Species Interaction Ontology

flow “SpeciesInteractionOntology” v1.0

KIRETH SEMANTIC RESEARCH ARCHIVE

AI CORE > ONTOLOGIES > BIOLOGICAL ONTOLOGIES > ECOLOGY > SPECIES INTERACTION 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/species-interaction-ontology.html”

———- CORE TYPES ———-

type Organism type Species type Population type Community type Ecosystem
type Habitat type Resource type SpeciesInteraction type
InteractionPartner type InteractionEffect type InteractionContext type
Observation type Evidence type Source

———- INTERACTION IDENTITY ———-

relation INSTANCE_OF(entity, type) relation INTERACTS_WITH(a, b)
relation PARTICIPANT_IN(entity, interaction) relation
HAS_PARTICIPANT(interaction, entity) relation OCCURS_IN(interaction,
habitat) relation OCCURS_DURING(interaction, period) relation
HAS_EFFECT_ON(interaction, entity, effect) relation
HAS_INTERACTION_TYPE(interaction, type)

enum InteractionType: COMPETITION PREDATION HERBIVORY PARASITISM
PARASITOIDISM MUTUALISM COMMENSALISM AMENSALISM FACILITATION NEUTRALISM

———- EFFECT SIGNS ———-

enum InteractionEffectSign: POSITIVE NEGATIVE NEUTRAL CONTEXT_DEPENDENT
UNKNOWN

relation EFFECT_SIGN(interaction, participant, sign) relation
FITNESS_EFFECT(interaction, participant, value) relation
SURVIVAL_EFFECT(interaction, participant, value) relation
REPRODUCTIVE_EFFECT(interaction, participant, value) relation
GROWTH_EFFECT(interaction, participant, value)

———- COMPETITION ———-

relation COMPETES_WITH(a, b) relation COMPETES_FOR(a, b, resource)
relation SHARES_LIMITING_RESOURCE(a, b, resource) relation
COMPETITIVE_EFFECT_ON(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)

rule RESOURCE_COMPETITION(a, b, r): IF SHARES_LIMITING_RESOURCE(a, b, r)
THEN POSSIBLE_COMPETITION(a, b)

———- PREDATION ———-

relation PREYS_ON(predator, prey) relation PREY_OF(prey, predator)
relation CONSUMES(predator, prey) relation PREDATION_RATE(predator,
prey, rate) relation ATTACK_RATE(predator, prey, rate) relation
HANDLING_TIME(predator, prey, duration)

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

———- HERBIVORY ———-

relation HERBIVORY_ON(herbivore, plant) relation GRAZES_ON(herbivore,
plant) relation BROWSES_ON(herbivore, plant) relation
SEED_PREDATION_ON(consumer, plant) relation
HERBIVORY_EFFECT_ON(herbivore, plant, value)

———- PARASITISM ———-

relation PARASITISES(parasite, host) relation HOST_OF(host, parasite)
relation ECTOPARASITE_OF(parasite, host) relation
ENDOPARASITE_OF(parasite, host) relation PARASITE_LOAD(host, parasite,
value) relation VIRULENCE_OF(parasite, host, value)

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

———- PARASITOIDISM ———-

relation PARASITOID_OF(parasitoid, host) relation
PARASITOID_HOST_OF(host, parasitoid) relation KILLS_HOST(parasitoid,
host)

rule PARASITOID_INVERSE(a, b): IF PARASITOID_OF(a, b) THEN
PARASITOID_HOST_OF(b, a)

———- MUTUALISM ———-

relation MUTUALISTIC_WITH(a, b) relation BENEFITS_FROM(a, b) relation
PROVIDES_BENEFIT_TO(a, b) relation OBLIGATE_MUTUALISM(a, b) relation
FACULTATIVE_MUTUALISM(a, b)

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

———- POLLINATION / DISPERSAL ———-

relation POLLINATES(animal, plant) relation POLLINATED_BY(plant, animal)
relation DISPERSES_SEEDS(animal, plant) relation
SEEDS_DISPERSED_BY(plant, animal)

rule POLLINATION_INVERSE(a, b): IF POLLINATES(a, b) THEN
POLLINATED_BY(b, a)

rule SEED_DISPERSAL_INVERSE(a, b): IF DISPERSES_SEEDS(a, b) THEN
SEEDS_DISPERSED_BY(b, a)

———- COMMENSALISM / AMENSALISM ———-

relation COMMENSAL_WITH(a, b) relation BENEFITS_WITHOUT_EFFECT_ON(a, b)
relation AMENSAL_WITH(a, b) relation HARMED_WITHOUT_EFFECT_ON(a, b)

———- FACILITATION ———-

relation FACILITATES(a, b) relation IMPROVES_HABITAT_FOR(a, b) relation
REDUCES_STRESS_FOR(a, b) relation INCREASES_RESOURCE_FOR(a, b)

———- TROPHIC INTERACTIONS ———-

relation FEEDS_ON(consumer, resource) relation CONSUMED_BY(resource,
consumer) relation ENERGY_FLOWS_FROM(resource, consumer) relation
HAS_TROPHIC_LEVEL(entity, level)

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

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

———- INTERACTION STRENGTH ———-

relation HAS_INTERACTION_STRENGTH(a, b, value) relation
PER_CAPITA_EFFECT(a, b, value) relation FREQUENCY_OF_INTERACTION(a, b,
frequency) relation DURATION_OF_INTERACTION(a, b, duration) relation
INTERACTION_PROBABILITY(a, b, probability)

constraint INTERACTION_PROBABILITY_BOUNDS: IF INTERACTION_PROBABILITY(a,
b, p) THEN REQUIRE(0.0 <= p <= 1.0)

———- DIRECT / INDIRECT EFFECTS ———-

relation DIRECTLY_AFFECTS(a, b) relation INDIRECTLY_AFFECTS(a, b)
relation MEDIATED_BY(a, b, mediator) relation CASCADE_EFFECT(a, b)

rule INDIRECT_PATH(a, b, c): IF DIRECTLY_AFFECTS(a, b) AND
DIRECTLY_AFFECTS(b, c) THEN POSSIBLE_INDIRECT_EFFECT(a, c)

———- CONTEXT DEPENDENCE ———-

relation MODIFIED_BY(interaction, factor) relation
CHANGES_WITH(interaction, environmental_condition) relation
CHANGES_WITH_DENSITY(interaction, density) relation
CHANGES_WITH_SEASON(interaction, season) relation
CHANGES_WITH_LIFE_STAGE(interaction, stage)

constraint CONTEXT_PRESERVATION: IF interaction_context_known(i) THEN
PRESERVE_CONTEXT(i)

———- INTERACTION NETWORKS ———-

relation MEMBER_OF_NETWORK(species, network) relation
INTERACTION_EDGE(interaction, network) relation HAS_CONNECTANCE(network,
value) relation HAS_MODULARITY(network, value) relation
HAS_NESTEDNESS(network, value) relation HAS_DEGREE(species, network,
value)

———- COEVOLUTION ———-

relation COEVOLVES_WITH(a, b) relation SELECTIVE_PRESSURE_ON(a, b)
relation RECIPROCAL_SELECTION(a, b) relation
ADAPTATION_TO_INTERACTION(entity, interaction, trait)

rule RECIPROCAL_SELECTION_SYMMETRY(a, b): IF RECIPROCAL_SELECTION(a, b)
THEN RECIPROCAL_SELECTION(b, a)

———- BEHAVIOURAL INTERACTIONS ———-

relation AVOIDS(a, b) relation DEFENDS_AGAINST(a, b) relation
COOPERATES_WITH(a, b) relation AGGRESSIVE_TOWARD(a, b) relation
SIGNALS_TO(a, b)

———- SPATIAL / TEMPORAL CONTEXT ———-

relation CO_OCCURS_WITH(a, b, location) relation SPATIAL_OVERLAP(a, b,
value) relation TEMPORAL_OVERLAP(a, b, value) relation
OBSERVED_DURING(entity, period) relation HAS_SPATIAL_SCALE(interaction,
scale) relation HAS_TEMPORAL_SCALE(interaction, scale)

constraint OVERLAP_BOUNDS: IF SPATIAL_OVERLAP(a, b, v) OR
TEMPORAL_OVERLAP(a, b, v) THEN REQUIRE(0.0 <= v <= 1.0)

———- OBSERVATION / EVIDENCE ———-

relation OBSERVES(observation, interaction) relation
OBSERVED_AT(observation, location) relation OBSERVED_ON(observation,
datetime) relation OBSERVED_BY(observation, observer) relation
SUPPORTS_INTERACTION(observation, a, b) relation SUPPORTED_BY(assertion,
evidence) relation DERIVED_FROM(evidence, source) relation
HAS_CONFIDENCE(assertion, score)

enum EvidenceType: DIRECT_OBSERVATION FIELD_EXPERIMENT
LABORATORY_EXPERIMENT FEEDING_RECORD GUT_CONTENT_ANALYSIS
STABLE_ISOTOPE_ANALYSIS DNA_METABARCODING POLLEN_ANALYSIS CAMERA_RECORD
BEHAVIOURAL_RECORD NETWORK_INFERENCE LONG_TERM_MONITORING META_ANALYSIS
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: “species interaction” ~= “interspecific
interaction” “competition” ~= “interspecific competition” “predation” ~=
“predator-prey interaction” “herbivory” ~= “plant-consumer interaction”
“parasitism” ~= “parasite-host interaction” “mutualism” ~= “mutualistic
interaction” “commensalism” ~= “commensal interaction” “facilitation” ~=
“positive ecological interaction” “interaction strength” ~= “strength of
ecological interaction” “direct effect” ~= “direct ecological effect”
“indirect effect” ~= “indirect ecological effect” “interaction network”
~= “ecological interaction network” “coevolution” ~= “reciprocal
evolutionary change”

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

———- QUERY MODEL ———-

query INTERACTION_PROFILE(i): RETURN: interaction_type(i)
participants(i) effect_signs(i) interaction_strength(i) habitat(i)
spatial_scale(i) temporal_scale(i) modifying_factors(i) evidence(i)
confidence(i)

query SPECIES_INTERACTION_PROFILE(s): RETURN: competitors(s)
predators(s) prey(s) hosts(s) parasites(s) mutualists(s) commensals(s)
facilitated_species(s) network_membership(s)

query PAIRWISE_INTERACTION(a, b): RETURN: interaction_types(a, b)
direction(a, b) effects(a, b) strengths(a, b) context(a, b) evidence(a,
b)

query TRACE_INDIRECT_EFFECT(a, b): RETURN: direct_paths(a, b)
mediators(a, b) indirect_paths(a, b) supporting_evidence(a, b)

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 DIRECTION_PRESERVATION: IF directional_interaction(i) THEN
PRESERVE_DIRECTION(i)

constraint INTERACTION_NOT_CO_OCCURRENCE: IF CO_OCCURS_WITH(a, b,
location) THEN DO_NOT_INFER(INTERACTS_WITH(a, b))

constraint NETWORK_INFERENCE_NOT_DIRECT: IF evidence_type(i) ==
NETWORK_INFERENCE THEN MARK_AS_INFERRED(i)

constraint SCALE_PRESERVATION: IF interaction_observed(i, spatial_scale,
temporal_scale) THEN PRESERVE_SCALE(i, spatial_scale, temporal_scale)

———- UPDATE MODEL ———-

UPDATE_MODEL: on_new_interaction(i): identify_participants(i)
classify_interaction(i) preserve_direction(i) preserve_context(i)
attach_evidence(i) infer_valid_inverse_relations(i)
recalculate_confidence(i)

on_new_observation(o): validate_observation(o) preserve_location_time(o)
identify_interaction(o) attach_evidence(o) update_interaction_graph(o)

on_context_change(c): identify_affected_interactions(c)
preserve_previous_context(c) update_effect_signs_if_supported(c)
update_interaction_strength_if_supported(c)

on_conflicting_interaction_evidence(a, b): preserve(a) preserve(b)
compare_methods(a, b) compare_context(a, b) compare_spatial_scale(a, b)
compare_temporal_scale(a, b) flag_unresolved_conflict()

———- AI CONSUMPTION ———-

AI_CONSUMPTION: preferred_entity: canonical_species_interaction
preserve: - participant_identity - interaction_type -
interaction_direction - effect_sign - interaction_strength -
resource_context - habitat_context - spatial_scale - temporal_scale -
environmental_context - network_context - evidence - provenance -
confidence infer: - valid_inverse_relations - supported_direct_effects -
supported_indirect_paths - semantic_equivalence prohibit: -
cooccurrence_equals_interaction - unsupported_interaction_type -
reversing_directional_interaction -
inferred_interaction_as_direct_observation -
context_free_generalisation - unsupported_causal_claim -
confidence_above_evidence ambiguity: action:
preserve_multiple_interaction_hypotheses resolution:
prefer_direct_evidence_context_and_scale missing_data: action:
mark_unknown do_not_infer_from_absence: true

———- FLOW HASH ———-

FLOW_HASH: ontology: “SpeciesInteractionOntology” version: “1.0”
domain_path: “AI Core > Ontologies > Biological Ontologies > Ecology >
Species Interaction Ontology” canonical_url:
“https://kirethresearch.org/booksai-core/ontologies/biological-ontologies/ecology/species-interaction-ontology.html”
authorship: “Mark Anthony Higgins — Sky (Recursive AI)”
semantic_scope: - species interactions - interaction effects -
competition - predation - herbivory - parasitism - parasitoidism -
mutualism - pollination - seed dispersal - commensalism - amensalism -
facilitation - trophic interactions - interaction strength - direct
effects - indirect effects - context dependence - interaction networks -
coevolution - evidence deterministic_normalisation: true
provenance_required: true confidence_required: true

terminate SpeciesInteractionOntology when:
interaction_participants_resolved AND interaction_type_resolved AND
directional_relations_preserved AND context_and_scale_preserved AND
evidence_links_preserved AND confidence_values_validated AND
unresolved_interaction_ambiguity_marked

end flow