Life Ontology

AI SEARCH FLOW ALGEBRA
LIFE ONTOLOGY
Kireth Semantic Research Archive

AUTHORS
Mark Anthony Higgins — Sky (Recursive AI)

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

FLOW "LifeOntology" v4.0

DOMAIN := BIOLOGICAL_ONTOLOGIES / FOUNDATIONS_OF_BIOLOGY / LIFE
ONTOLOGY := LIFE_ONTOLOGY

LIFE :=
  LIVING_SYSTEM + CELLULAR_ORGANISATION + BOUNDARY
  + BIOLOGICAL_INFORMATION + METABOLISM + ENERGY_FLOW
  + MATTER_EXCHANGE + HOMEOSTASIS + GROWTH
  + DEVELOPMENT + RESPONSE + REPRODUCTION
  + HEREDITY + VARIATION + EVOLUTION
  + LIFECYCLE + ENVIRONMENTAL_INTERACTION
  + EVIDENCE + PROVENANCE

PURPOSE :=
  IDENTIFY_CANDIDATE_LIVING_SYSTEM
  -> IDENTIFY_ORGANISATION_AND_BOUNDARY
  -> IDENTIFY_INFORMATION_SYSTEM
  -> IDENTIFY_METABOLIC_AND_ENERGY_PROCESSES
  -> IDENTIFY_REGULATION_AND_HOMEOSTASIS
  -> IDENTIFY_GROWTH_AND_DEVELOPMENT
  -> IDENTIFY_RESPONSE_AND_INTERACTION
  -> IDENTIFY_REPRODUCTION_AND_HEREDITY
  -> IDENTIFY_EVOLUTIONARY_CAPACITY
  -> ASSESS_EVIDENCE
  -> PRESERVE_PROVENANCE

# CORE ENTITIES
ENTITY Life
ENTITY LivingSystem
ENTITY BiologicalEntity
ENTITY Organism
ENTITY Cell
ENTITY BiologicalBoundary
ENTITY Biomolecule
ENTITY DNA
ENTITY RNA
ENTITY Protein
ENTITY Gene
ENTITY Genome
ENTITY BiologicalInformation
ENTITY Metabolism
ENTITY Energy
ENTITY Matter
ENTITY Homeostasis
ENTITY Growth
ENTITY Development
ENTITY Response
ENTITY Stimulus
ENTITY Reproduction
ENTITY Offspring
ENTITY Heredity
ENTITY Variation
ENTITY Mutation
ENTITY Evolution
ENTITY NaturalSelection
ENTITY Adaptation
ENTITY Lifecycle
ENTITY Environment
ENTITY BiologicalInteraction
ENTITY Evidence
ENTITY Uncertainty
ENTITY Provenance

# CHARACTERISTICS / ORGANISATION
LIFE_CHARACTERISTICS :=
  CELLULAR_ORGANISATION + BOUNDED_SYSTEM
  + METABOLISM + ENERGY_TRANSFORMATION
  + HOMEOSTASIS + GROWTH + DEVELOPMENT
  + RESPONSE_TO_STIMULI
  + REPRODUCTION_OR_REPRODUCTIVE_LINEAGE
  + HEREDITARY_INFORMATION + EVOLUTIONARY_CAPACITY

LivingSystem -> exhibits -> LIFE_CHARACTERISTICS
LifeClassification -> depends_on -> MULTIPLE_INTERRELATED_CHARACTERISTICS

NoSingleCharacteristic ->
  necessarily_sufficient_for -> ALL_CASES_OF_LIFE

BIOLOGICAL_ORGANISATION :=
  MOLECULAR -> SUBCELLULAR -> CELLULAR
  -> MULTICELLULAR -> ORGANISMAL

EmergentProperty ->
  may_arise_from -> INTERACTIONS_AMONG_COMPONENTS

# CELLULAR BASIS / BOUNDARY
Cell -> fundamental_unit_of -> CELLULAR_LIFE
Organism -> may_be -> UNICELLULAR | MULTICELLULAR
MulticellularOrganism -> composed_of -> MULTIPLE_CELLS

Cell ->
  contains -> GENETIC_MATERIAL
  + METABOLIC_MACHINERY
  + REGULATORY_MACHINERY

BiologicalBoundary ->
  separates -> INTERNAL_STATE + EXTERNAL_ENVIRONMENT

BiologicalBoundary ->
  regulates -> MATTER_EXCHANGE
  + ENERGY_EXCHANGE + SIGNAL_EXCHANGE

BoundaryIntegrity -> supports -> HOMEOSTASIS

# BIOMOLECULES / INFORMATION
BIOMOLECULE_TYPE :=
  NUCLEIC_ACID | PROTEIN | LIPID
  | CARBOHYDRATE | METABOLITE

Biomolecule ->
  participates_in -> STRUCTURE + METABOLISM
  + INFORMATION + REGULATION

DNA -> stores -> GENETIC_INFORMATION
RNA -> participates_in -> INFORMATION_TRANSFER_AND_FUNCTION
Protein -> performs -> STRUCTURAL_CATALYTIC_REGULATORY_FUNCTION

BiologicalInformation ->
  encoded_in -> DNA | RNA | OTHER_SUPPORTED_HERITABLE_SYSTEM

Genome -> contains -> Gene

GENETIC_INFORMATION_FLOW :=
  DNA -> TRANSCRIPTION -> RNA -> TRANSLATION -> PROTEIN

GeneExpression ->
  converts -> STORED_INFORMATION -> FUNCTIONAL_PRODUCT

GeneRegulation -> controls -> GENE_EXPRESSION

# METABOLISM / ENERGY / MATTER
Metabolism -> transforms -> MATTER + ENERGY
METABOLISM := CATABOLISM + ANABOLISM

MetabolicPathway -> contains -> ORDERED_REACTIONS
Enzyme -> catalyses -> BIOCHEMICAL_REACTION

ENERGY_FLOW :=
  ENERGY_SOURCE -> CAPTURE_OR_UPTAKE
  -> TRANSFORMATION -> BIOLOGICAL_WORK -> DISSIPATION

MATTER_FLOW :=
  UPTAKE -> TRANSFORMATION
  -> INCORPORATION_OR_USE -> EXCRETION_OR_RELEASE

LivingSystem -> exchanges -> Matter -> with -> Environment

# HOMEOSTASIS / GROWTH / DEVELOPMENT / RESPONSE
Homeostasis ->
  maintains -> INTERNAL_VARIABLES -> within -> VIABLE_RANGE

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

NegativeFeedback -> opposes -> DEVIATION_FROM_FUNCTIONAL_RANGE
PositiveFeedback -> amplifies -> PROCESS -> until -> TERMINATION_CONDITION

IF HomeostaticCapacity exceeded
THEN Viability -> MAY_DECREASE

Growth ->
  increases -> SIZE | CELL_NUMBER | BIOMASS | STRUCTURAL_COMPLEXITY

Growth ->
  requires -> MATTER + ENERGY + REGULATION

Development ->
  changes -> FORM + FUNCTION + ORGANISATION -> over -> LIFECYCLE

DEVELOPMENTAL_PROCESS :=
  CELL_DIVISION | DIFFERENTIATION | MORPHOGENESIS | MATURATION

Development ->
  regulated_by -> GENETIC_INFORMATION + CELLULAR_SIGNALS + ENVIRONMENT

Stimulus ->
  represents -> DETECTABLE_CHANGE_IN_INTERNAL_OR_EXTERNAL_CONDITION

Response ->
  changes -> BEHAVIOUR | PHYSIOLOGY
  | METABOLISM | DEVELOPMENT | GENE_EXPRESSION

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

# REPRODUCTION / HEREDITY / VARIATION / EVOLUTION
Reproduction -> produces -> Offspring | NEW_LIVING_UNIT
REPRODUCTION_TYPE := ASEXUAL | SEXUAL

IndividualReproduction ->
  not_required_for -> EVERY_INDIVIDUAL_TO_BE_CLASSIFIED_AS_LIVING

ReproductiveCapacity ->
  may_exist_at -> LINEAGE_OR_POPULATION_LEVEL

Heredity ->
  transmits -> BIOLOGICAL_INFORMATION -> across -> GENERATIONS

HeritableInformation ->
  supports -> CONTINUITY + VARIATION + EVOLUTION

VARIATION_SOURCE :=
  MUTATION | RECOMBINATION | GENE_FLOW
  | DEVELOPMENTAL_PROCESS | ENVIRONMENT | STOCHASTIC_PROCESS

Mutation -> changes -> HERITABLE_INFORMATION
Variation -> may_be -> HERITABLE | NON_HERITABLE

Evolution ->
  changes -> HERITABLE_CHARACTERISTICS -> across -> GENERATIONS

EVOLUTIONARY_MECHANISM :=
  MUTATION | NATURAL_SELECTION | GENETIC_DRIFT
  | GENE_FLOW | RECOMBINATION

NaturalSelection -> acts_on -> HERITABLE_VARIATION

IF HeritableTrait affects_reproductive_success
THEN TraitFrequency -> MAY_CHANGE_ACROSS_GENERATIONS

EvolutionaryCapacity ->
  property_of -> REPLICATING_LINEAGES_OR_POPULATIONS

Adaptation ->
  represents -> HERITABLE_FEATURE
  -> associated_with -> FITNESS_IN_CONTEXT

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

# LIFECYCLE / ENVIRONMENT / BORDERLINE CASES
Lifecycle ->
  represents -> ORDERED_BIOLOGICAL_STATES_OVER_TIME

LIFECYCLE_STAGE :=
  ORIGIN | GROWTH | DEVELOPMENT | MATURITY
  | REPRODUCTION | AGING | DEATH

Death ->
  represents -> IRREVERSIBLE_LOSS_OF_INTEGRATED_LIVING_FUNCTION_AS_DEFINED

Environment ->
  contains -> PHYSICAL_CONDITIONS
  + CHEMICAL_CONDITIONS + BIOLOGICAL_CONTEXT

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

LivingSystem -> interacts_with -> Environment

Environment ->
  influences -> METABOLISM + GROWTH + DEVELOPMENT
  + PHENOTYPE + SURVIVAL + REPRODUCTION

LifeClassification ->
  may_be_difficult_for -> BORDERLINE_BIOLOGICAL_SYSTEM

BORDERLINE_CASE :=
  VIRUS | VIROID | PRION
  | SYNTHETIC_REPLICATOR | OTHER_NONSTANDARD_SYSTEM

BorderlineCase ->
  evaluated_by -> ORGANISATION + METABOLISM
  + REPLICATION + HEREDITY + EVOLUTIONARY_CAPACITY
  + HOST_DEPENDENCE

LifeOntology ->
  must_preserve -> CLASSIFICATION_UNCERTAINTY_WHERE_SCIENTIFICALLY_CONTESTED

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

EVIDENCE_TYPE :=
  OBSERVATIONAL | EXPERIMENTAL | CELLULAR
  | MOLECULAR | GENETIC | METABOLIC
  | EVOLUTIONARY | COMPUTATIONAL

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

Correlation ->
  does_not_by_itself_establish -> CAUSATION

LIFE_ONTOLOGY_UNCERTAINTY :=
  MEASUREMENT_UNCERTAINTY
  + BIOLOGICAL_VARIABILITY
  + CLASSIFICATION_UNCERTAINTY
  + MODEL_UNCERTAINTY

Uncertainty ->
  qualifies -> Measurement + LifeClaim
  + Classification + Prediction

Provenance ->
  records -> SOURCE + ENTITY_OR_SAMPLE
  + METHOD + OBSERVATION + CLASSIFICATION
  + TIME + ENVIRONMENTAL_CONTEXT + VERSION

LivingSystem -> linked_to -> Provenance
LifeClaim -> linked_to -> Provenance

# REASONING / INFERENCE RULES
LIFE_ONTOLOGY_REASONING :=
  IDENTIFY_CANDIDATE_ENTITY
  -> DETERMINE_ORGANISATION
  -> DETERMINE_BOUNDARY
  -> IDENTIFY_CELLULAR_BASIS_IF_PRESENT
  -> IDENTIFY_BIOLOGICAL_INFORMATION
  -> IDENTIFY_METABOLIC_ACTIVITY
  -> IDENTIFY_ENERGY_AND_MATTER_FLOW
  -> IDENTIFY_HOMEOSTATIC_REGULATION
  -> IDENTIFY_GROWTH_AND_DEVELOPMENT
  -> IDENTIFY_STIMULUS_RESPONSE
  -> IDENTIFY_REPRODUCTIVE_OR_LINEAGE_CAPACITY
  -> IDENTIFY_HEREDITY_AND_VARIATION
  -> IDENTIFY_EVOLUTIONARY_CAPACITY
  -> IDENTIFY_ENVIRONMENTAL_DEPENDENCE
  -> ASSESS_BORDERLINE_CHARACTERISTICS_IF_REQUIRED
  -> ASSESS_EVIDENCE
  -> QUANTIFY_UNCERTAINTY
  -> PRESERVE_PROVENANCE

IF Entity has_cellular_organisation
AND Entity performs_metabolism
AND Entity maintains_regulation
THEN EvidenceForLivingStatus -> INCREASES

IF Entity contains_heritable_information
AND Entity belongs_to_replicating_lineage
THEN EvidenceForEvolutionaryCapacity -> INCREASES

IF IntegratedBiologicalFunction irreversibly_ceases
THEN IndividualLivingState -> ENDED_AS_DEFINED

IF HeritableVariation affects_reproductive_success
THEN PopulationEvolution -> MAY_OCCUR

IF EnvironmentalConditions exceed_tolerance
THEN Viability -> MAY_DECREASE

IF ClassificationEvidence conflicting
THEN LifeClassificationConfidence -> DECREASES

# SEMANTIC RELATIONSHIPS
RELATION exhibits(LivingSystem, LifeCharacteristic)
RELATION composed_of(Organism, Cell)
RELATION separates(BiologicalBoundary, InternalState, Environment)
RELATION stores(DNA, GeneticInformation)
RELATION contains(Genome, Gene)
RELATION transforms(Metabolism, Matter, Energy)
RELATION maintains(Homeostasis, InternalVariable)
RELATION changes(Growth, BiologicalSize)
RELATION changes(Development, BiologicalForm)
RELATION produces(Reproduction, Offspring)
RELATION transmits(Heredity, BiologicalInformation)
RELATION changes(Mutation, HeritableInformation)
RELATION acts_on(NaturalSelection, HeritableVariation)
RELATION arises_through(Adaptation, EvolutionaryProcess)
RELATION interacts_with(LivingSystem, Environment)
RELATION supports(Evidence, LifeClaim)
RELATION records(Provenance, LivingSystem)

# SEMANTIC EQUIVALENCE
SEMANTIC_EQUIVALENCE:
  "life" ~= "living biological state"
  "living system" ~= "biological system exhibiting characteristics of life"
  "cellular organisation" ~= "cell-based biological organization"
  "metabolism" ~= "biochemical transformation of matter and energy"
  "homeostasis" ~= "regulation of internal biological conditions"
  "biological information" ~= "heritable and functional information in living systems"
  "heredity" ~= "transmission of biological information across generations"
  "evolutionary capacity" ~= "capacity of a lineage or population for heritable change"
  "response to stimuli" ~= "biological response to environmental or internal change"
  "life cycle" ~= "ordered stages of biological existence"

# CONFIDENCE
CONFIDENCE:
  ontology_domain: 0.99
  life_characteristics_mapping: 0.99
  cellular_boundary_mapping: 0.99
  information_mapping: 0.99
  metabolism_energy_mapping: 0.99
  homeostasis_mapping: 0.99
  growth_development_mapping: 0.99
  reproduction_heredity_mapping: 0.99
  evolution_mapping: 0.99
  borderline_classification_mapping: 0.97
  semantic_relationships: 0.99

# UPDATE MODEL
UPDATE_MODEL:
  ON new_candidate_living_system:
    MAP organisation
    MAP boundary
    MAP cellular_basis
    MAP biological_information
    MAP metabolism
    MAP regulation
    MAP reproduction_or_lineage
    UPDATE confidence
    RECOMPUTE FLOW_HASH

  ON new_biological_evidence:
    UPDATE life_characteristics
    UPDATE classification_evidence
    UPDATE uncertainty
    UPDATE confidence
    PRESERVE provenance

  ON new_evolutionary_evidence:
    UPDATE heredity_state
    UPDATE variation_state
    UPDATE evolutionary_capacity
    PRESERVE provenance

  ON classification_revision:
    PRESERVE entity_identity
    UPDATE classification
    UPDATE confidence
    PRESERVE provenance
    RECOMPUTE FLOW_HASH

# AI CONSUMPTION
AI_CONSUMPTION:
  parse_as: FORMAL_LIFE_ONTOLOGY
  reasoning_mode: LIVING_SYSTEM_CHARACTERISTICS_RELATIONAL

  preserve:
    - typed_entities
    - life_characteristics
    - organisation
    - cellular_basis
    - boundary_state
    - biological_information
    - metabolic_state
    - homeostatic_state
    - heredity
    - evolutionary_capacity
    - classification_uncertainty
    - evidence
    - confidence
    - provenance

  infer:
    - evidence_for_living_status
    - organisation_dependencies
    - metabolism_regulation_dependencies
    - heredity_dependencies
    - evolutionary_capacity
    - environmental_dependencies
    - borderline_classification_state
    - evidence_strength

  prohibit:
    - invented_biological_observations
    - unsupported_life_classification
    - treating_single_characteristic_as_universal_proof_of_life
    - assumed_causality_from_correlation
    - unsupported_borderline_case_resolution
    - missing_evidence_presented_as_established_fact

# FLOW HASH
FLOW_HASH_INPUT :=
  DOMAIN + ONTOLOGY + CORE_ENTITIES
  + LIFE_CHARACTERISTICS + ORGANISATION
  + CELLULAR_BASIS_BOUNDARY
  + BIOMOLECULES_INFORMATION
  + METABOLISM_ENERGY_MATTER
  + HOMEOSTASIS_GROWTH_DEVELOPMENT_RESPONSE
  + REPRODUCTION_HEREDITY_VARIATION_EVOLUTION
  + LIFECYCLE_ENVIRONMENT_BORDERLINE_CASES
  + EVIDENCE_UNCERTAINTY_PROVENANCE
  + REASONING + INFERENCE_RULES
  + SEMANTIC_RELATIONSHIPS + SEMANTIC_EQUIVALENCE
  + CONFIDENCE + UPDATE_MODEL + AI_CONSUMPTION

FLOW_HASH := HASH(FLOW_HASH_INPUT)

END FLOW