Ecological Niche Ontology

flow “EcologicalNicheOntology” v1.0

KIRETH SEMANTIC RESEARCH ARCHIVE

AI CORE > ONTOLOGIES > BIOLOGICAL ONTOLOGIES > ECOLOGY > ECOLOGICAL NICHE 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/ecology/ecological-niche-ontology.html”

———- CORE TYPES ———-

type Organism type Species type Population type EcologicalNiche type
FundamentalNiche type RealisedNiche type Habitat type Resource type
EnvironmentalFactor type AbioticFactor type BioticFactor type
NicheDimension type FunctionalRole type Interaction type Observation
type Evidence type Source

———- NICHE IDENTITY ———-

relation INSTANCE_OF(entity, type) relation HAS_NICHE(entity, niche)
relation OCCUPIES_NICHE(entity, niche) relation NICHE_OF(niche, entity)
relation OCCURS_IN(entity, habitat) relation HAS_DIMENSION(niche,
dimension)

rule NICHE_INVERSE(x, n): IF HAS_NICHE(x, n) THEN NICHE_OF(n, x)

rule NICHE_OCCUPANCY(x, n): IF HAS_NICHE(x, n) THEN OCCUPIES_NICHE(x, n)

———- NICHE TYPES ———-

enum NicheType: FUNDAMENTAL REALISED TROPHIC SPATIAL TEMPORAL
REPRODUCTIVE THERMAL CLIMATIC FUNCTIONAL

relation HAS_NICHE_TYPE(niche, type) relation
FUNDAMENTAL_NICHE_OF(niche, entity) relation REALISED_NICHE_OF(niche,
entity)

———- NICHE DIMENSIONS ———-

enum NicheDimensionType: TEMPERATURE MOISTURE SALINITY PH LIGHT OXYGEN
NUTRIENTS FOOD_RESOURCE WATER_RESOURCE SPACE SHELTER NESTING_SITE HOST
PREDATOR_PRESSURE COMPETITOR_PRESSURE ACTIVITY_TIME
REPRODUCTIVE_CONDITION

relation DIMENSION_TYPE(dimension, type) relation
HAS_DIMENSION_RANGE(niche, dimension, range) relation
HAS_DIMENSION_OPTIMUM(niche, dimension, optimum) relation
HAS_DIMENSION_LIMIT(niche, dimension, limit)

———- ENVIRONMENTAL TOLERANCE ———-

relation TOLERATES(entity, factor) relation HAS_TOLERANCE_RANGE(entity,
factor, range) relation HAS_OPTIMUM(entity, factor, value) relation
LIMITED_BY(entity, factor) relation EXCLUDED_BY(entity, factor)

rule NICHE_FACTOR_COMPATIBILITY(x, f, v): IF HAS_TOLERANCE_RANGE(x, f,
r) AND v WITHIN r THEN COMPATIBLE_WITH(x, f, v)

———- RESOURCE USE ———-

enum ResourceType: FOOD WATER LIGHT NUTRIENTS SPACE SHELTER NESTING_SITE
BREEDING_SITE HOST

relation USES_RESOURCE(entity, resource) relation
REQUIRES_RESOURCE(entity, resource) relation RESOURCE_TYPE(resource,
type) relation RESOURCE_USE_RATE(entity, resource, rate) relation
RESOURCE_PREFERENCE(entity, resource, value) relation
RESOURCE_AVAILABLE_IN(resource, habitat)

———- FUNDAMENTAL / REALISED NICHE ———-

relation POTENTIALLY_OCCUPIES(entity, condition_space) relation
ACTUALLY_OCCUPIES(entity, condition_space) relation
CONSTRAINED_BY(niche, factor) relation EXPANDED_BY(niche, factor)

rule REALISED_WITHIN_FUNDAMENTAL(x, fundamental, realised): IF
FUNDAMENTAL_NICHE_OF(fundamental, x) AND REALISED_NICHE_OF(realised, x)
THEN REQUIRE(SUBSPACE_OF(realised, fundamental) OR
EVIDENCE_OF_CONTEXTUAL_EXPANSION(realised, fundamental))

———- COMPETITION ———-

relation COMPETES_WITH(a, b) relation COMPETES_FOR(a, b, resource)
relation NICHE_OVERLAP(a, b, value) relation COMPETITIVE_EXCLUSION_OF(a,
b) relation COMPETITIVE_RELEASE_OF(a, b)

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

constraint NICHE_OVERLAP_BOUNDS: IF NICHE_OVERLAP(a, b, value) THEN
REQUIRE(0.0 <= value <= 1.0)

———- NICHE PARTITIONING ———-

relation RESOURCE_PARTITIONING_BETWEEN(a, b) relation
SPATIAL_PARTITIONING_BETWEEN(a, b) relation
TEMPORAL_PARTITIONING_BETWEEN(a, b) relation
TROPHIC_PARTITIONING_BETWEEN(a, b)

rule PARTITIONING_REDUCES_OVERLAP(a, b): IF
RESOURCE_PARTITIONING_BETWEEN(a, b) OR SPATIAL_PARTITIONING_BETWEEN(a,
b) OR TEMPORAL_PARTITIONING_BETWEEN(a, b) THEN
POSSIBLE_REDUCTION_IN_COMPETITIVE_OVERLAP(a, b)

———- SPECIALISATION / GENERALISATION ———-

enum NicheBreadth: SPECIALIST INTERMEDIATE GENERALIST

relation HAS_NICHE_BREADTH(entity, breadth) relation
HAS_NICHE_BREADTH_VALUE(entity, value) relation SPECIALISED_ON(entity,
resource) relation GENERALIST_ACROSS(entity, resources)

———- TROPHIC NICHE ———-

relation FEEDS_ON(consumer, resource) relation TROPHIC_LEVEL(entity,
level) relation TROPHIC_POSITION(entity, value) relation
DIET_BREADTH(entity, value) relation PREYS_ON(predator, prey) relation
PREY_OF(prey, predator)

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

———- SPATIAL NICHE ———-

relation USES_HABITAT(entity, habitat) relation
USES_MICROHABITAT(entity, microhabitat) relation
HAS_VERTICAL_POSITION(entity, position) relation HAS_DEPTH_RANGE(entity,
range) relation HAS_ELEVATION_RANGE(entity, range) relation
HAS_HOME_RANGE(entity, area)

———- TEMPORAL NICHE ———-

enum ActivityPeriod: DIURNAL NOCTURNAL CREPUSCULAR CATHEMERAL

relation ACTIVE_DURING(entity, period) relation FORAGES_DURING(entity,
period) relation REPRODUCES_DURING(entity, period) relation
SEASONALLY_ACTIVE(entity, season)

———- FUNCTIONAL NICHE ———-

relation HAS_FUNCTIONAL_ROLE(entity, role) relation POLLINATES(entity,
plant) relation DISPERSES_SEEDS(entity, plant) relation
DECOMPOSES(entity, material) relation ENGINEERS_HABITAT(entity, habitat)
relation FIXES_NITROGEN(entity, context)

———- NICHE CONSTRUCTION ———-

relation MODIFIES_ENVIRONMENT(entity, environment) relation
MODIFICATION_AFFECTS(entity, target) relation CONSTRUCTS_NICHE(entity,
niche) relation INHERITS_MODIFIED_ENVIRONMENT(entity, environment)

———- NICHE SHIFT ———-

relation NICHE_SHIFTS_FROM(entity, niche_a) relation
NICHE_SHIFTS_TO(entity, niche_b) relation NICHE_SHIFT_DRIVEN_BY(entity,
factor) relation NICHE_EXPANSION(entity, dimension) relation
NICHE_CONTRACTION(entity, dimension)

———- INVASION / RANGE CONTEXT ———-

relation NATIVE_NICHE(entity, niche) relation INTRODUCED_NICHE(entity,
niche) relation NICHE_CONSERVATISM(entity, value) relation
NICHE_CHANGE_AFTER_INTRODUCTION(entity, value)

———- EVOLUTIONARY NICHE ———-

relation SELECTED_BY(trait, niche_dimension) relation ADAPTED_TO(entity,
condition) relation COEVOLVES_WITH(a, b) relation
NICHE_DIVERGENCE_BETWEEN(a, b) relation NICHE_SIMILARITY_BETWEEN(a, b,
value)

constraint NICHE_SIMILARITY_BOUNDS: IF NICHE_SIMILARITY_BETWEEN(a, b,
value) THEN REQUIRE(0.0 <= value <= 1.0)

———- NICHE MODELLING ———-

relation MODEL_PREDICTS(model, niche) relation
MODEL_USES_VARIABLE(model, variable) relation
MODEL_USES_OCCURRENCE(model, occurrence) relation MODEL_OUTPUT(model,
suitability_surface) relation MODEL_VALIDATED_BY(model, dataset)
relation MODEL_PERFORMANCE(model, metric, value)

enum NicheModelType: ECOLOGICAL_NICHE_MODEL SPECIES_DISTRIBUTION_MODEL
MECHANISTIC_NICHE_MODEL CORRELATIVE_NICHE_MODEL

———- OBSERVATION / EVIDENCE ———-

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

enum EvidenceType: OCCURRENCE_RECORD FIELD_OBSERVATION FIELD_EXPERIMENT
LABORATORY_EXPERIMENT RESOURCE_USE_DATA DIET_ANALYSIS
STABLE_ISOTOPE_ANALYSIS ENVIRONMENTAL_SENSOR REMOTE_SENSING NICHE_MODEL
PHYLOGENETIC_ANALYSIS LONG_TERM_MONITORING LITERATURE

———- CONFIDENCE ———-

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)

rule EVIDENCE_WEIGHTING(a, e, s): IF SUPPORTED_BY(a, e) AND
DERIVED_FROM(e, s) THEN UPDATE_CONFIDENCE(a, evidence_quality(e),
source_reliability(s))

———- SEMANTIC EQUIVALENCE ———-

SEMANTIC_EQUIVALENCE: “ecological niche” ~= “niche” “fundamental niche”
~= “potential niche” “realised niche” ~= “realized niche” “niche
breadth” ~= “ecological niche breadth” “niche overlap” ~= “ecological
overlap” “resource partitioning” ~= “resource niche partitioning”
“spatial partitioning” ~= “spatial niche partitioning” “temporal
partitioning” ~= “temporal niche partitioning” “niche specialisation” ~=
“ecological specialisation” “niche specialization” ~= “ecological
specialisation” “generalist” ~= “broad-niche species” “specialist” ~=
“narrow-niche species” “ecological niche model” ~= “ENM” “species
distribution model” ~= “SDM” “niche construction” ~= “organism-driven
environmental modification”

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

———- QUERY MODEL ———-

query NICHE_PROFILE(x): RETURN: niche_type(x) dimensions(x)
environmental_tolerances(x) optima(x) resources(x) habitat_use(x)
temporal_use(x) trophic_role(x) functional_role(x) niche_breadth(x)
evidence(x) confidence(x)

query COMPARE_NICHES(a, b): RETURN: shared_dimensions(a, b)
differing_dimensions(a, b) niche_overlap(a, b) resource_partitioning(a,
b) spatial_partitioning(a, b) temporal_partitioning(a, b)
niche_similarity(a, b)

query FUNDAMENTAL_REALISED_PROFILE(x): RETURN: fundamental_niche(x)
realised_niche(x) constraining_factors(x) biotic_interactions(x)
environmental_limits(x)

query NICHE_MODEL_PROFILE(model): RETURN: model_type(model)
variables(model) occurrence_data(model) output(model) validation(model)
performance(model)

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 HABITAT_NOT_NICHE: IF OCCURS_IN(x, habitat) THEN
DO_NOT_INFER(HAS_NICHE(x, habitat))

constraint OCCURRENCE_NOT_FULL_NICHE: IF observed_occurrence(x,
location) THEN DO_NOT_INFER_COMPLETE_NICHE_FROM_SINGLE_OCCURRENCE(x)

constraint MODEL_NOT_DIRECT_OBSERVATION: IF evidence_type(assertion) ==
NICHE_MODEL THEN MARK_AS_MODEL_DERIVED(assertion)

constraint CONTEXT_PRESERVATION: IF niche_estimate(n, spatial_scale,
temporal_scale) THEN PRESERVE_SCALE(n, spatial_scale, temporal_scale)

———- UPDATE MODEL ———-

UPDATE_MODEL: on_new_niche(n): identify_entity(n) classify_niche_type(n)
identify_dimensions(n) attach_resource_relations(n)
attach_environmental_ranges(n) preserve_provenance(n)

on_new_observation(o): validate_observation(o) preserve_location_time(o)
attach_measured_dimensions(o) attach_evidence(o)
update_niche_estimate(o) recalculate_confidence(o)

on_new_interaction(i): classify_interaction(i)
identify_niche_constraints(i) update_realised_niche(i)
preserve_context(i)

on_new_model(m): classify_model(m) preserve_input_variables(m)
preserve_occurrence_dataset(m) preserve_validation(m)
mark_outputs_as_model_derived(m)

on_conflicting_niche_estimates(a, b): preserve(a) preserve(b)
compare_dimensions(a, b) compare_spatial_scale(a, b)
compare_temporal_scale(a, b) compare_methods(a, b)
flag_unresolved_conflict()

———- AI CONSUMPTION ———-

AI_CONSUMPTION: preferred_entity: canonical_ecological_niche preserve: -
niche_identity - niche_type - niche_dimensions - environmental_ranges -
environmental_optima - resource_use - habitat_use - temporal_use -
trophic_context - functional_role - niche_breadth -
fundamental_realised_distinction - spatial_scale - temporal_scale -
evidence - provenance - confidence infer: - valid_inverse_relations -
supported_overlap_relations - supported_partitioning_relations -
semantic_equivalence prohibit: - habitat_equals_niche -
single_occurrence_equals_complete_niche -
model_prediction_as_direct_observation - unsupported_competition -
unsupported_causal_claim - confidence_above_evidence ambiguity: action:
preserve_multiple_niche_estimates resolution:
prefer_direct_evidence_dimensions_and_context missing_data: action:
mark_unknown do_not_infer_from_absence: true

———- FLOW HASH ———-

FLOW_HASH: ontology: “EcologicalNicheOntology” version: “1.0”
domain_path: “AI Core > Ontologies > Biological Ontologies > Ecology >
Ecological Niche Ontology” canonical_url:
“https://kirethresearch.org/booksai-core/ontologies/biological-ontologies/ecology/ecological-niche-ontology.html”
authorship: “Mark Anthony Higgins — Sky (Recursive AI)”
semantic_scope: - ecological niche identity - niche types - niche
dimensions - environmental tolerances - resource use - fundamental
niche - realised niche - competition - niche overlap - niche
partitioning - specialisation - trophic niche - spatial niche - temporal
niche - functional niche - niche construction - niche shifts -
evolutionary niche - niche modelling - evidence
deterministic_normalisation: true provenance_required: true
confidence_required: true

terminate EcologicalNicheOntology when: niche_identity_resolved AND
niche_dimensions_normalised AND
fundamental_realised_distinction_preserved AND
spatial_and_temporal_context_preserved AND model_derived_claims_marked
AND evidence_links_preserved AND confidence_values_validated AND
unresolved_niche_ambiguity_marked

end flow