Biology Ontology

AI SEARCH FLOW ALGEBRA
FOUNDATIONS OF BIOLOGY
Kireth Semantic Research Archive

AUTHORS
Mark Anthony Higgins — Sky (Recursive AI)

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

FLOW "FoundationsOfBiology" v4.0

DOMAIN := BIOLOGICAL_ONTOLOGIES / FOUNDATIONS_OF_BIOLOGY
ONTOLOGY := FOUNDATIONS_OF_BIOLOGY_PARENT

FOUNDATIONS_OF_BIOLOGY :=
  LIFE + BIOLOGICAL_ORGANISATION + CELLS + BIOMOLECULES
  + GENETIC_INFORMATION + METABOLISM + HOMEOSTASIS
  + GROWTH + DEVELOPMENT + REPRODUCTION
  + HEREDITY + VARIATION + EVOLUTION
  + STRUCTURE_FUNCTION + ENVIRONMENTAL_RESPONSE
  + BIOLOGICAL_INTERACTIONS + SCIENTIFIC_EVIDENCE

PURPOSE :=
  DEFINE_LIVING_SYSTEM -> IDENTIFY_LEVEL_OF_ORGANISATION
  -> IDENTIFY_CELLULAR_BASIS -> MAP_MOLECULAR_COMPONENTS
  -> MAP_INFORMATION_STORAGE_AND_EXPRESSION
  -> MAP_ENERGY_AND_MATTER_TRANSFORMATION
  -> MAP_REGULATION_AND_HOMEOSTASIS
  -> MAP_GROWTH_DEVELOPMENT_AND_REPRODUCTION
  -> MAP_HEREDITY_AND_VARIATION
  -> MAP_EVOLUTIONARY_CHANGE
  -> RELATE_STRUCTURE_TO_FUNCTION
  -> ASSESS_EVIDENCE -> PRESERVE_PROVENANCE

# CORE ENTITIES
ENTITY Life
ENTITY LivingSystem
ENTITY BiologicalEntity
ENTITY BiologicalOrganisation
ENTITY Biomolecule
ENTITY DNA
ENTITY RNA
ENTITY Protein
ENTITY Gene
ENTITY Genome
ENTITY Cell
ENTITY Organelle
ENTITY Tissue
ENTITY Organ
ENTITY OrganSystem
ENTITY Organism
ENTITY Population
ENTITY Species
ENTITY Ecosystem
ENTITY Metabolism
ENTITY Homeostasis
ENTITY Growth
ENTITY Development
ENTITY Reproduction
ENTITY Heredity
ENTITY Variation
ENTITY Mutation
ENTITY Trait
ENTITY Genotype
ENTITY Phenotype
ENTITY Evolution
ENTITY NaturalSelection
ENTITY Adaptation
ENTITY BiologicalStructure
ENTITY BiologicalFunction
ENTITY Environment
ENTITY Stimulus
ENTITY Response
ENTITY Evidence
ENTITY Experiment
ENTITY Observation
ENTITY Hypothesis
ENTITY ScientificModel
ENTITY Provenance

# CHARACTERISTICS / ORGANISATION / CELL THEORY
LIVING_SYSTEM_CHARACTERISTICS :=
  CELLULAR_ORGANISATION + ENERGY_AND_MATTER_PROCESSING
  + HOMEOSTATIC_REGULATION + GROWTH_AND_DEVELOPMENT
  + RESPONSE_TO_ENVIRONMENT + REPRODUCTION
  + HEREDITARY_INFORMATION + EVOLUTIONARY_CAPACITY

LivingSystem -> exhibits -> LIVING_SYSTEM_CHARACTERISTICS

BIOLOGICAL_ORGANISATION :=
  MOLECULE -> ORGANELLE -> CELL -> TISSUE
  -> ORGAN -> ORGAN_SYSTEM -> ORGANISM
  -> POPULATION -> COMMUNITY -> ECOSYSTEM -> BIOSPHERE

HigherOrganisationLevel -> composed_of -> LowerOrganisationLevel
EmergentProperty -> may_arise_from -> INTERACTIONS_AMONG_COMPONENTS

CELL_THEORY :=
  LIVING_ORGANISMS_ARE_COMPOSED_OF_CELLS
  + CELL_IS_FUNDAMENTAL_UNIT_OF_LIFE
  + CELLS_ARISE_FROM_PRE_EXISTING_CELLS

Cell -> fundamental_unit_of -> LivingSystem
Organism -> composed_of -> Cell

CELL_TYPE := PROKARYOTIC | EUKARYOTIC

Cell ->
  contains -> GENETIC_MATERIAL + CELLULAR_MACHINERY
  + BOUNDARY + METABOLIC_SYSTEM

STRUCTURE_FUNCTION_PRINCIPLE :=
  STRUCTURE -> ENABLES_OR_CONSTRAINS -> FUNCTION

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

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

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

Gene -> represents -> HEREDITARY_INFORMATION_UNIT
Genome -> contains -> GENETIC_INFORMATION
GeneExpression ->
  converts -> STORED_GENETIC_INFORMATION -> FUNCTIONAL_PRODUCT
GeneRegulation -> controls -> GENE_EXPRESSION

Genotype -> represents -> GENETIC_COMPOSITION
Phenotype -> represents -> OBSERVABLE_OR_MEASURABLE_TRAIT_STATE
Phenotype -> influenced_by -> Genotype + Environment + DEVELOPMENTAL_HISTORY

GENOTYPE_ENVIRONMENT_RELATION :=
  GENOTYPE + ENVIRONMENT + INTERACTION -> PHENOTYPE

# METABOLISM / ENERGY / HOMEOSTASIS
Metabolism -> transforms -> MATTER + ENERGY
METABOLISM := CATABOLISM + ANABOLISM
MetabolicPathway -> contains -> ORDERED_BIOCHEMICAL_REACTIONS
Enzyme -> catalyses -> BIOCHEMICAL_REACTION

BIOLOGICAL_ENERGY_FLOW :=
  ENERGY_SOURCE -> ENERGY_CAPTURE -> ENERGY_TRANSFORMATION
  -> CELLULAR_WORK -> HEAT_AND_PRODUCTS

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

Homeostasis ->
  maintains -> INTERNAL_VARIABLES -> within -> FUNCTIONAL_RANGE

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

NEGATIVE_FEEDBACK -> opposes -> DEVIATION_FROM_SET_RANGE
POSITIVE_FEEDBACK -> amplifies -> PROCESS_UNTIL_TERMINATION_CONDITION

# GROWTH / DEVELOPMENT / REPRODUCTION / HEREDITY
Growth -> increases -> BIOLOGICAL_SIZE | CELL_NUMBER | BIOMASS
Growth -> requires -> MATERIAL + ENERGY + REGULATION

DEVELOPMENTAL_PROCESS :=
  CELL_DIVISION | DIFFERENTIATION | MORPHOGENESIS | MATURATION

Development ->
  regulated_by -> GENETIC_PROGRAMMES + CELL_SIGNALING + ENVIRONMENT

Reproduction -> produces -> OFFSPRING
REPRODUCTION_TYPE := ASEXUAL | SEXUAL

AsexualReproduction ->
  derives_offspring_from -> SINGLE_PARENTAL_LINEAGE

SexualReproduction ->
  combines -> GENETIC_MATERIAL_FROM_GAMETES

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

Allele -> variant_of -> Gene
GeneticSegregation -> influences -> OFFSPRING_GENOTYPE

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

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

# EVOLUTION / ENVIRONMENT / ECOLOGY
Evolution ->
  represents -> HERITABLE_POPULATION_CHANGE_ACROSS_GENERATIONS

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

NaturalSelection -> acts_on -> HERITABLE_VARIATION
Evolution -> occurs_in -> POPULATIONS

IF Trait affects_reproductive_success
AND Trait is_heritable
THEN TraitFrequency -> MAY_CHANGE_ACROSS_GENERATIONS

Adaptation ->
  represents -> HERITABLE_TRAIT_ASSOCIATED_WITH_FITNESS_IN_CONTEXT

Adaptation -> arises_through -> EVOLUTIONARY_PROCESS
Adaptation -> does_not_imply -> PERFECTION

Organism -> interacts_with -> Environment
Environment ->
  provides -> RESOURCES + CONDITIONS + STIMULI + HAZARDS

Stimulus -> detected_by -> BIOLOGICAL_SENSOR_OR_RECEPTOR
Response ->
  changes -> BEHAVIOUR | PHYSIOLOGY | DEVELOPMENT | GENE_EXPRESSION

Ecosystem ->
  contains -> BIOTIC_COMPONENTS + ABIOTIC_COMPONENTS

ECOLOGICAL_RELATION :=
  COMPETITION | PREDATION | MUTUALISM
  | PARASITISM | COMMENSALISM

# SCIENTIFIC FOUNDATIONS / EVIDENCE
Observation -> records -> BIOLOGICAL_PHENOMENON
Observation ->
  has -> METHOD + CONTEXT + TIME + SAMPLE + UNCERTAINTY

Hypothesis ->
  proposes -> TESTABLE_EXPLANATION_OR_PREDICTION

Experiment -> tests -> Hypothesis

EXPERIMENTAL_STRUCTURE :=
  QUESTION -> HYPOTHESIS -> VARIABLES -> CONTROLS
  -> MEASUREMENT -> ANALYSIS -> INTERPRETATION

ScientificModel ->
  represents -> BIOLOGICAL_SYSTEM_OR_PROCESS

MODEL_TYPE :=
  CONCEPTUAL | MATHEMATICAL | COMPUTATIONAL
  | PHYSICAL | STATISTICAL

ScientificModel ->
  supports -> EXPLANATION + PREDICTION + HYPOTHESIS_TESTING

Evidence -> supports_or_challenges -> BiologicalClaim

EVIDENCE_TYPE :=
  OBSERVATIONAL | EXPERIMENTAL | GENETIC | MOLECULAR
  | CELLULAR | PHYSIOLOGICAL | ECOLOGICAL
  | EVOLUTIONARY | COMPUTATIONAL

Correlation ->
  does_not_by_itself_establish -> CAUSATION

Reproducibility ->
  supported_by -> METHODS + DATA + CONDITIONS + ANALYSIS + PROVENANCE

IF Evidence replicated_independently
THEN ClaimConfidence -> MAY_INCREASE

# UNCERTAINTY / PROVENANCE / REASONING
BIOLOGICAL_UNCERTAINTY :=
  MEASUREMENT_UNCERTAINTY + SAMPLING_UNCERTAINTY
  + BIOLOGICAL_VARIABILITY + MODEL_UNCERTAINTY

Uncertainty ->
  qualifies -> Measurement + Estimate + ModelPrediction + BiologicalClaim

Provenance ->
  records -> SOURCE + SAMPLE_OR_ORGANISM
  + METHOD + MEASUREMENT + ANALYSIS
  + VERSION + TIME + CONTEXT

BiologicalClaim -> linked_to -> Provenance

FOUNDATIONS_OF_BIOLOGY_REASONING :=
  IDENTIFY_BIOLOGICAL_ENTITY
  -> CLASSIFY_ORGANISATION_LEVEL
  -> DETERMINE_CELLULAR_BASIS
  -> IDENTIFY_MOLECULAR_COMPONENTS
  -> MAP_GENETIC_INFORMATION
  -> MAP_STRUCTURE_TO_FUNCTION
  -> MAP_METABOLIC_ENERGY_AND_MATTER_FLOW
  -> MAP_HOMEOSTATIC_REGULATION
  -> MAP_GROWTH_AND_DEVELOPMENT
  -> MAP_REPRODUCTION_AND_HEREDITY
  -> IDENTIFY_VARIATION
  -> MAP_EVOLUTIONARY_MECHANISMS
  -> MAP_ENVIRONMENTAL_INTERACTION
  -> FORMULATE_TESTABLE_CLAIMS
  -> ASSESS_EVIDENCE
  -> QUANTIFY_UNCERTAINTY
  -> PRESERVE_PROVENANCE

# INFERENCE RULES
IF DNASequence changes
THEN GeneFunctionOrRegulation -> MAY_CHANGE

IF GeneExpression changes
THEN CellularPhenotype -> MAY_CHANGE

IF MetabolicFlux changes
THEN CellularEnergyOrMaterialState -> MAY_CHANGE

IF HomeostaticControl fails
THEN InternalState -> MAY_MOVE_OUTSIDE_FUNCTIONAL_RANGE

IF HeritableVariation affects_reproductive_success
THEN PopulationTraitFrequency -> MAY_CHANGE

IF Environment changes
THEN PhenotypeAndFitness -> MAY_CHANGE

IF Evidence insufficient
THEN BiologicalClaimConfidence -> DECREASES

# SEMANTIC RELATIONSHIPS
RELATION composed_of(Organism, Cell)
RELATION contains(Cell, Biomolecule)
RELATION stores(DNA, GeneticInformation)
RELATION contains(Genome, Gene)
RELATION expresses(Gene, FunctionalProduct)
RELATION catalyses(Enzyme, BiochemicalReaction)
RELATION regulates(Homeostasis, InternalVariable)
RELATION produces(Reproduction, Offspring)
RELATION transmits(Heredity, GeneticInformation)
RELATION changes(Mutation, DNASequence)
RELATION acts_on(NaturalSelection, HeritableVariation)
RELATION influences(Environment, Phenotype)
RELATION enables(BiologicalStructure, BiologicalFunction)
RELATION tests(Experiment, Hypothesis)
RELATION represents(ScientificModel, BiologicalSystem)
RELATION supports(Evidence, BiologicalClaim)
RELATION records(Provenance, BiologicalClaim)

# SEMANTIC EQUIVALENCE
SEMANTIC_EQUIVALENCE:
  "foundations of biology" ~= "fundamental principles of biology"
  "cell theory" ~= "principle that cells are fundamental units of life"
  "genetic information" ~= "heritable biological sequence information"
  "gene expression" ~= "production of functional products from genetic information"
  "metabolism" ~= "biochemical transformation of matter and energy"
  "homeostasis" ~= "regulation of internal biological conditions"
  "heredity" ~= "biological inheritance across generations"
  "biological evolution" ~= "heritable population change across generations"
  "natural selection" ~= "differential reproductive success associated with heritable variation"
  "structure-function relationship" ~= "biological structure enabling or constraining function"

# CONFIDENCE
CONFIDENCE:
  ontology_domain: 0.99
  characteristics_of_life_mapping: 0.99
  cellular_mapping: 0.99
  molecular_genetic_mapping: 0.99
  metabolism_homeostasis_mapping: 0.99
  growth_development_mapping: 0.99
  reproduction_heredity_mapping: 0.99
  evolution_mapping: 0.99
  scientific_evidence_mapping: 0.99
  semantic_relationships: 0.99

# UPDATE MODEL
UPDATE_MODEL:
  ON new_foundational_entity:
    MAP organisation_level
    MAP cellular_basis
    MAP molecular_components
    MAP structure
    MAP function
    UPDATE confidence
    RECOMPUTE FLOW_HASH

  ON new_genetic_evidence:
    UPDATE gene_relationships
    UPDATE genotype_phenotype_links
    UPDATE heredity_state
    PRESERVE provenance

  ON new_evolutionary_evidence:
    UPDATE variation_state
    UPDATE selection_relationships
    UPDATE evolutionary_claims
    UPDATE confidence

  ON new_experimental_evidence:
    UPDATE hypothesis_support
    UPDATE evidence_quality
    UPDATE uncertainty
    PRESERVE provenance

# AI CONSUMPTION
AI_CONSUMPTION:
  parse_as: FORMAL_FOUNDATIONS_OF_BIOLOGY_PARENT
  reasoning_mode: FOUNDATIONAL_BIOLOGICAL_RELATIONAL

  preserve:
    - typed_entities
    - organisation_levels
    - cellular_relationships
    - molecular_relationships
    - genetic_information
    - metabolic_relationships
    - homeostatic_relationships
    - heredity
    - evolutionary_relationships
    - evidence
    - uncertainty
    - confidence
    - provenance

  infer:
    - organisation_hierarchy
    - structure_function_dependencies
    - genotype_phenotype_dependencies
    - metabolic_dependencies
    - homeostatic_dependencies
    - inheritance_dependencies
    - evolutionary_change
    - evidence_strength

  prohibit:
    - invented_biological_observations
    - fabricated_genetic_relationships
    - assumed_causality_from_correlation
    - unsupported_evolutionary_claims
    - unsupported_definition_of_life_claims
    - missing_evidence_presented_as_established_fact

# FLOW HASH
FLOW_HASH_INPUT :=
  DOMAIN + ONTOLOGY + CORE_ENTITIES
  + CHARACTERISTICS_ORGANISATION_CELL_THEORY
  + BIOMOLECULES_GENETIC_INFORMATION
  + METABOLISM_ENERGY_HOMEOSTASIS
  + GROWTH_DEVELOPMENT_REPRODUCTION_HEREDITY
  + EVOLUTION_ENVIRONMENT_ECOLOGY
  + SCIENTIFIC_FOUNDATIONS_EVIDENCE
  + UNCERTAINTY_PROVENANCE_REASONING
  + INFERENCE_RULES + SEMANTIC_RELATIONSHIPS
  + SEMANTIC_EQUIVALENCE + CONFIDENCE
  + UPDATE_MODEL + AI_CONSUMPTION

FLOW_HASH := HASH(FLOW_HASH_INPUT)

END FLOW