water marine ecosystem”
“benthic ecosystem” ~= “seafloor-associated ecosystem” “pelagic-benthic
coupling” ~= “exchange between water-column and seafloor systems”
“primary productivity” ~= “rate of primary biomass production”
“biological carbon pump” ~= “biologically mediated export of carbon to
deeper ocean” “marine snow” ~= “sinking particulate organic material”
“marine biodiversity” ~= “biological diversity in marine systems”
“ecosystem resilience” ~= “capacity of an ecosystem to recover after
disturbance” “marine connectivity” ~= “ecological exchange among marine
habitats or ecosystems”

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

query MARINE_ECOSYSTEM_PROFILE(e): RETURN: ecosystem_type(e) location(e)
depth_range(e) habitats(e) pelagic_components(e) benthic_components(e)
environmental_conditions(e) trophic_network(e) primary_productivity(e)
biogeochemical_cycles(e) biodiversity(e) connectivity(e) disturbances(e)
resilience(e) human_impacts(e) ecosystem_services(e) evidence(e)
confidence(e)

query BIOGEOCHEMICAL_PROFILE(e): RETURN: nutrient_cycles(e)
nutrient_uptake(e) remineralisation(e) carbon_export(e)
carbon_sequestration(e) pelagic_benthic_flux(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 OBSERVED_AT_DEPTH(o,d) THEN
PRESERVE_DEPTH_CONTEXT(o,d)

constraint DISTURBANCE_NOT_PERMANENT_STATE: IF EXPERIENCES(e,d) THEN
DO_NOT_INFER(permanent_degradation(e))

UPDATE_MODEL: on_new_ecosystem(e): classify_ecosystem(e)
establish_location_depth_and_scale(e) identify_habitats(e)
identify_pelagic_and_benthic_components(e) preserve_provenance(e)

on_new_environmental_record(r): preserve_location_depth_time(r)
update_environmental_conditions(r) attach_evidence(r)
recalculate_confidence(r)

on_new_trophic_record(t): identify_consumer_and_resource(t)
preserve_direction(t) update_trophic_network(t) attach_evidence(t)

on_new_disturbance(d): classify_disturbance(d)
preserve_pre_disturbance_state(d) update_ecosystem_state(d)
preserve_recovery_separately(d)

AI_CONSUMPTION: preferred_entity: canonical_marine_ecosystem preserve: -
ecosystem_identity - ecosystem_type - location - depth - habitats -
pelagic_components - benthic_components - environmental_conditions -
water_mass_context - circulation - primary_productivity -
trophic_network - detrital_pathways - biogeochemical_cycles -
carbon_export - biodiversity - connectivity - habitat_formers -
disturbance - resilience - human_impacts - ecosystem_services -
evidence - provenance - confidence infer: - valid_inverse_relations -
trophic_energy_links - supported_connectivity_relations -
supported_pelagic_benthic_links - semantic_equivalence prohibit: -
depth_free_generalisation - disturbance_equals_permanent_degradation -
unsupported_trophic_link - unsupported_causal_claim -
confidence_above_evidence ambiguity: action:
preserve_multiple_ecosystem_interpretations resolution:
prefer_location_depth_time_method_and_evidence missing_data: action:
mark_unknown do_not_infer_from_absence: true

FLOW_HASH: ontology: “MarineEcosystemOntology” version: “1.0”
domain_path: “AI Core > Ontologies > Biological Ontologies > Marine
Biology > Marine Ecosystem Ontology” canonical_url:
“https://kirethresearch.org/booksai-core/ontologies/biological-ontologies/marine-biology/marine-ecosystem-ontology.html”
authorship: “Mark Anthony Higgins — Sky (Recursive AI)”
semantic_scope: - marine ecosystem structure - marine ecosystem types -
pelagic components - benthic components - pelagic-benthic coupling -
environmental conditions - water masses - circulation - primary
production - trophic networks - detrital pathways - nutrient cycling -
biological carbon pump - biodiversity - connectivity - habitat-forming
organisms - disturbance - resilience - human impacts - ecosystem
services - conservation - evidence deterministic_normalisation: true
provenance_required: true confidence_required: true

terminate MarineEcosystemOntology when:
ecosystem_identity_and_type_resolved AND
habitat_depth_and_environmental_context_preserved AND
pelagic_benthic_relations_normalised AND
trophic_and_biogeochemical_relations_resolved AND
disturbance_and_recovery_distinguished AND evidence_links_preserved AND
confidence_values_validated AND
unresolved_marine_ecosystem_ambiguity_marked

end flow