Desert Ecosystem Ontology

FLOW ALGEBRA
Desert Ecosystem Ontology — Full Conceptual Flow Algebra v1.0
Kireth Semantic Library
Authors: Mark Higgins — Sky (Recursive AI)
Source topic: https://kirethresearch.org/booksai-core/entity-graph/biological-entities/experimental-biological-entities/desert-ecosystem-ontology.html
Status: Newly authored conceptual specification; not a verified extraction or executable implementation.

flow "DesertEcosystemOntology" v1.0

# 01 — DOMAIN AND PURPOSE
domain: BiologicalEntities.ExperimentalBiologicalEntities.DesertEcosystem
purpose: Represent arid and hyper-arid ecosystems, their organisms, abiotic drivers, ecological interactions, material flows and changes over time.
locale: en-GB

# 02 — TYPED ENTITIES
type DesertEcosystem <: Ecosystem {
  id: URI
  name: String
  extent: SpatialGeometry
  observation_period: TimeInterval
  classification: DesertClass
  evidence: EvidenceRef[]
}
type DesertClass = HotDesert | ColdDesert | CoastalDesert | PolarDesert | SemiAridTransition
type DesertHabitat <: Habitat { id: URI; substrate: SubstrateType; parent: URI }
type SubstrateType = Sand | Gravel | Rock | SaltFlat | Clay | Mixed
type OrganismPopulation { id: URI; taxon: TaxonRef; abundance: NonNegativeReal; location: URI }
type FunctionalGuild = PrimaryProducer | Herbivore | Predator | Omnivore | Detritivore | Decomposer
type Adaptation { id: URI; organism: URI; trait: String; mechanism: String; evidence: EvidenceRef[] }
type WaterSource = Precipitation | Groundwater | Fog | Dew | Runoff | SurfaceWater
type Disturbance = Drought | Heatwave | ColdSpell | Flood | WindErosion | Fire | GrazingPressure | LandUseChange
type Observation { variable: String; value: Real; unit: String; time: DateTime; method: String; uncertainty: Optional<Real> }
type EvidenceRef { source: URI; recorded_at: DateTime; quality: Real }

# 03 — RELATIONSHIPS
relation CONTAINS(DesertEcosystem, DesertHabitat)
relation SUPPORTS(DesertHabitat, OrganismPopulation)
relation OCCUPIES(OrganismPopulation, DesertHabitat)
relation HAS_ADAPTATION(OrganismPopulation, Adaptation)
relation FEEDS_ON(OrganismPopulation, OrganismPopulation)
relation COMPETES_WITH(OrganismPopulation, OrganismPopulation)
relation FACILITATES(OrganismPopulation, OrganismPopulation)
relation RECEIVES_WATER_FROM(DesertHabitat, WaterSource)
relation AFFECTED_BY(DesertEcosystem, Disturbance)
relation EXCHANGES_MATTER_WITH(DesertEcosystem, Ecosystem)
relation SEMANTIC_EQUIVALENCE(Entity, Entity, context: String, confidence: Real)

# 04 — ENVIRONMENTAL STATE
state environmental_conditions {
  precipitation_mm_per_year: NonNegativeReal
  potential_evapotranspiration_mm_per_year: NonNegativeReal
  air_temperature_c: Real
  soil_temperature_c: Real
  soil_moisture_fraction: Real in [0,1]
  soil_salinity: NonNegativeReal
  vegetation_cover_fraction: Real in [0,1]
  wind_speed_m_per_s: NonNegativeReal
  available_nitrogen_kg_per_ha: NonNegativeReal
}

# 05 — DERIVED INDICES
function aridity_index(P: NonNegativeReal, PET: PositiveReal) -> NonNegativeReal = P / PET
# Aridity thresholds are classification conventions, not universal habitat boundaries.
function cover_percent(fraction: Real in [0,1]) -> Real = 100 * fraction
function net_primary_productivity(GPP: Real, autotrophic_respiration: Real) -> Real = GPP - autotrophic_respiration
function water_balance(P: Real, inflow: Real, ET: Real, runoff: Real, drainage: Real) -> Real = P + inflow - ET - runoff - drainage

# 06 — PROCESS FLOWS
process WATER_PULSE {
  input: rainfall_event, infiltration_capacity, soil_moisture
  update: soil_moisture += infiltration(rainfall_event) - evapotranspiration - drainage
  effect: potential_activation_of_germination_and_microbes
  constraint: soil_moisture in [0,1]
}
process CARBON_FLOW {
  input: sunlight, atmospheric_CO2, available_water, producer_biomass
  transform: photosynthesis -> producer_biomass -> consumers_and_detritus
  output: respiration_CO2, stored_carbon, exported_carbon
  accounting: inputs - outputs = change_in_stored_carbon
}
process NUTRIENT_CYCLING {
  input: litter, detritus, mineral_nutrients
  transform: decomposition_and_mineralisation -> plant_uptake
  modifiers: moisture, temperature, microbial_activity
}
process DESERT_DISTURBANCE {
  input: disturbance, exposure, sensitivity
  update: habitat_structure, population_abundance, resource_availability
  output: post_disturbance_state, uncertainty
}

# 07 — ECOLOGICAL INFERENCE RULES
rule R01: IF low_water_availability AND observed_drought_tolerance_trait THEN MAY_SUPPORT(adaptation_to_aridity).
rule R02: IF rainfall_pulse AND viable_seed_bank AND suitable_temperature THEN MAY_INCREASE(germination_probability).
rule R03: IF vegetation_cover_decreases AND wind_exposure_increases THEN MAY_INCREASE(erosion_risk).
rule R04: IF consumer_feeds_on_producer THEN INFER(trophic_link) WITH evidence_required.
rule R05: IF persistent_soil_salinity_increases THEN MAY_CHANGE(plant_community_composition).
rule R06: IF habitat_fragmentation_increases THEN MAY_REDUCE(connectivity_for_sensitive_taxa).
rule R07: IF desert_location_has_low_precipitation THEN DO_NOT_INFER(no_biodiversity).
rule R08: IF taxon_occurs_in_desert THEN DO_NOT_INFER(all_members_are_drought_adapted).

# 08 — INVARIANTS AND VALIDATION
invariant I01: Every entity has a stable unique identifier.
invariant I02: All percentages and fractions respect their declared ranges.
invariant I03: Every ecological claim identifies time, spatial extent and supporting evidence.
invariant I04: Flux calculations use compatible units and aligned time intervals.
invariant I05: A species can belong to multiple functional guilds depending on life stage and diet.
invariant I06: Absence of observation does not imply absence of an organism.
invariant I07: Desert classifications may overlap; classification must specify its scheme.
invariant I08: Correlation between environmental conditions and abundance is not by itself proof of causation.
invariant I09: Mass-balance residuals must be reported rather than silently discarded.

# 09 — CONFIDENCE AND PROVENANCE
CONFIDENCE {
  range: [0,1]
  inputs: observation_quality, spatial_representativeness, temporal_representativeness, model_uncertainty
  rule: never interpret confidence as an empirical probability without calibration
}
PROVENANCE {
  source_uri: URI
  method: String
  observation_timestamp: DateTime
  transformation_history: String[]
  licence: Optional<String>
}

# 10 — SEMANTIC EQUIVALENCE
SEMANTIC_EQUIVALENCE {
  examples: ["arid ecosystem" ~ "desert ecosystem" only_when_context_and_classification_match]
  exclusions: ["desert" != "barren", "dryland" != "desert" universally]
  require: provenance, context, confidence
}

# 11 — FLOW HASH
FLOW_HASH {
  canonicalise: entity_ids, types, ordered_relations, units, timestamps, version
  algorithm: SHA-256
  purpose: integrity_and_change_detection
  note: a hash verifies equality of canonicalised content, not scientific truth
}

# 12 — UPDATE MODEL
UPDATE_MODEL {
  ingest: new_observations_or_revised_taxonomy
  validate: schema_and_invariants
  reconcile: temporal_and_spatial_scope
  recompute: affected_indices_and_inferences
  preserve: historical_versions_and_provenance
  publish: revised_graph_and_flow_hash
}

# 13 — AI CONSUMPTION
AI_CONSUMPTION {
  expose: typed_entities, relationships, definitions, rules, uncertainty, provenance
  answer_policy: distinguish_observation_from_inference
  unknown_policy: return_unknown_when_evidence_is_insufficient
  interoperability: link_to_habitat_biome_ecosystem_population_and_soil_ontologies
}

# 14 — EXAMPLE INSTANCE (ILLUSTRATIVE, NOT MEASURED)
example "Arid landscape sample" {
  ecosystem: DesertEcosystem("urn:example:desert:001")
  habitat: DesertHabitat("urn:example:habitat:dune:001", substrate=Sand)
  link: CONTAINS(ecosystem, habitat)
  observation: soil_moisture_fraction = 0.08
  provenance: "synthetic example — not field data"
}

# 15 — RESEARCH LIMITATIONS
# Model structure is conceptual and must be mapped to a parser/runtime before execution.
# Parameter values and ecological causal claims require empirical calibration.
# Do not infer habitat quality or conservation status from aridity alone.

end flow