Biodiversity Ontology

flow “BiodiversityOntology” v1.0

KIRETH SEMANTIC RESEARCH ARCHIVE

AI CORE > ONTOLOGIES > BIOLOGICAL ONTOLOGIES > ECOLOGY > BIODIVERSITY 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/biodiversity-ontology.html”

type Organism type Species type Population type Community type Ecosystem
type Habitat type Region type Biodiversity type Trait type Observation
type Evidence type Source

enum BiodiversityLevel: GENETIC_DIVERSITY SPECIES_DIVERSITY
FUNCTIONAL_DIVERSITY PHYLOGENETIC_DIVERSITY ECOSYSTEM_DIVERSITY
LANDSCAPE_DIVERSITY

relation INSTANCE_OF(entity,type) relation
HAS_BIODIVERSITY(entity,biodiversity) relation
HAS_DIVERSITY_LEVEL(biodiversity,level) relation
MEASURED_IN(biodiversity,spatial_unit) relation
MEASURED_DURING(biodiversity,temporal_unit)

———- GENETIC DIVERSITY ———-

relation HAS_ALLELE(population,allele) relation
HAS_ALLELE_FREQUENCY(population,allele,frequency) relation
HAS_HETEROZYGOSITY(population,value) relation
HAS_NUCLEOTIDE_DIVERSITY(population,value) relation
HAS_GENETIC_RICHNESS(population,value) relation
HAS_EFFECTIVE_POPULATION_SIZE(population,value) relation
GENE_FLOW_BETWEEN(population_a,population_b)

constraint ALLELE_FREQUENCY_BOUNDS: IF HAS_ALLELE_FREQUENCY(p,a,f) THEN
REQUIRE(0.0 <= f <= 1.0)

———- SPECIES DIVERSITY ———-

relation HAS_SPECIES(entity,species) relation
HAS_SPECIES_RICHNESS(entity,richness) relation
HAS_SPECIES_EVENNESS(entity,evenness) relation
HAS_SPECIES_DIVERSITY(entity,diversity) relation
HAS_ABUNDANCE(entity,species,abundance) relation
HAS_RELATIVE_ABUNDANCE(entity,species,value)

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

———- ALPHA / BETA / GAMMA ———-

relation HAS_ALPHA_DIVERSITY(entity,value) relation
BETA_DIVERSITY_BETWEEN(a,b,value) relation
HAS_GAMMA_DIVERSITY(region,value) relation
SPECIES_TURNOVER_BETWEEN(a,b,value)

———- FUNCTIONAL / PHYLOGENETIC ———-

relation HAS_FUNCTIONAL_TRAIT(species,trait) relation
HAS_FUNCTIONAL_RICHNESS(entity,value) relation
HAS_FUNCTIONAL_EVENNESS(entity,value) relation
HAS_FUNCTIONAL_DIVERGENCE(entity,value) relation
HAS_FUNCTIONAL_REDUNDANCY(entity,value) relation
HAS_PHYLOGENETIC_DIVERSITY(entity,value) relation
EVOLUTIONARY_DISTINCTIVENESS(species,value)

———- ECOSYSTEM DIVERSITY ———-

relation HAS_ECOSYSTEM(entity,ecosystem) relation
HAS_HABITAT(entity,habitat) relation
HAS_ECOSYSTEM_RICHNESS(region,value) relation
HAS_HABITAT_RICHNESS(region,value) relation
HAS_HABITAT_HETEROGENEITY(region,value)

———- DIVERSITY INDICES ———-

enum DiversityIndex: SHANNON_INDEX SIMPSON_INDEX INVERSE_SIMPSON_INDEX
BERGER_PARKER_INDEX PIELOU_EVENNESS HILL_NUMBER

relation USES_DIVERSITY_INDEX(metric,index) relation
HAS_DIVERSITY_VALUE(entity,metric,value)

———- ENDEMISM / RARITY ———-

relation ENDEMIC_TO(species,region) relation
HAS_ENDEMIC_SPECIES(region,species) relation
RANGE_RESTRICTED_TO(species,region) relation
HAS_RANGE_SIZE(species,area) relation HAS_LOCAL_ABUNDANCE(species,value)

rule ENDEMISM_INVERSE(s,r): IF ENDEMIC_TO(s,r) THEN
HAS_ENDEMIC_SPECIES(r,s)

———- CONSERVATION STATUS ———-

enum ConservationStatus: LEAST_CONCERN NEAR_THREATENED VULNERABLE
ENDANGERED CRITICALLY_ENDANGERED EXTINCT_IN_WILD EXTINCT DATA_DEFICIENT

relation HAS_CONSERVATION_STATUS(species,status) relation
ASSESSED_ON(species,date) relation ASSESSED_BY(species,authority)

———- THREATS ———-

enum ThreatType: HABITAT_LOSS HABITAT_FRAGMENTATION OVEREXPLOITATION
POLLUTION INVASIVE_SPECIES CLIMATE_CHANGE DISEASE HUMAN_DISTURBANCE
ALTERED_FIRE_REGIME HYDROLOGICAL_CHANGE

relation THREATENED_BY(entity,threat) relation THREAT_TYPE(threat,type)
relation THREAT_SEVERITY(threat,severity) relation
THREAT_SCOPE(threat,scope)

———- LOSS / RECOVERY ———-

relation DECLINES_IN(entity,metric) relation
SPECIES_LOSS_FROM(species,region) relation
LOCAL_EXTINCTION_OF(species,region) relation
GLOBAL_EXTINCTION_OF(species) relation
GENETIC_EROSION_IN(population,value) relation
FUNCTIONAL_LOSS_IN(entity,value) relation
HOMOGENISATION_BETWEEN(a,b,value) relation INCREASES_IN(entity,metric)
relation COLONISATION_OF(species,region) relation
RECOVERY_OF(entity,metric) relation REINTRODUCED_TO(species,region)

constraint LOCAL_NOT_GLOBAL_EXTINCTION: IF LOCAL_EXTINCTION_OF(s,r) THEN
DO_NOT_INFER(GLOBAL_EXTINCTION_OF(s))

———- CONSERVATION ACTIONS ———-

enum ConservationActionType: HABITAT_PROTECTION HABITAT_RESTORATION
SPECIES_PROTECTION REINTRODUCTION CAPTIVE_BREEDING
INVASIVE_SPECIES_CONTROL POLLUTION_REDUCTION SUSTAINABLE_HARVEST
CONNECTIVITY_RESTORATION GENETIC_RESCUE

relation PROTECTED_BY(entity,action) relation
CONSERVATION_ACTION_TYPE(action,type) relation TARGETS(action,entity)
relation IMPLEMENTED_IN(action,region) relation
HAS_OUTCOME(action,outcome)

———- ECOSYSTEM FUNCTION / SERVICES ———-

relation SUPPORTS_FUNCTION(biodiversity,function) relation
FUNCTION_DEPENDS_ON(function,biodiversity_component) relation
CONTRIBUTES_TO_RESILIENCE(biodiversity,ecosystem) relation
SUPPORTS_SERVICE(biodiversity,service)

———- TEMPORAL CHANGE ———-

relation OBSERVED_DURING(entity,period) relation
CHANGES_OVER(entity,period) relation HAS_LONG_TERM_TREND(entity,trend)
relation BASELINE_AT(entity,date,value) relation
CURRENT_VALUE(entity,value)

enum BiodiversityTrend: INCREASING STABLE DECREASING FLUCTUATING UNKNOWN

———- SAMPLING ———-

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

relation USES_SAMPLING_METHOD(observation,method) relation
HAS_SAMPLE_SIZE(observation,size) relation
HAS_SAMPLING_EFFORT(observation,effort) relation
HAS_DETECTION_PROBABILITY(observation,probability)

———- EVIDENCE ———-

relation OBSERVES(observation,entity) relation
OBSERVED_AT(observation,location) relation
OBSERVED_ON(observation,datetime) relation ESTIMATES(observation,metric)
relation SUPPORTED_BY(assertion,evidence) relation
DERIVED_FROM(evidence,source) relation HAS_CONFIDENCE(assertion,score)

enum EvidenceType: SPECIES_INVENTORY POPULATION_SURVEY GENETIC_DATA
FUNCTIONAL_TRAIT_DATA PHYLOGENETIC_DATA REMOTE_SENSING ENVIRONMENTAL_DNA
LONG_TERM_MONITORING EXPERIMENTAL 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)

———- SEMANTIC EQUIVALENCE ———-

SEMANTIC_EQUIVALENCE: “biodiversity” ~= “biological diversity” “genetic
diversity” ~= “within-species genetic variation” “species diversity” ~=
“diversity of species” “functional diversity” ~= “diversity of
ecological traits” “phylogenetic diversity” ~= “evolutionary diversity”
“ecosystem diversity” ~= “diversity of ecosystems” “species richness” ~=
“number of species” “species evenness” ~= “abundance evenness” “alpha
diversity” ~= “within-site diversity” “beta diversity” ~= “between-site
diversity” “gamma diversity” ~= “regional diversity” “species turnover”
~= “compositional turnover” “biodiversity loss” ~= “decline in
biological diversity” “genetic erosion” ~= “loss of genetic diversity”

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

———- QUERIES ———-

query BIODIVERSITY_PROFILE(x): RETURN: biodiversity_levels(x)
species_richness(x) species_evenness(x) species_diversity(x)
genetic_diversity(x) functional_diversity(x) phylogenetic_diversity(x)
ecosystem_diversity(x) threats(x) trend(x) evidence(x) confidence(x)

query CONSERVATION_PROFILE(x): RETURN: conservation_status(x) threats(x)
protection(x) conservation_actions(x) outcomes(x)

query CHANGE_PROFILE(x): RETURN: baseline(x) current_value(x)
long_term_trend(x) losses(x) gains(x) restoration_effects(x)

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

———- CONSISTENCY ———-

constraint NON_NEGATIVE_RICHNESS: IF HAS_SPECIES_RICHNESS(x,r) THEN
REQUIRE(r >= 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
biodiversity_measurement(x,spatial_scale,temporal_scale) THEN
PRESERVE_SCALE(x,spatial_scale,temporal_scale)

constraint SAMPLING_LIMIT: IF incomplete_sampling(o) THEN
DO_NOT_TREAT_OBSERVED_RICHNESS_AS_COMPLETE_RICHNESS(o)

constraint METRIC_PRESERVATION: IF biodiversity_value(x,metric) THEN
PRESERVE_METRIC_DEFINITION(x,metric)

———- UPDATE MODEL ———-

UPDATE_MODEL: on_new_biodiversity_record(r):
identify_biodiversity_level(r) preserve_spatial_scale(r)
preserve_temporal_scale(r) preserve_metric(r) attach_evidence(r)
recalculate_confidence(r)

on_new_species_record(s): validate_taxonomic_identity(s)
update_species_inventory(s) update_richness_if_supported(s)
preserve_provenance(s)

on_new_threat(t): classify_threat(t) identify_affected_entities(t)
preserve_severity_scope(t) attach_evidence(t)

on_conflicting_estimates(a,b): preserve(a) preserve(b)
compare_metrics(a,b) compare_sampling_effort(a,b)
compare_spatial_scale(a,b) compare_temporal_scale(a,b)
flag_unresolved_conflict()

———- AI CONSUMPTION ———-

AI_CONSUMPTION: preferred_entity: canonical_biodiversity_measurement
preserve: - biodiversity_level - taxonomic_context - spatial_scale -
temporal_scale - metric_definition - sampling_method - sampling_effort -
genetic_metrics - species_metrics - functional_metrics -
phylogenetic_metrics - ecosystem_metrics - threats -
conservation_actions - trends - evidence - provenance - confidence
infer: - valid_inverse_relations - supported_diversity_relations -
supported_change_relations - semantic_equivalence prohibit: -
local_extinction_equals_global_extinction -
incomplete_sample_equals_complete_inventory -
metric_free_diversity_comparison - scale_free_generalisation -
unsupported_causal_claim - confidence_above_evidence ambiguity: action:
preserve_multiple_estimates resolution:
prefer_metric_sampling_scale_and_evidence missing_data: action:
mark_unknown do_not_infer_from_absence: true

———- FLOW HASH ———-

FLOW_HASH: ontology: “BiodiversityOntology” version: “1.0” domain_path:
“AI Core > Ontologies > Biological Ontologies > Ecology > Biodiversity
Ontology” canonical_url:
“https://kirethresearch.org/booksai-core/ontologies/biological-ontologies/ecology/biodiversity-ontology.html”
authorship: “Mark Anthony Higgins — Sky (Recursive AI)”
semantic_scope: - genetic diversity - species diversity - functional
diversity - phylogenetic diversity - ecosystem diversity - alpha
diversity - beta diversity - gamma diversity - diversity indices -
endemism - rarity - conservation status - biodiversity threats -
biodiversity loss - biodiversity recovery - conservation actions -
ecosystem function - ecosystem services - sampling - evidence
deterministic_normalisation: true provenance_required: true
confidence_required: true

terminate BiodiversityOntology when: biodiversity_level_resolved AND
metric_definition_preserved AND spatial_and_temporal_scale_preserved AND
sampling_context_preserved AND evidence_links_preserved AND
confidence_values_validated AND unresolved_biodiversity_ambiguity_marked

end flow