Ecology

flow “EcologyOntology” v1.0

KIRETH SEMANTIC RESEARCH ARCHIVE

AI CORE > ONTOLOGIES > BIOLOGICAL ONTOLOGIES > ECOLOGY

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/ecology.html”

type Organism type Species type Population type Community type Ecosystem
type Biome type Habitat type Niche type Environment type Resource type
AbioticFactor type BioticFactor type Interaction type Process type
FoodWeb type Disturbance type Observation type Evidence type Source

———- ECOLOGICAL HIERARCHY ———-

relation INSTANCE_OF(entity, type) relation MEMBER_OF(entity,
collection) relation POPULATION_OF(population, species) relation
COMMUNITY_CONTAINS(community, population) relation
ECOSYSTEM_CONTAINS(ecosystem, community) relation BIOME_CONTAINS(biome,
ecosystem) relation OCCURS_IN(entity, habitat) relation
OCCUPIES_NICHE(entity, niche) relation REQUIRES_RESOURCE(entity,
resource)

rule ORGANISM_POPULATION(x, p): IF INSTANCE_OF(x, Organism) AND
MEMBER_OF(x, p) THEN INSTANCE_OF(p, Population)

rule POPULATION_COMMUNITY(p, c): IF COMMUNITY_CONTAINS(c, p) THEN
INSTANCE_OF(c, Community)

rule COMMUNITY_ECOSYSTEM(c, e): IF ECOSYSTEM_CONTAINS(e, c) THEN
INSTANCE_OF(e, Ecosystem)

———- HABITAT / ENVIRONMENT ———-

enum HabitatType: TERRESTRIAL FRESHWATER MARINE ESTUARINE WETLAND FOREST
GRASSLAND DESERT TUNDRA SOIL CAVE URBAN

entity TEMPERATURE : AbioticFactor entity WATER : AbioticFactor entity
LIGHT : AbioticFactor entity SALINITY : AbioticFactor entity PH :
AbioticFactor entity OXYGEN : AbioticFactor entity NUTRIENTS :
AbioticFactor entity CLIMATE : AbioticFactor

relation EXPOSED_TO(entity, factor) relation RESPONDS_TO(entity, factor)
relation LIMITED_BY(entity, factor) relation ADAPTED_TO(entity, factor)
relation HAS_TOLERANCE_RANGE(entity, factor, range)

———- POPULATION ECOLOGY ———-

relation HAS_POPULATION_SIZE(population, size) relation
HAS_DENSITY(population, density) relation HAS_BIRTH_RATE(population,
rate) relation HAS_DEATH_RATE(population, rate) relation
HAS_IMMIGRATION_RATE(population, rate) relation
HAS_EMIGRATION_RATE(population, rate) relation
HAS_GROWTH_RATE(population, rate) relation
HAS_CARRYING_CAPACITY(environment, capacity)

rule POPULATION_NET_CHANGE(p): IF HAS_BIRTH_RATE(p, b) AND
HAS_DEATH_RATE(p, d) AND HAS_IMMIGRATION_RATE(p, i) AND
HAS_EMIGRATION_RATE(p, e) THEN NET_CHANGE(p, (b + i) - (d + e))

———- ECOLOGICAL INTERACTIONS ———-

enum InteractionType: COMPETITION PREDATION HERBIVORY PARASITISM
MUTUALISM COMMENSALISM AMENSALISM FACILITATION

relation INTERACTS_WITH(a, b) relation COMPETES_WITH(a, b) relation
PREYS_ON(predator, prey) relation PREY_OF(prey, predator) relation
CONSUMES(consumer, resource) relation PARASITISES(parasite, host)
relation HOST_OF(host, parasite) relation MUTUALISTIC_WITH(a, b)
relation COMMENSAL_WITH(a, b) relation FACILITATES(a, b)

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

rule PARASITISM_INVERSE(a, b): IF PARASITISES(a, b) THEN HOST_OF(b, a)

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

———- TROPHIC ECOLOGY ———-

enum TrophicRole: PRIMARY_PRODUCER PRIMARY_CONSUMER SECONDARY_CONSUMER
TERTIARY_CONSUMER OMNIVORE DETRITIVORE DECOMPOSER

relation HAS_TROPHIC_ROLE(entity, role) relation FEEDS_ON(consumer,
resource) relation ENERGY_FLOWS_FROM(source, receiver) relation
MEMBER_OF_FOOD_WEB(entity, food_web)

rule TROPHIC_TRANSFER(resource, consumer): IF FEEDS_ON(consumer,
resource) THEN ENERGY_FLOWS_FROM(resource, consumer)

———- PRODUCTIVITY ———-

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

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

———- BIOGEOCHEMICAL CYCLES ———-

enum BiogeochemicalCycle: CARBON_CYCLE NITROGEN_CYCLE PHOSPHORUS_CYCLE
WATER_CYCLE SULFUR_CYCLE

relation PARTICIPATES_IN(entity, cycle) relation TRANSFERS(element,
source, destination) relation STORES(element, reservoir) relation
RELEASES(entity, substance) relation ABSORBS(entity, substance) relation
DECOMPOSES(entity, material)

———- COMMUNITY ECOLOGY ———-

relation HAS_SPECIES_RICHNESS(community, richness) relation
HAS_SPECIES_DIVERSITY(community, diversity) relation
HAS_EVENNESS(community, evenness) relation DOMINATED_BY(community,
species) relation KEYSTONE_SPECIES(community, species) relation
FOUNDATION_SPECIES(community, species)

———- SUCCESSION ———-

enum SuccessionType: PRIMARY_SUCCESSION SECONDARY_SUCCESSION

relation UNDERGOES_SUCCESSION(ecosystem, type) relation
PRECEDES(stage_a, stage_b) relation FOLLOWS(stage_b, stage_a) relation
COLONISED_BY(stage, species)

rule SUCCESSION_INVERSE(a, b): IF PRECEDES(a, b) THEN FOLLOWS(b, a)

———- DISTURBANCE ———-

enum DisturbanceType: FIRE FLOOD DROUGHT STORM VOLCANISM DISEASE
LAND_USE_CHANGE POLLUTION INVASIVE_SPECIES

relation EXPERIENCES(ecosystem, disturbance) relation
DISTURBANCE_TYPE(disturbance, type) relation HAS_INTENSITY(disturbance,
intensity) relation HAS_FREQUENCY(disturbance, frequency) relation
RECOVERS_FROM(ecosystem, disturbance) relation RESISTANT_TO(ecosystem,
disturbance) relation RESILIENT_TO(ecosystem, disturbance)

———- SPATIAL ECOLOGY ———-

relation DISTRIBUTED_IN(entity, region) relation CONNECTED_TO(habitat_a,
habitat_b) relation FRAGMENTED_BY(habitat, factor) relation
DISPERSAL_BETWEEN(population_a, population_b) relation
MIGRATES_BETWEEN(entity, region_a, region_b) relation
HAS_RANGE_SIZE(species, area)

———- EVOLUTIONARY ECOLOGY ———-

relation SELECTED_BY(trait, environment) relation
INCREASES_FITNESS(trait, context) relation DECREASES_FITNESS(trait,
context) relation ADAPTATION_TO(trait, environment) relation
COEVOLVES_WITH(a, b)

rule ECOLOGICAL_SELECTION(t, e): IF SELECTED_BY(t, e) AND
INCREASES_FITNESS(t, e) THEN ADAPTATION_TO(t, e)

———- CONSERVATION ———-

enum ConservationStatus: LEAST_CONCERN NEAR_THREATENED VULNERABLE
ENDANGERED CRITICALLY_ENDANGERED EXTINCT_IN_WILD EXTINCT DATA_DEFICIENT

relation HAS_CONSERVATION_STATUS(species, status) relation
THREATENED_BY(entity, threat) relation PROTECTED_BY(entity, measure)
relation RESTORED_BY(ecosystem, action)

———- ECOSYSTEM SERVICES ———-

enum EcosystemService: PROVISIONING REGULATING CULTURAL SUPPORTING

relation PROVIDES_SERVICE(ecosystem, service) relation BENEFITS(service,
beneficiary) relation DEPENDS_ON(service, process)

———- EVIDENCE ———-

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_OBSERVATION EXPERIMENTAL REMOTE_SENSING
SENSOR_DATA POPULATION_SURVEY SPECIES_INVENTORY MOLECULAR MODELLING
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: “ecology” ~= “ecological science” “habitat” ~=
“living environment” “ecological niche” ~= “niche” “food web” ~=
“trophic network” “food chain” ~= “trophic chain” “primary producer” ~=
“autotrophic producer” “consumer” ~= “heterotrophic consumer”
“decomposer” ~= “decomposition organism” “species richness” ~= “number
of species” “carrying capacity” ~= “maximum sustainable population”
“ecological succession” ~= “successional change” “ecosystem resilience”
~= “ecological resilience”

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

———- CAUSAL MODEL ———-

relation CAUSES(a, b) relation INFLUENCES(a, b) relation REGULATES(a, b)
relation FEEDBACK_ON(a, b)

constraint CAUSATION_REQUIRES_EVIDENCE: IF CAUSES(a, b) THEN REQUIRE
SUPPORTED_BY(CAUSES(a,b), Evidence)

———- QUERIES ———-

query ECOLOGICAL_PROFILE(x): RETURN: organisational_level(x) habitat(x)
niche(x) resources(x) interactions(x) trophic_role(x)
environmental_factors(x) spatial_distribution(x) evidence(x)
confidence(x)

query ECOSYSTEM_PROFILE(e): RETURN: communities(e) species(e)
trophic_network(e) productivity(e) nutrient_cycles(e) disturbances(e)
ecosystem_services(e) resilience(e)

query POPULATION_PROFILE(p): RETURN: species(p) population_size(p)
density(p) growth_rate(p) limiting_factors(p) interactions(p)

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 SCALE_PRESERVATION: IF ecological_pattern_observed(x, scale)
THEN PRESERVE_SCALE(x, scale)

constraint CONTEXT_PRESERVATION: IF
ecological_relation_context_dependent(r) THEN PRESERVE_CONTEXT(r)

———- UPDATE MODEL ———-

UPDATE_MODEL: on_new_observation(o): validate_observation(o)
identify_ecological_level(o) preserve_space_time_scale(o)
attach_evidence(o) update_entity_graph(o) recalculate_confidence(o)

on_new_interaction(i): classify_interaction(i) identify_participants(i)
preserve_context(i) attach_evidence(i) infer_valid_inverse_relations(i)

on_environmental_change(c): identify_affected_entities(c)
update_factor_relations(c) preserve_before_after_state(c)
recalculate_supported_predictions(c)

on_conflicting_evidence(a, b): preserve(a) preserve(b) compare_scale(a,
b) compare_context(a, b) compare_methodology(a, b)
flag_unresolved_conflict()

———- AI CONSUMPTION ———-

AI_CONSUMPTION: preferred_entity: canonical_ecological_entity
preserve: - taxonomic_identity - organisational_level - habitat -
niche - spatial_scale - temporal_scale - environmental_context -
population_context - species_interactions - trophic_relations -
ecosystem_processes - evidence - provenance - confidence infer: -
valid_inverse_relations - trophic_links - organisational_membership -
semantic_equivalence prohibit: - unsupported_causal_claim -
invented_species_interaction - scale_free_generalisation -
context_free_generalisation - confidence_above_evidence -
absence_equals_extinction ambiguity: action:
preserve_multiple_interpretations resolution:
prefer_evidence_scale_and_context missing_data: action: mark_unknown
do_not_infer_from_absence: true

———- FLOW HASH ———-

FLOW_HASH: ontology: “EcologyOntology” version: “1.0” domain_path: “AI
Core > Ontologies > Biological Ontologies > Ecology” canonical_url:
“https://kirethresearch.org/booksai-core/ontologies/biological-ontologies/ecology.html”
authorship: “Mark Anthony Higgins — Sky (Recursive AI)”
semantic_scope: - ecological hierarchy - habitats and niches -
population ecology - community ecology - species interactions - trophic
ecology - ecosystem processes - succession - disturbance - spatial
ecology - conservation - evidence deterministic_normalisation: true
provenance_required: true confidence_required: true

terminate EcologyOntology when: ecological_entities_resolved AND
semantic_relations_normalised AND scale_and_context_preserved AND
evidence_links_preserved AND confidence_values_validated AND
unresolved_ambiguity_marked

end flow