Habitat Ontology

flow “HabitatOntology” v1.0

KIRETH SEMANTIC RESEARCH ARCHIVE

AI CORE > ONTOLOGIES > BIOLOGICAL ONTOLOGIES > ECOLOGY > HABITAT 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/habitat-ontology.html”

———- CORE TYPES ———-

type Habitat type Microhabitat type Ecosystem type Biome type Organism
type Species type Population type Community type Resource type
AbioticFactor type BioticFactor type EnvironmentalCondition type
SpatialUnit type HabitatPatch type Corridor type Ecotone type
Disturbance type Observation type Evidence type Source

———- HABITAT STRUCTURE ———-

relation INSTANCE_OF(entity, type) relation PART_OF(part, whole)
relation SUBHABITAT_OF(child, parent) relation
MICROHABITAT_OF(microhabitat, habitat) relation HABITAT_OF(habitat,
entity) relation OCCURS_IN(entity, habitat) relation CONTAINS(habitat,
entity) relation LOCATED_IN(habitat, region) relation
PART_OF_ECOSYSTEM(habitat, ecosystem) relation PART_OF_BIOME(habitat,
biome)

rule HABITAT_OCCUPANCY(h, x): IF HABITAT_OF(h, x) THEN OCCURS_IN(x, h)

rule HABITAT_CONTAINMENT(h, x): IF OCCURS_IN(x, h) THEN CONTAINS(h, x)

rule SUBHABITAT_TRANSITIVITY(a, b, c): IF SUBHABITAT_OF(a, b) AND
SUBHABITAT_OF(b, c) THEN SUBHABITAT_OF(a, c)

———- HABITAT TYPES ———-

enum HabitatType: FOREST WOODLAND GRASSLAND SAVANNA DESERT TUNDRA ALPINE
FRESHWATER RIVER STREAM LAKE POND WETLAND MARSH SWAMP BOG MARINE
OPEN_OCEAN CORAL_REEF ESTUARY INTERTIDAL COASTAL MANGROVE SOIL CAVE
SUBTERRANEAN URBAN AGRICULTURAL HOST_ASSOCIATED

relation HAS_HABITAT_TYPE(habitat, type)

———- PHYSICAL CHARACTERISTICS ———-

entity TEMPERATURE : AbioticFactor entity WATER_AVAILABILITY :
AbioticFactor entity MOISTURE : AbioticFactor entity LIGHT :
AbioticFactor entity SALINITY : AbioticFactor entity PH : AbioticFactor
entity OXYGEN : AbioticFactor entity NUTRIENTS : AbioticFactor entity
SUBSTRATE : AbioticFactor entity SOIL_TYPE : AbioticFactor entity DEPTH
: AbioticFactor entity ELEVATION : AbioticFactor entity FLOW_RATE :
AbioticFactor entity WAVE_EXPOSURE : AbioticFactor

relation HAS_FACTOR(habitat, factor) relation HAS_VALUE(factor, value)
relation HAS_RANGE(factor, range) relation
HAS_SEASONAL_VARIATION(factor, variation) relation
HAS_SPATIAL_VARIATION(factor, variation)

———- BIOTIC CHARACTERISTICS ———-

relation HAS_VEGETATION(habitat, vegetation) relation
HAS_DOMINANT_SPECIES(habitat, species) relation HAS_COMMUNITY(habitat,
community) relation HAS_POPULATION(habitat, population) relation
HAS_BIOTIC_FACTOR(habitat, factor)

———- RESOURCES ———-

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

relation PROVIDES_RESOURCE(habitat, resource) relation
RESOURCE_TYPE(resource, type) relation REQUIRES_RESOURCE(entity,
resource) relation RESOURCE_AVAILABILITY(habitat, resource, value)
relation RESOURCE_LIMITED_IN(resource, habitat)

rule RESOURCE_SUPPORT(h, x, r): IF PROVIDES_RESOURCE(h, r) AND
REQUIRES_RESOURCE(x, r) THEN POTENTIALLY_SUPPORTS(h, x)

———- HABITAT SUITABILITY ———-

relation SUITABLE_FOR(habitat, entity) relation UNSUITABLE_FOR(habitat,
entity) relation HAS_SUITABILITY_SCORE(habitat, entity, score) relation
TOLERANCE_RANGE(entity, factor, range) relation OPTIMUM_RANGE(entity,
factor, range) relation LIMITED_BY(entity, factor)

rule FACTOR_SUITABILITY(h, x, f): IF HAS_FACTOR(h, f) AND HAS_VALUE(f,
v) AND TOLERANCE_RANGE(x, f, r) AND v WITHIN r THEN FACTOR_COMPATIBLE(h,
x, f)

constraint SUITABILITY_SCORE_BOUNDS: IF HAS_SUITABILITY_SCORE(h, x, s)
THEN REQUIRE(0.0 <= s <= 1.0)

———- HABITAT OCCUPANCY ———-

relation OCCUPIED_BY(habitat, entity) relation UNOCCUPIED_BY(habitat,
entity) relation BREEDS_IN(entity, habitat) relation FORAGES_IN(entity,
habitat) relation SHELTERS_IN(entity, habitat) relation RESTS_IN(entity,
habitat) relation MIGRATES_THROUGH(entity, habitat)

rule OCCUPANCY_INVERSE(h, x): IF OCCUPIED_BY(h, x) THEN OCCURS_IN(x, h)

constraint ABSENCE_NOT_UNSUITABILITY: IF UNOCCUPIED_BY(h, x) THEN
DO_NOT_INFER(UNSUITABLE_FOR(h, x))

———- HABITAT PATCHES ———-

relation PATCH_OF(patch, habitat) relation HAS_PATCH_AREA(patch, area)
relation HAS_PATCH_QUALITY(patch, quality) relation
HAS_EDGE_LENGTH(patch, length) relation HAS_CORE_AREA(patch, area)
relation DISTANCE_BETWEEN(patch_a, patch_b, distance)

———- CONNECTIVITY ———-

relation CONNECTED_TO(habitat_a, habitat_b) relation
CONNECTED_BY(habitat_a, habitat_b, corridor) relation
CORRIDOR_BETWEEN(corridor, habitat_a, habitat_b) relation
DISPERSAL_BETWEEN(population_a, population_b) relation
MOVEMENT_BETWEEN(entity, habitat_a, habitat_b) relation
HAS_CONNECTIVITY_SCORE(habitat, score)

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

———- FRAGMENTATION ———-

enum FragmentationCause: ROAD URBANISATION AGRICULTURE DEFORESTATION DAM
FENCE RESOURCE_EXTRACTION NATURAL_BARRIER

relation FRAGMENTED_BY(habitat, cause) relation SPLIT_INTO(habitat,
patch) relation ISOLATES(cause, patch) relation
REDUCES_CONNECTIVITY(cause, habitat) relation
INCREASES_EDGE_EFFECT(cause, habitat)

———- EDGE EFFECTS / ECOTONES ———-

relation BORDERS(habitat_a, habitat_b) relation HAS_ECOTONE(habitat_a,
habitat_b, ecotone) relation EDGE_EFFECT_ON(edge, entity) relation
HAS_EDGE_CONDITION(edge, condition)

———- HABITAT SELECTION ———-

relation SELECTS_HABITAT(entity, habitat) relation
AVOIDS_HABITAT(entity, habitat) relation PREFERS(entity, habitat_a,
habitat_b) relation USES_HABITAT(entity, habitat) relation
HABITAT_USE_FREQUENCY(entity, habitat, frequency)

———- HABITAT CHANGE ———-

enum HabitatChange: SUCCESSION DEGRADATION RESTORATION CONVERSION
FRAGMENTATION EXPANSION CONTRACTION CLIMATE_SHIFT

relation UNDERGOES_CHANGE(habitat, change) relation
CHANGES_FROM(habitat, state_a) relation CHANGES_TO(habitat, state_b)
relation CHANGE_RATE(habitat, rate) relation DRIVEN_BY(change, factor)

———- DISTURBANCE ———-

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

relation EXPERIENCES(habitat, disturbance) relation
DISTURBANCE_TYPE(disturbance, type) relation HAS_INTENSITY(disturbance,
intensity) relation HAS_FREQUENCY(disturbance, frequency) relation
HAS_DURATION(disturbance, duration) relation RECOVERS_FROM(habitat,
disturbance)

———- HABITAT QUALITY ———-

relation HAS_HABITAT_QUALITY(habitat, quality) relation
HAS_STRUCTURAL_COMPLEXITY(habitat, value) relation
HAS_RESOURCE_DIVERSITY(habitat, value) relation
HAS_DISTURBANCE_LEVEL(habitat, value) relation
HAS_CONTAMINATION_LEVEL(habitat, value)

———- CONSERVATION / RESTORATION ———-

relation THREATENED_BY(habitat, threat) relation PROTECTED_BY(habitat,
measure) relation RESTORED_BY(habitat, action) relation
MANAGED_BY(habitat, action) relation MONITORED_BY(habitat, programme)

———- TEMPORAL DIMENSION ———-

relation OBSERVED_DURING(habitat, period) relation
SEASONAL_STATE(habitat, season, state) relation CHANGES_OVER(habitat,
period) relation HAS_LONG_TERM_TREND(habitat, trend)

———- OBSERVATION / EVIDENCE ———-

relation OBSERVES(observation, habitat) relation
OBSERVED_AT(observation, location) relation OBSERVED_ON(observation,
datetime) relation OBSERVED_BY(observation, observer) relation
USES_METHOD(observation, method) relation SUPPORTED_BY(assertion,
evidence) relation DERIVED_FROM(evidence, source) relation
HAS_CONFIDENCE(assertion, score)

enum EvidenceType: FIELD_SURVEY VEGETATION_SURVEY SPECIES_SURVEY
ENVIRONMENTAL_SENSOR REMOTE_SENSING GIS_ANALYSIS AERIAL_IMAGERY
SATELLITE_IMAGERY HABITAT_MODEL LONG_TERM_MONITORING EXPERIMENTAL
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: “habitat” ~= “living environment” “microhabitat”
~= “small-scale habitat” “habitat patch” ~= “discrete habitat area”
“habitat suitability” ~= “environmental suitability” “habitat quality”
~= “ecological habitat quality” “habitat connectivity” ~= “landscape
connectivity” “habitat fragmentation” ~= “fragmentation of habitat”
“ecotone” ~= “habitat transition zone” “corridor” ~= “ecological
corridor” “habitat restoration” ~= “ecological habitat restoration”
“habitat selection” ~= “selection of habitat” “habitat use” ~= “use of
habitat”

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)

———- QUERY MODEL ———-

query HABITAT_PROFILE(h): RETURN: habitat_type(h) location(h)
ecosystem(h) abiotic_factors(h) biotic_factors(h) resources(h)
communities(h) populations(h) quality(h) connectivity(h)
fragmentation(h) disturbance(h) evidence(h) confidence(h)

query HABITAT_SUITABILITY(h, x): RETURN: resource_compatibility(h, x)
factor_compatibility(h, x) tolerance_matches(h, x) suitability_score(h,
x) occupancy_evidence(h, x)

query CONNECTIVITY_PROFILE(h): RETURN: connected_habitats(h)
corridors(h) patches(h) isolation(h) fragmentation(h) movement_links(h)

query HABITAT_CHANGE_PROFILE(h): RETURN: historical_states(h)
current_state(h) change_drivers(h) disturbance_history(h) restoration(h)
long_term_trend(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 SPATIAL_BOUNDARY_REQUIRED: IF INSTANCE_OF(h, Habitat) THEN
REQUIRE spatial_definition(h) OR MARK_BOUNDARY_UNKNOWN(h)

constraint TEMPORAL_CONTEXT_REQUIRED: IF habitat_state_asserted(h) THEN
PRESERVE_TEMPORAL_CONTEXT(h)

constraint OCCUPANCY_NOT_SUITABILITY: IF OCCURS_IN(x, h) THEN
DO_NOT_INFER_FULL_SUITABILITY(h, x)

———- UPDATE MODEL ———-

UPDATE_MODEL: on_new_habitat(h): classify_habitat(h)
establish_spatial_boundary(h) identify_abiotic_factors(h)
identify_biotic_components(h) identify_resources(h)
preserve_provenance(h)

on_new_observation(o): validate_observation(o) preserve_location_time(o)
attach_habitat(o) attach_evidence(o) update_habitat_state(o)
recalculate_confidence(o)

on_new_occupancy_record(r): identify_entity(r) identify_habitat(r)
preserve_time(r) preserve_detection_method(r) update_occupancy_graph(r)

on_habitat_change(c): preserve_previous_state(c) classify_change(c)
identify_driver(c) update_current_state(c) preserve_change_provenance(c)

on_conflicting_evidence(a, b): preserve(a) preserve(b)
compare_spatial_resolution(a, b) compare_temporal_context(a, b)
compare_methods(a, b) flag_unresolved_conflict()

———- AI CONSUMPTION ———-

AI_CONSUMPTION: preferred_entity: canonical_habitat preserve: -
habitat_identity - habitat_type - spatial_boundary - temporal_context -
ecosystem_context - abiotic_conditions - biotic_conditions - resources -
occupancy - suitability - quality - connectivity - fragmentation -
disturbance - habitat_change - evidence - provenance - confidence
infer: - valid_containment_relations - valid_connectivity_relations -
resource_support_relations - semantic_equivalence prohibit: -
absence_equals_unsuitability - occupancy_equals_optimal_habitat -
unsupported_causal_claim - boundary_free_generalisation -
time_free_habitat_state - confidence_above_evidence ambiguity: action:
preserve_multiple_interpretations resolution:
prefer_evidence_spatial_temporal_context missing_data: action:
mark_unknown do_not_infer_from_absence: true

———- FLOW HASH ———-

FLOW_HASH: ontology: “HabitatOntology” version: “1.0” domain_path: “AI
Core > Ontologies > Biological Ontologies > Ecology > Habitat Ontology”
canonical_url:
“https://kirethresearch.org/booksai-core/ontologies/biological-ontologies/ecology/habitat-ontology.html”
authorship: “Mark Anthony Higgins — Sky (Recursive AI)”
semantic_scope: - habitat identity - habitat classification -
microhabitats - physical conditions - biotic conditions - resources -
habitat suitability - occupancy - habitat patches - connectivity -
fragmentation - edge effects - habitat selection - habitat change -
disturbance - habitat quality - conservation - restoration - evidence
deterministic_normalisation: true provenance_required: true
confidence_required: true

terminate HabitatOntology when: habitat_identity_resolved AND
spatial_boundary_preserved AND environmental_conditions_normalised AND
occupancy_and_suitability_distinguished AND
connectivity_relations_resolved AND evidence_links_preserved AND
confidence_values_validated AND unresolved_ambiguity_marked

end flow