Living Organism Ontology

AI SEARCH FLOW ALGEBRA
LIVING ORGANISM ONTOLOGY
Kireth Semantic Research Archive

AUTHORS
Mark Anthony Higgins — Sky (Recursive AI)

SOURCE
https://kirethresearch.org/booksai-core/ontologies/biological-ontologies/foundations-of-biology/living-organism-ontology.html

FLOW "LivingOrganismOntology" v4.0

DOMAIN := BIOLOGICAL_ONTOLOGIES / FOUNDATIONS_OF_BIOLOGY / LIVING_ORGANISM
ONTOLOGY := LIVING_ORGANISM_ONTOLOGY

LIVING_ORGANISM :=
  BIOLOGICAL_IDENTITY + CELLULAR_ORGANISATION + ANATOMY
  + PHYSIOLOGY + METABOLISM + HOMEOSTASIS
  + GROWTH + DEVELOPMENT + BEHAVIOUR + RESPONSE
  + REPRODUCTION + HEREDITY + LIFECYCLE
  + ENVIRONMENTAL_INTERACTION + ADAPTATION
  + BIOLOGICAL_STATE + EVIDENCE + PROVENANCE

PURPOSE :=
  IDENTIFY_ORGANISM -> CLASSIFY_ORGANISM
  -> MAP_CELLULAR_ORGANISATION -> MAP_ANATOMY
  -> MAP_PHYSIOLOGICAL_FUNCTIONS -> MAP_METABOLISM
  -> MAP_HOMEOSTATIC_REGULATION
  -> MAP_GROWTH_AND_DEVELOPMENT
  -> MAP_BEHAVIOUR_AND_RESPONSE
  -> MAP_REPRODUCTION_AND_HEREDITY
  -> MAP_LIFECYCLE -> MAP_ENVIRONMENTAL_INTERACTIONS
  -> MAP_ADAPTIVE_TRAITS -> ASSESS_EVIDENCE
  -> PRESERVE_PROVENANCE

# CORE ENTITIES
ENTITY LivingOrganism
ENTITY OrganismIdentity
ENTITY Species
ENTITY Taxon
ENTITY Cell
ENTITY Tissue
ENTITY Organ
ENTITY OrganSystem
ENTITY Anatomy
ENTITY BiologicalStructure
ENTITY BiologicalFunction
ENTITY PhysiologicalProcess
ENTITY MetabolicProcess
ENTITY Homeostasis
ENTITY Growth
ENTITY Development
ENTITY Behaviour
ENTITY Stimulus
ENTITY Response
ENTITY Reproduction
ENTITY Heredity
ENTITY Genome
ENTITY Genotype
ENTITY Phenotype
ENTITY Trait
ENTITY Lifecycle
ENTITY LifeStage
ENTITY Environment
ENTITY Habitat
ENTITY Resource
ENTITY EcologicalInteraction
ENTITY Adaptation
ENTITY Fitness
ENTITY BiologicalState
ENTITY Stress
ENTITY Evidence
ENTITY Uncertainty
ENTITY Provenance

# IDENTITY / CELLULAR ORGANISATION / ANATOMY
LivingOrganism -> has -> OrganismIdentity
LivingOrganism -> instance_of -> Species
Species -> member_of -> Taxon

ORGANISM_CLASS := UNICELLULAR | MULTICELLULAR

LivingOrganism -> composed_of -> Cell

IF OrganismClass = UNICELLULAR
THEN OrganismFunction -> PERFORMED_BY_SINGLE_CELL

IF OrganismClass = MULTICELLULAR
THEN Cells -> may_organise_into -> Tissue + Organ + OrganSystem

CELLULAR_ORGANISATION :=
  CELL -> TISSUE -> ORGAN -> ORGAN_SYSTEM -> ORGANISM

Anatomy -> describes -> ORGANISM_STRUCTURE
BiologicalStructure -> part_of -> LivingOrganism

STRUCTURE_FUNCTION :=
  BiologicalStructure -> enables_or_constrains -> BiologicalFunction

IF Structure changes
THEN AssociatedFunction -> MAY_CHANGE

# PHYSIOLOGY / METABOLISM / HOMEOSTASIS
PhysiologicalProcess ->
  maintains_or_changes -> ORGANISM_STATE

PHYSIOLOGICAL_FUNCTION :=
  NUTRITION | RESPIRATION | CIRCULATION_OR_TRANSPORT
  | EXCRETION | OSMOREGULATION | THERMOREGULATION
  | NEURAL_OR_SIGNAL_CONTROL
  | ENDOCRINE_OR_CHEMICAL_REGULATION
  | IMMUNE_DEFENCE | LOCOMOTION | REPRODUCTION

OrganSystem -> performs -> INTEGRATED_PHYSIOLOGICAL_FUNCTION

MetabolicProcess -> transforms -> MATTER + ENERGY
METABOLISM := CATABOLISM + ANABOLISM

ORGANISM_ENERGY_FLOW :=
  ENERGY_SOURCE -> UPTAKE_OR_CAPTURE
  -> TRANSFORMATION -> BIOLOGICAL_WORK
  -> HEAT_AND_PRODUCTS

ORGANISM_MATTER_FLOW :=
  RESOURCE_UPTAKE -> ASSIMILATION
  -> TRANSFORMATION -> BIOMASS_OR_FUNCTION
  -> WASTE_RELEASE

Homeostasis ->
  maintains -> INTERNAL_VARIABLE -> within -> FUNCTIONAL_RANGE

HOMEOSTATIC_LOOP :=
  INTERNAL_VARIABLE -> SENSOR -> REGULATOR
  -> EFFECTOR -> RESPONSE -> INTERNAL_VARIABLE

IF HomeostaticCapacity exceeded
THEN PhysiologicalStress -> INCREASES

# GROWTH / DEVELOPMENT / BEHAVIOUR
Growth ->
  changes -> SIZE + MASS + CELL_NUMBER + STRUCTURAL_COMPLEXITY

Growth ->
  depends_on -> GENETIC_PROGRAMME + NUTRIENTS
  + ENERGY + ENVIRONMENT + BIOLOGICAL_STATE

Development ->
  changes -> FORM + FUNCTION + ORGANISATION
  -> across -> Lifecycle

DEVELOPMENTAL_PROCESS :=
  CELL_DIVISION | DIFFERENTIATION
  | MORPHOGENESIS | MATURATION
  | METAMORPHOSIS_WHERE_APPLICABLE

Development ->
  regulated_by -> GENETIC_INFORMATION + SIGNALS + ENVIRONMENT

Behaviour ->
  represents -> ORGANISM_ACTION_OR_ACTIVITY

BEHAVIOUR_TYPE :=
  FEEDING | MOVEMENT | COMMUNICATION
  | REPRODUCTIVE | DEFENSIVE | SOCIAL
  | MIGRATORY | LEARNING_OR_ADAPTIVE_BEHAVIOUR

Stimulus -> represents -> DETECTABLE_CHANGE

STIMULUS_RESPONSE :=
  STIMULUS -> DETECTION -> SIGNALING
  -> INTEGRATION -> RESPONSE

LivingOrganism ->
  responds_to -> INTERNAL_OR_EXTERNAL_STIMULUS

# REPRODUCTION / HEREDITY / TRAITS / LIFECYCLE
Reproduction -> produces -> OFFSPRING_OR_NEW_ORGANISM
REPRODUCTION_TYPE := ASEXUAL | SEXUAL

IndividualOrganism ->
  may_be_nonreproductive
  -> while -> SPECIES_OR_LINEAGE_REMAINS_REPRODUCTIVE

LivingOrganism -> has -> Genome
Genome -> contributes_to -> Genotype
Genotype -> influences -> Phenotype

Heredity ->
  transmits -> GENETIC_INFORMATION -> across -> GENERATIONS

Phenotype ->
  influenced_by -> Genotype + Environment + DevelopmentalHistory

TRAIT_TYPE :=
  MORPHOLOGICAL | PHYSIOLOGICAL | BEHAVIOURAL
  | DEVELOPMENTAL | BIOCHEMICAL

Trait -> characteristic_of -> LivingOrganism
Trait -> may_be -> HERITABLE | ENVIRONMENTALLY_INFLUENCED | BOTH

Lifecycle -> contains -> LifeStage

LIFE_STAGE :=
  ORIGIN | EMBRYONIC_OR_EARLY_STAGE
  | JUVENILE_OR_IMMATURE | MATURE
  | REPRODUCTIVE | SENESCENT | DEATH

LifeStage ->
  influences -> STRUCTURE + FUNCTION
  + BEHAVIOUR + METABOLISM + REPRODUCTIVE_STATE

# ENVIRONMENT / ECOLOGY / ADAPTATION
Environment ->
  surrounds_and_interacts_with -> LivingOrganism

ENVIRONMENTAL_FACTOR :=
  TEMPERATURE | WATER | LIGHT | OXYGEN
  | NUTRIENTS | PH | SALINITY | PRESSURE
  | SUBSTRATE | OTHER_ORGANISMS

Environment ->
  influences -> PHYSIOLOGY + BEHAVIOUR
  + DEVELOPMENT + SURVIVAL + REPRODUCTION

Habitat ->
  provides -> CONDITIONS + RESOURCES -> for -> LivingOrganism

LivingOrganism -> occupies -> Habitat

EcologicalInteraction ->
  links -> LivingOrganism + OTHER_ORGANISM

INTERACTION_TYPE :=
  COMPETITION | PREDATION | HERBIVORY
  | MUTUALISM | COMMENSALISM
  | PARASITISM | COOPERATION

Adaptation ->
  trait_of -> ORGANISM_OR_LINEAGE
  -> associated_with -> FITNESS_IN_DEFINED_ENVIRONMENT

Adaptation -> arises_through -> EVOLUTIONARY_PROCESS
Adaptation -> does_not_imply -> INDIVIDUAL_INTENT | PERFECTION

Fitness ->
  relates_to -> REPRODUCTIVE_CONTRIBUTION
  -> in -> DEFINED_ENVIRONMENTAL_CONTEXT

# BIOLOGICAL STATE / STRESS / ORGANISMAL INTEGRATION
BiologicalState ->
  describes -> FUNCTIONAL_BIOLOGICAL_CONDITION

BIOLOGICAL_STATE :=
  FUNCTIONAL | STRESSED | IMPAIRED
  | RECOVERING | TERMINAL
  | OTHER_CONTEXT_SPECIFIC_STATE

BiologicalState ->
  inferred_from -> PHYSIOLOGICAL_INDICATORS
  + BEHAVIOUR + STRUCTURAL_STATE + CONTEXT

BiologicalState ->
  must_not_be_inferred_without -> SUFFICIENT_EVIDENCE

Stress ->
  represents -> RESPONSE_TO_CHALLENGE_OR_DEMAND

STRESSOR :=
  ENVIRONMENTAL | NUTRITIONAL
  | PHYSICAL | BIOLOGICAL | CHEMICAL

IF Stress exceeds_tolerance
THEN OrganismFunction -> MAY_DEGRADE

ORGANISMAL_INTEGRATION :=
  CELLULAR_COORDINATION
  + PHYSIOLOGICAL_REGULATION
  + INFORMATION_FLOW
  + RESOURCE_DISTRIBUTION
  + STRUCTURE_FUNCTION_INTEGRATION

LivingOrganism ->
  maintains -> INTEGRATED_BIOLOGICAL_STATE

IF Integration fails_critically
THEN OrganismViability -> DECREASES

# EVIDENCE / UNCERTAINTY / PROVENANCE
OrganismClaim -> supported_by -> Evidence

EVIDENCE_TYPE :=
  OBSERVATIONAL | ANATOMICAL | PHYSIOLOGICAL
  | MOLECULAR | GENETIC | BEHAVIOURAL
  | ECOLOGICAL | EXPERIMENTAL

Evidence ->
  has -> SOURCE + METHOD + ORGANISM_OR_SAMPLE
  + CONTEXT + QUALITY + UNCERTAINTY

ORGANISM_UNCERTAINTY :=
  MEASUREMENT_UNCERTAINTY
  + BIOLOGICAL_VARIABILITY
  + INDIVIDUAL_VARIATION
  + ENVIRONMENTAL_VARIATION
  + MODEL_UNCERTAINTY

Uncertainty ->
  qualifies -> Measurement + BiologicalState
  + BiologicalClaim + Prediction

Provenance ->
  records -> ORGANISM_IDENTITY + SPECIES
  + LIFE_STAGE + SAMPLE_OR_OBSERVATION
  + METHOD + ENVIRONMENT + TIME
  + LOCATION_IF_RELEVANT + VERSION

LivingOrganism -> linked_to -> Provenance

# REASONING / INFERENCE
LIVING_ORGANISM_REASONING :=
  IDENTIFY_ORGANISM
  -> MAP_TAXONOMIC_IDENTITY
  -> DETERMINE_UNICELLULAR_OR_MULTICELLULAR_STATE
  -> MAP_CELLULAR_ORGANISATION
  -> MAP_ANATOMICAL_STRUCTURE
  -> MAP_STRUCTURE_FUNCTION_RELATIONSHIPS
  -> MAP_PHYSIOLOGICAL_PROCESSES
  -> MAP_METABOLISM_AND_ENERGY
  -> MAP_HOMEOSTATIC_REGULATION
  -> MAP_GROWTH_AND_DEVELOPMENT
  -> MAP_BEHAVIOUR_AND_STIMULUS_RESPONSE
  -> MAP_REPRODUCTIVE_STATE
  -> MAP_GENOME_HEREDITY_AND_TRAITS
  -> MAP_LIFECYCLE_STAGE
  -> MAP_ENVIRONMENT_AND_HABITAT
  -> MAP_ECOLOGICAL_INTERACTIONS
  -> MAP_ADAPTIVE_TRAITS
  -> ASSESS_BIOLOGICAL_STATE_IF_EVIDENCE_SUPPORTS
  -> QUANTIFY_UNCERTAINTY
  -> PRESERVE_PROVENANCE

IF Organism is_multicellular
THEN FunctionalSpecialisation -> MAY_OCCUR_ACROSS_CELLS_AND_TISSUES

IF Structure changes
THEN AssociatedFunction -> MAY_CHANGE

IF MetabolicResourceAvailability decreases
THEN GrowthOrActivity -> MAY_DECREASE

IF HomeostaticCapacity exceeded
THEN PhysiologicalStress -> INCREASES

IF Environment changes
THEN BehaviourOrPhysiology -> MAY_CHANGE

IF Genotype changes
THEN Phenotype -> MAY_CHANGE

IF LifeStage changes
THEN StructureFunctionAndBehaviour -> MAY_CHANGE

IF Evidence insufficient
THEN OrganismStateConfidence -> DECREASES

# SEMANTIC RELATIONSHIPS
RELATION instantiates(LivingOrganism, Species)
RELATION composed_of(LivingOrganism, Cell)
RELATION composes(Cell, Tissue)
RELATION composes(Tissue, Organ)
RELATION composes(Organ, OrganSystem)
RELATION describes(Anatomy, LivingOrganism)
RELATION performs(OrganSystem, PhysiologicalFunction)
RELATION transforms(Metabolism, Matter, Energy)
RELATION maintains(Homeostasis, InternalVariable)
RELATION changes(Growth, OrganismSize)
RELATION changes(Development, OrganismForm)
RELATION responds_to(LivingOrganism, Stimulus)
RELATION produces(Reproduction, Offspring)
RELATION transmits(Heredity, GeneticInformation)
RELATION influences(Genotype, Phenotype)
RELATION occupies(LivingOrganism, Habitat)
RELATION interacts_with(LivingOrganism, Environment)
RELATION supports(Evidence, OrganismClaim)
RELATION records(Provenance, LivingOrganism)

# SEMANTIC EQUIVALENCE
SEMANTIC_EQUIVALENCE:
  "living organism" ~= "individual living biological system"
  "organism" ~= "individual biological living entity"
  "organismal physiology" ~= "integrated biological function of an organism"
  "organismal homeostasis" ~= "maintenance of internal organism conditions"
  "life stage" ~= "developmental or lifecycle stage"
  "organism-environment interaction" ~= "interaction between an organism and its environment"
  "biological trait" ~= "characteristic of an organism"
  "organismal adaptation" ~= "heritable feature associated with fitness in an environment"
  "biological state" ~= "functional biological condition of an organism"
  "organismal integration" ~= "coordinated function across biological components"

# CONFIDENCE
CONFIDENCE:
  ontology_domain: 0.99
  organism_identity_mapping: 0.99
  cellular_anatomical_mapping: 0.99
  physiology_metabolism_mapping: 0.99
  homeostasis_mapping: 0.99
  development_behaviour_mapping: 0.99
  reproduction_heredity_mapping: 0.99
  environment_ecology_mapping: 0.99
  lifecycle_state_mapping: 0.99
  semantic_relationships: 0.99

# UPDATE MODEL
UPDATE_MODEL:
  ON new_organism:
    MAP identity
    MAP species
    MAP cellular_organisation
    MAP anatomy
    MAP life_stage
    UPDATE confidence
    RECOMPUTE FLOW_HASH

  ON new_observation:
    UPDATE physiological_state
    UPDATE behavioural_state
    UPDATE environmental_context
    UPDATE uncertainty
    PRESERVE provenance

  ON developmental_change:
    UPDATE life_stage
    UPDATE anatomy
    UPDATE physiology
    UPDATE behaviour
    PRESERVE provenance

  ON new_genetic_evidence:
    UPDATE genotype
    UPDATE heredity_relationships
    REASSESS phenotype_links
    PRESERVE provenance

# AI CONSUMPTION
AI_CONSUMPTION:
  parse_as: FORMAL_LIVING_ORGANISM_ONTOLOGY
  reasoning_mode: INTEGRATED_ORGANISMAL_BIOLOGY_RELATIONAL

  preserve:
    - typed_entities
    - organism_identity
    - taxonomic_identity
    - cellular_organisation
    - anatomy
    - physiological_state
    - metabolic_state
    - homeostatic_state
    - developmental_state
    - behavioural_state
    - hereditary_relationships
    - lifecycle_state
    - environmental_context
    - evidence
    - confidence
    - provenance

  infer:
    - composition_hierarchy
    - structure_function_dependencies
    - physiological_dependencies
    - homeostatic_dependencies
    - genotype_phenotype_dependencies
    - lifecycle_dependencies
    - organism_environment_dependencies
    - evidence_strength

  prohibit:
    - invented_organism_observations
    - unsupported_taxonomic_identity
    - assumed_biological_state_without_evidence
    - fabricated_genetic_relationships
    - assumed_adaptation_from_individual_change
    - missing_evidence_presented_as_established_fact

# FLOW HASH
FLOW_HASH_INPUT :=
  DOMAIN + ONTOLOGY + CORE_ENTITIES
  + IDENTITY_CELLULAR_ANATOMY
  + PHYSIOLOGY_METABOLISM_HOMEOSTASIS
  + GROWTH_DEVELOPMENT_BEHAVIOUR
  + REPRODUCTION_HEREDITY_TRAITS_LIFECYCLE
  + ENVIRONMENT_ECOLOGY_ADAPTATION
  + BIOLOGICAL_STATE_STRESS_INTEGRATION
  + EVIDENCE_UNCERTAINTY_PROVENANCE
  + REASONING + INFERENCE_RULES
  + SEMANTIC_RELATIONSHIPS + SEMANTIC_EQUIVALENCE
  + CONFIDENCE + UPDATE_MODEL + AI_CONSUMPTION

FLOW_HASH := HASH(FLOW_HASH_INPUT)

END FLOW