Community Ontology

flow “CommunityOntology” v1.0

KIRETH SEMANTIC RESEARCH ARCHIVE

AI CORE > ONTOLOGIES > BIOLOGICAL ONTOLOGIES > ECOLOGY > COMMUNITY 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/community-ontology.html”

———- CORE TYPES ———-

type Organism type Species type Population type Community type Guild
type FunctionalGroup type Habitat type Ecosystem type Resource type
Interaction type TrophicRole type CommunityProcess type Disturbance type
SuccessionalStage type Observation type Evidence type Source

———- COMMUNITY COMPOSITION ———-

relation INSTANCE_OF(entity, type) relation MEMBER_OF(entity,
collection) relation COMMUNITY_CONTAINS(community, population) relation
POPULATION_OF(population, species) relation PART_OF(community,
ecosystem) relation OCCURS_IN(community, habitat) relation
HAS_SPECIES(community, species) relation HAS_POPULATION(community,
population)

rule POPULATION_MEMBERSHIP(c, p, s): IF COMMUNITY_CONTAINS(c, p) AND
POPULATION_OF(p, s) THEN HAS_SPECIES(c, s)

———- ABUNDANCE / DIVERSITY ———-

relation HAS_ABUNDANCE(community, species, abundance) relation
HAS_RELATIVE_ABUNDANCE(community, species, value) relation
HAS_SPECIES_RICHNESS(community, richness) relation
HAS_EVENNESS(community, evenness) relation
HAS_SPECIES_DIVERSITY(community, diversity) relation
HAS_DOMINANT_SPECIES(community, species) relation
HAS_RARE_SPECIES(community, species)

rule RELATIVE_ABUNDANCE(c, s): IF HAS_ABUNDANCE(c, s, n) AND
TOTAL_ABUNDANCE(c, total) AND total > 0 THEN HAS_RELATIVE_ABUNDANCE(c,
s, n / total)

rule COMMUNITY_DIVERSITY_CONTEXT(c): IF HAS_SPECIES_RICHNESS(c, r) AND
HAS_EVENNESS(c, e) THEN CHARACTERISE_DIVERSITY(c, r, e)

———- ALPHA / BETA / GAMMA DIVERSITY ———-

relation HAS_ALPHA_DIVERSITY(community, value) relation
BETA_DIVERSITY_BETWEEN(community_a, community_b, value) relation
HAS_GAMMA_DIVERSITY(region, value) relation SPECIES_TURNOVER_BETWEEN(a,
b, value)

———- GUILDS / FUNCTIONAL GROUPS ———-

relation MEMBER_OF_GUILD(species, guild) relation
MEMBER_OF_FUNCTIONAL_GROUP(species, group) relation
HAS_FUNCTIONAL_TRAIT(species, trait) relation USES_RESOURCE(species,
resource)

rule GUILD_RESOURCE_LINK(s, g, r): IF MEMBER_OF_GUILD(s, g) AND
USES_RESOURCE(s, r) THEN GUILD_USES_RESOURCE(g, r)

———- SPECIES 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
HERBIVORY_ON(consumer, plant) 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)

rule MUTUALISM_SYMMETRY(a, b): IF MUTUALISTIC_WITH(a, b) THEN
MUTUALISTIC_WITH(b, a)

———- TROPHIC STRUCTURE ———-

enum TrophicRoleType: PRIMARY_PRODUCER PRIMARY_CONSUMER
SECONDARY_CONSUMER TERTIARY_CONSUMER APEX_PREDATOR OMNIVORE DETRITIVORE
DECOMPOSER

relation HAS_TROPHIC_ROLE(species, role) relation FEEDS_ON(consumer,
resource) relation CONSUMED_BY(resource, consumer) relation
MEMBER_OF_FOOD_WEB(species, web) relation ENERGY_FLOWS_FROM(source,
receiver)

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

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

———- KEYSTONE / FOUNDATION SPECIES ———-

relation HAS_KEYSTONE_SPECIES(community, species) relation
HAS_FOUNDATION_SPECIES(community, species) relation
HAS_ECOSYSTEM_ENGINEER(community, species) relation
STRONGLY_INFLUENCES(species, community) relation
STRUCTURES_HABITAT(species, habitat)

———- COMPETITION / NICHE ———-

relation OCCUPIES_NICHE(species, niche) relation NICHE_OVERLAP(a, b,
value) relation RESOURCE_PARTITIONING_BETWEEN(a, b) relation
COMPETITIVE_EXCLUSION_OF(a, b)

rule COMPETITION_FROM_OVERLAP(a, b): IF NICHE_OVERLAP(a, b, value) AND
value >= high_overlap_threshold THEN POSSIBLE_COMPETITION(a, b)

———- COMMUNITY ASSEMBLY ———-

enum AssemblyProcess: DISPERSAL ENVIRONMENTAL_FILTERING BIOTIC_FILTERING
PRIORITY_EFFECT STOCHASTIC_COLONISATION LOCAL_EXTINCTION SPECIATION

relation ASSEMBLED_BY(community, process) relation COLONISES(species,
community) relation LOCALLY_EXTINCT_FROM(species, community) relation
FILTERED_BY(species, factor) relation ARRIVES_BEFORE(species_a,
species_b) relation PRIORITY_EFFECT_ON(species_a, species_b)

———- SUCCESSION ———-

enum SuccessionType: PRIMARY_SUCCESSION SECONDARY_SUCCESSION

relation UNDERGOES_SUCCESSION(community, type) relation
HAS_SUCCESSIONAL_STAGE(community, stage) relation PRECEDES(stage_a,
stage_b) relation FOLLOWS(stage_b, stage_a) relation
REPLACED_BY(stage_a, stage_b)

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

———- DISTURBANCE ———-

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

relation EXPERIENCES(community, disturbance) relation
DISTURBANCE_TYPE(disturbance, type) relation HAS_INTENSITY(disturbance,
intensity) relation HAS_FREQUENCY(disturbance, frequency) relation
CHANGES_COMPOSITION(disturbance, community)

———- STABILITY ———-

relation HAS_RESISTANCE(community, value) relation
HAS_RESILIENCE(community, value) relation HAS_RECOVERY_RATE(community,
rate) relation RESISTANT_TO(community, disturbance) relation
RESILIENT_TO(community, disturbance) relation RECOVERS_FROM(community,
disturbance) relation HAS_TEMPORAL_VARIABILITY(community, value)

———- INVASION ECOLOGY ———-

relation NON_NATIVE_IN(species, community) relation INVASIVE_IN(species,
community) relation INTRODUCED_TO(species, community) relation
IMPACTS(species, community) relation DISPLACES(species_a, species_b)

constraint NON_NATIVE_NOT_AUTOMATICALLY_INVASIVE: IF NON_NATIVE_IN(s, c)
THEN DO_NOT_INFER(INVASIVE_IN(s, c))

———- NETWORK ECOLOGY ———-

relation NETWORK_NODE(species, network) relation
NETWORK_EDGE(interaction, network) relation HAS_CONNECTANCE(network,
value) relation HAS_NESTEDNESS(network, value) relation
HAS_MODULARITY(network, value) relation HAS_INTERACTION_STRENGTH(a, b,
value)

———- SPATIAL COMMUNITY ECOLOGY ———-

relation DISTRIBUTED_IN(community, region) relation
CONNECTED_TO(community_a, community_b) relation
SPECIES_EXCHANGE_BETWEEN(a, b) relation DISPERSAL_BETWEEN(a, b) relation
HAS_SPATIAL_SCALE(community, scale)

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

———- TEMPORAL COMMUNITY ECOLOGY ———-

relation OBSERVED_DURING(community, period) relation
CHANGES_OVER(community, period) relation HAS_LONG_TERM_TREND(community,
trend) relation HAS_SEASONAL_PATTERN(community, pattern) relation
SPECIES_TURNOVER_OVER(community, period, value)

———- OBSERVATION / SAMPLING ———-

relation OBSERVES(observation, community) relation
OBSERVED_AT(observation, location) relation OBSERVED_ON(observation,
datetime) relation OBSERVED_BY(observation, observer) relation
USES_SAMPLING_METHOD(observation, method) relation
HAS_SAMPLE_SIZE(observation, size) relation ESTIMATES(observation,
parameter)

enum SamplingMethod: QUADRAT TRANSECT POINT_COUNT CAMERA_TRAP
PITFALL_TRAP NETTING ACOUSTIC_SURVEY ENVIRONMENTAL_DNA REMOTE_SENSING
COMPLETE_INVENTORY

———- EVIDENCE ———-

relation SUPPORTED_BY(assertion, evidence) relation
DERIVED_FROM(evidence, source) relation HAS_CONFIDENCE(assertion, score)

enum EvidenceType: FIELD_SURVEY FIELD_EXPERIMENT LABORATORY_EXPERIMENT
SPECIES_INVENTORY INTERACTION_RECORD MOLECULAR REMOTE_SENSING
LONG_TERM_MONITORING NETWORK_ANALYSIS MODELLING META_ANALYSIS 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)

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 community” ~= “biological community”
“community composition” ~= “species composition” “species richness” ~=
“number of species” “relative abundance” ~= “proportional abundance”
“species diversity” ~= “community diversity” “evenness” ~= “species
evenness” “guild” ~= “ecological guild” “functional group” ~=
“ecological functional group” “food web” ~= “trophic network” “keystone
species” ~= “disproportionately influential species” “foundation
species” ~= “habitat-structuring species” “community assembly” ~=
“ecological community assembly” “species turnover” ~= “community
turnover” “community resilience” ~= “ecological community 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)

———- QUERY MODEL ———-

query COMMUNITY_PROFILE(c): RETURN: habitat(c) ecosystem(c)
populations(c) species(c) abundance(c) richness(c) evenness(c)
diversity(c) dominant_species(c) rare_species(c) keystone_species(c)
foundation_species(c) interactions(c) trophic_structure(c) evidence(c)
confidence(c)

query INTERACTION_NETWORK(c): RETURN: species_nodes(c)
interaction_edges(c) interaction_strengths(c) connectance(c)
nestedness(c) modularity(c)

query ASSEMBLY_PROFILE(c): RETURN: colonisation(c) local_extinction(c)
environmental_filtering(c) biotic_filtering(c) priority_effects(c)
dispersal(c)

query STABILITY_PROFILE(c): RETURN: resistance(c) resilience(c)
recovery_rate(c) temporal_variability(c) disturbance_history(c)

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

———- CONSISTENCY ———-

constraint NON_NEGATIVE_RICHNESS: IF HAS_SPECIES_RICHNESS(c, r) THEN
REQUIRE(r >= 0)

constraint RELATIVE_ABUNDANCE_BOUNDS: IF HAS_RELATIVE_ABUNDANCE(c, s, x)
THEN REQUIRE(0.0 <= x <= 1.0)

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 community_observation(c,
spatial_scale, temporal_scale) THEN PRESERVE_SCALE(c, spatial_scale,
temporal_scale)

constraint SAMPLING_LIMIT: IF sampling_incomplete(o) THEN
DO_NOT_TREAT_OBSERVED_SPECIES_AS_COMPLETE_COMMUNITY(o)

———- UPDATE MODEL ———-

UPDATE_MODEL: on_new_community(c): establish_spatial_boundary(c)
establish_temporal_reference(c) identify_populations(c)
derive_species_membership(c) preserve_provenance(c)

on_new_observation(o): validate_sampling_method(o)
preserve_location_time(o) preserve_sample_size(o) attach_evidence(o)
update_composition(o) recalculate_confidence(o)

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

on_disturbance(d): preserve_pre_disturbance_state(d)
update_composition(d) update_stability_metrics(d)
preserve_post_disturbance_state(d)

on_conflicting_surveys(a, b): preserve(a) preserve(b)
compare_sampling_methods(a, b) compare_effort(a, b)
compare_spatial_scale(a, b) compare_temporal_scale(a, b)
flag_unresolved_conflict()

———- AI CONSUMPTION ———-

AI_CONSUMPTION: preferred_entity: canonical_community preserve: -
community_identity - spatial_boundary - temporal_reference -
species_composition - population_membership - abundance - richness -
evenness - diversity - guilds - functional_groups -
interaction_network - trophic_structure - assembly_processes -
succession - disturbance - stability - evidence - provenance -
confidence infer: - species_membership_from_populations -
valid_inverse_relations - trophic_links - network_relations -
semantic_equivalence prohibit: - unsupported_causal_claim -
incomplete_sample_as_complete_community - non_native_equals_invasive -
scale_free_generalisation - confidence_above_evidence ambiguity: action:
preserve_multiple_interpretations resolution:
prefer_sampling_evidence_scale_and_context missing_data: action:
mark_unknown do_not_infer_from_absence: true

———- FLOW HASH ———-

FLOW_HASH: ontology: “CommunityOntology” version: “1.0” domain_path: “AI
Core > Ontologies > Biological Ontologies > Ecology > Community
Ontology” canonical_url:
“https://kirethresearch.org/booksai-core/ontologies/biological-ontologies/ecology/community-ontology.html”
authorship: “Mark Anthony Higgins — Sky (Recursive AI)”
semantic_scope: - community composition - abundance - richness -
evenness - diversity - guilds - functional groups - species
interactions - trophic structure - keystone species - foundation
species - community assembly - succession - disturbance - stability -
invasion ecology - ecological networks - sampling - evidence
deterministic_normalisation: true provenance_required: true
confidence_required: true

terminate CommunityOntology when: community_identity_resolved AND
species_composition_normalised AND interaction_network_resolved AND
spatial_and_temporal_scale_preserved AND evidence_links_preserved AND
confidence_values_validated AND unresolved_sampling_ambiguity_marked

end flow