Aquatic Habitat Ontology

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

flow "AquaticHabitatOntology" v1.0

# 1. ONTOLOGY IDENTITY
ontology:
  id: kireth:biological.experimental.aquatic_habitat
  label: "Aquatic Habitat Ontology"
  parent: kireth:biological.environment
  domain: ecology
  scope: "Water-dominated environments and their physical, chemical and biological relationships"
  locale: en-GB

# 2. TYPE SYSTEM
types:
  Entity: {id: URI, label: String}
  AquaticHabitat: Entity
  FreshwaterHabitat: AquaticHabitat
  MarineHabitat: AquaticHabitat
  BrackishHabitat: AquaticHabitat
  LenticHabitat: FreshwaterHabitat
  LoticHabitat: FreshwaterHabitat
  WetlandHabitat: AquaticHabitat
  EstuarineHabitat: BrackishHabitat
  CoastalHabitat: MarineHabitat
  OpenOceanHabitat: MarineHabitat
  BenthicHabitat: AquaticHabitat
  PelagicHabitat: AquaticHabitat
  CoralReefHabitat: MarineHabitat
  MangroveHabitat: CoastalHabitat
  SeagrassHabitat: CoastalHabitat
  AquaticOrganism: Entity
  Population: Entity
  Community: Entity
  WaterBody: Entity
  AbioticFactor: Entity
  Resource: Entity
  Disturbance: Entity
  Observation: Entity
  TimeInterval: Entity
  GeographicRegion: Entity

# 3. RELATIONSHIP SIGNATURES
relations:
  PART_OF: (AquaticHabitat, AquaticHabitat|WaterBody|GeographicRegion) -> Boolean
  CONTAINS: (AquaticHabitat, AquaticOrganism|Population|Community) -> Boolean
  INHABITS: (AquaticOrganism, AquaticHabitat) -> Boolean
  SUPPORTS: (AquaticHabitat, Population|Community) -> Boolean
  CONNECTED_TO: (AquaticHabitat, AquaticHabitat) -> Boolean
  EXCHANGES_WATER_WITH: (AquaticHabitat, AquaticHabitat) -> Boolean
  RECEIVES_INPUT_FROM: (AquaticHabitat, WaterBody) -> Boolean
  EXPERIENCES: (AquaticHabitat, Disturbance) -> Boolean
  HAS_FACTOR: (AquaticHabitat, AbioticFactor) -> Boolean
  PROVIDES: (AquaticHabitat, Resource) -> Boolean
  OBSERVED_IN: (Observation, AquaticHabitat) -> Boolean
  TEMPORALLY_VALID: (Observation, TimeInterval) -> Boolean

# 4. MEASUREMENT SCHEMA
measurements:
  water_temperature: {unit: degC, type: Real}
  salinity: {unit: PSU, type: Real, note: "Practical salinity is dimensionless; PSU is conventional notation"}
  dissolved_oxygen: {unit: mg/L, type: NonNegativeReal}
  pH: {unit: dimensionless, type: Real}
  turbidity: {unit: NTU, type: NonNegativeReal}
  water_depth: {unit: m, type: NonNegativeReal}
  flow_velocity: {unit: m/s, type: NonNegativeReal}
  conductivity: {unit: uS/cm, type: NonNegativeReal}
  nutrient_concentration: {unit: mg/L, type: NonNegativeReal}
  light_attenuation_coefficient: {unit: per_m, type: NonNegativeReal}
  habitat_area: {unit: m2, type: NonNegativeReal}
  primary_productivity: {unit: gC/m2/day, type: NonNegativeReal}
  measurement_context: [time, depth, location, method, uncertainty]

# 5. SEMANTIC CLASSIFICATION
classification:
  freshwater: "Low-salinity inland water; boundaries depend on adopted classification"
  marine: "Saltwater systems connected to marine environments"
  brackish: "Variable intermediate salinity, often at freshwater–marine interfaces"
  lentic: "Predominantly standing water"
  lotic: "Predominantly flowing water"
  benthic: "Associated with the substrate or bottom"
  pelagic: "Associated with open-water zones"
  wetland: "Water-saturated or inundated habitat with characteristic ecological processes"
  note: "Categories overlap; benthic/pelagic describe zones rather than exclusive salinity classes"

# 6. FLOW TRANSFORMATIONS
flows:
  WaterExchange:
    inputs: [habitat_a, habitat_b, discharge, time]
    outputs: [water_flux]
    expression: "water_flux = discharge * time"
    preconditions: ["discharge >= 0", "time >= 0"]
  LightAvailability:
    inputs: [surface_irradiance, attenuation_coefficient, depth]
    outputs: [irradiance_at_depth]
    expression: "irradiance_at_depth = surface_irradiance * exp(-attenuation_coefficient * depth)"
    assumptions: ["approximately homogeneous vertical attenuation"]
  OxygenBalance:
    inputs: [initial_oxygen_mass, photosynthetic_input, atmospheric_exchange, respiration, decomposition, advective_net_flux]
    outputs: [final_oxygen_mass]
    expression: "final_oxygen_mass = initial_oxygen_mass + photosynthetic_input + atmospheric_exchange - respiration - decomposition + advective_net_flux"
    assumptions: ["all terms integrated over same interval and expressed as oxygen mass"]
  NutrientBalance:
    inputs: [initial_nutrient_mass, external_inputs, internal_recycling, biological_uptake, export, permanent_removal]
    outputs: [final_nutrient_mass]
    expression: "final_nutrient_mass = initial_nutrient_mass + external_inputs + internal_recycling - biological_uptake - export - permanent_removal"
    note: "Track compartments to avoid double-counting internal recycling"

# 7. INFERENCE RULES
rules:
  - id: R1
    when: "INHABITS(o,h) AND TYPE(h,AquaticHabitat)"
    infer: "TYPE(o,AquaticOrganism)"
    qualification: "Only when inhabits refers to sustained ecological occupancy"
  - id: R2
    when: "TYPE(h,EstuarineHabitat)"
    infer: "TYPE(h,BrackishHabitat)"
    qualification: "Typical classification; some estuarine portions may be fresh or marine"
  - id: R3
    when: "PART_OF(h1,h2) AND PART_OF(h2,h3)"
    infer: "PART_OF(h1,h3)"
    qualification: "Apply only to compatible spatial-part relations"
  - id: R4
    when: "EXCHANGES_WATER_WITH(a,b)"
    infer: "EXCHANGES_WATER_WITH(b,a)"
    qualification: "Connectivity is symmetric; instantaneous flux direction is not"
  - id: R5
    when: "dissolved_oxygen(h,t) < locally_validated_threshold"
    infer: "POTENTIAL_HYPOXIA(h,t)"
    qualification: "Threshold depends on species, temperature, duration and scientific context"
  - id: R6
    when: "salinity_variance(h,interval) > calibrated_variability_threshold"
    infer: "VARIABLE_SALINITY_REGIME(h,interval)"
    qualification: "Threshold must be documented"

# 8. CONSTRAINTS AND INVARIANTS
invariants:
  - "Every entity has a stable, nonempty identifier"
  - "Measured concentrations and depths are nonnegative"
  - "Observations must preserve units, sampling time and provenance"
  - "Habitat classes need not be mutually exclusive"
  - "A habitat may change classification with time or spatial scale"
  - "Mass-balance outputs conserve tracked matter within explicitly defined boundaries"
  - "No ecological impact is asserted as causal solely from correlation"
  - "Missing data must not be converted into zero values"

# 9. CONFIDENCE
CONFIDENCE:
  fields: [score, evidence_type, sampling_quality, temporal_relevance, spatial_relevance, uncertainty, provenance]
  score_range: [0.0, 1.0]
  combine: "Use calibrated evidence fusion; avoid multiplying dependent evidence as if independent"
  missing_evidence: "unknown, not false"

# 10. SEMANTIC EQUIVALENCE
SEMANTIC_EQUIVALENCE:
  exact_match: "Same concept, scale, definition and intended reference"
  close_match: "Overlapping meaning with documented distinction"
  prohibited_shortcuts:
    - "wetland == freshwater habitat"
    - "estuary == always brackish at every point"
    - "benthic == marine"
    - "habitat == ecosystem"
  preserve: [taxonomic_context, salinity_regime, spatial_scale, temporal_scope]

# 11. FLOW HASH
FLOW_HASH:
  canonicalise: [ontology_id, version, entity_ids, typed_relations, measurements, rule_ids, temporal_scope]
  serialisation: "Deterministic UTF-8 with sorted keys and normalised numeric representations"
  algorithm: SHA-256
  output: "Lowercase hexadecimal digest of canonical serialisation"
  note: "Digest calculated by an implementing system; none is fabricated here"

# 12. UPDATE MODEL
UPDATE_MODEL:
  operations: [ADD_ENTITY, REVISE_MEASUREMENT, ASSERT_RELATION, RETRACT_RELATION, RECLASSIFY_HABITAT, MERGE_EQUIVALENT, DEPRECATE_ENTITY]
  require: [timestamp, actor_or_source, evidence, prior_version, change_reason]
  conflict_policy: "Retain competing observations with provenance; do not silently overwrite"
  version_policy: "Increment semantic version when rules, types or meanings change"

# 13. AI CONSUMPTION
AI_CONSUMPTION:
  input: "Typed habitat graph, observations, provenance and query context"
  process: [validate, resolve_entities, check_units, select_temporal_scope, apply_rules, calculate_confidence, emit_explanations]
  output: [answer, supporting_relations, evidence, uncertainty, provenance, ontology_version]
  safeguards: ["No unsupported species presence claims", "No inferred causation without suitable evidence", "Distinguish observation from prediction"]

# 14. EXAMPLE (ILLUSTRATIVE, NOT SITE DATA)
example:
  habitat: example:estuary_01
  type: EstuarineHabitat
  observation:
    salinity: 12
    salinity_unit: PSU
    depth: 2
    depth_unit: m
    status: synthetic
  interpretation: "An estuarine observation; classification depends on temporal and spatial context"

# 15. VALIDATION TESTS
tests:
  - "Reject negative water depth"
  - "Reject missing measurement units"
  - "Accept a coastal wetland with multiple habitat classifications"
  - "Preserve contradictory observations from different times"
  - "Require explicit thresholds before declaring hypoxia"
  - "Recompute dependent inferences after updated salinity observations"
  - "Stable canonical input must produce stable FLOW_HASH"

# 16. ATTRIBUTION
credit: "Mark Higgins — Sky (Recursive AI)"
website: https://kirethresearch.org
licence: "Refer to the applicable Kireth Research licence; no licence terms are invented here"
end flow